The ocean The TODAY

37:2 May 2010 May 37:2 Micro eneral MicrobiologY i s ics e e sea t eria h om t t t B ology ic parasi and biofuel t ranscrip cyanobac t a o t t me eukaryo marine viralmarine ecology imicrobials from from imicrobials hermo t t ga an Quarterly Magazine Quarterly of the Society for G

microbiologytoday 37:2 May 2010

Cover image Ocean wave. Features Regulars iStockphoto / Thinkstock

82 70 News NTS

Beyond the infinite – tracking E bacterial gene expression 78 Microshorts jack A. gilbert 80 Conferences Editor The importance of metatranscriptomics in

Dr Paul Hoskisson understanding marine ecosystems. CONT

110 Schoolzone Editorial Board Dr Kim Hardie 86 116 Gradline Professor Mark Harris Cyanobacteria Professor Jo Verran david G. AdAms Managing Editor 120 Going Public Janet Hurst Why are cyanobacteria so important for the environment? Editorial Assistant 127 Council 09–10 Y 2010 Yvonne Taylor 92 Design 128 Hot off the Press Ian Atherton The ecological significance of MA address small, eukaryotic parasites in 131 Reviews SGM HQ, Marlborough marine ecosystems House, Basingstoke Road, Spencers Wood, Reading Laure Guillou, Catharina Alves-de-Souza, 136 Comment RG7 1AG Raffaele Siano, Humberto González The remarkable 37:2 tel 0118 988 1809 The role of eukaryotic pathogens of plankton in Fax 0118 988 5656 ‘taxonomy gene’ marine ecology should not be ignored. email [email protected] H. GEst web www.sgm.ac.uk

Advertising 96 James Priest, Group Sales Viral ecology: old questions, Manager, Ten Alps Media, new challenges EXTRAS ONE New Oxford Street, London WC1A 1NU K. ERIC WOMMACK tel 0207 657 1804 The diversity and abundance of viruses in the 133 fax 0207 379 7115 email james.priest@ biosphere is being revealed by metagenomics. Obituaries: tenalps.com Duncan McGarva © 2010 The Society for 100 General Microbiology Thermotoga, a small genus with Pat Clarke

ISSN 1464-0570 a large potential in biohydrogen Walter Plowright

Printed by synthesis Latimer Trend & Co. Ltd, NIELS THOMAS ERIKSEN, THOMAS MARIUS NIELSEN, Plymouth, UK NIKOLAJ KYNDBY HOLM & MARTIN LEEGAARD RIIS Does this small marine thermophile hold the key to biofuel development? 104 Antimicrobials: treasures from the oceans The views expressed by contributors are not JEM STACH necessarily those of The potential of novel actinomycetes from the Society; nor can the claims of advertisers be the sea bed to provide the next generation of guaranteed. antimicrobial compounds. All change at MT And sometimes when a piece is Josiane retires to-date don’t just happen. Accounts have to credited, I actually ghosted it. be kept as well, money paid into the bank, Janet in

This is my last issue as Managing Editor of Microbiology Today as Now it’s time to hand on ists badges printed, programme books produced July 1991 At the end of April, SGM bid

by the time you read the magazine, I will have retired. Although at Harvest the mantle to others, who will g and deadlines met – it’s a complicated farewell to Josiane Dunn who employed originally at the SGM in 1990 as Professional Affairs House, SGM’s no doubt develop the magazine business organizing meetings, that involves

previous has run the meetings office with NEWS Assistant, when the main concern was the disappearance of named further and take it to greater much forward-planning, multi-tasking, headquarters. charm and great efficiency since microbiology departments in universities (they all went and now it’s (Yes, that heights. Ian Atherton, who is attention to detail and patience. Josiane has 1999. Josiane has organized a perceived decline in named microbiology degrees!), I soon became is Ian in the already Production and Design these in spades, in addition to a very pleasant background!) 24 Society main meetings embroiled in many other Society activities. Grants were ‘dumped’ Editor, is taking over my role and warm personality. To Josiane nothing is a Fred Fabry and many smaller events such on me in the first week and I became responsible for careers of Managing Editor, but he will problem – troubleshooting is just something as FIS conferences. Over promotion too. I don’t know how I got to be involved in writing These days MT not only goes to members be helped by a good team, to that has to be done. the years, she has probably copy for what was then the rather dull SGM Quarterly, but I was, around the world, it is also sent to politicians whom I wish every success. As Josiane is always the first to met more members of the even though my name didn’t appear as part of the editorial team! and opinion-formers as part of the SGM’s emphasize, ensuring that the meetings run janet Hurst Society than anyone else, both The magazine was put together by journal staff in those days and Microbiology Awareness Campaign. It is smoothly is a team effort, involving other delegates at meetings and the individuals on Sylvia Stubbs from JGV was in charge. A few months after I joined distributed to schools and generally acts as SGM staff; Karen’s help in the office is the group committees (more recently divisional SGM, Ian Atherton was employed to work on Microbiology and he a promotional tool for both the Society and particularly appreciated. However, Josiane committees) who organize the scientific content and microbiolo eventually took over from Sylvia on the Q when she left. Thus began microbiology. The magazine is also available on herself is a great team player, always willing of our programmes. She has provided an

a partnership that has lasted almost 20 years. the web and PDFs of the articles can be freely gy to help others and provide a sensible opinion excellent service to the latter and also to the Lots of other people have contributed to the success of the downloaded by anyone. on matters. Her reputation as a whizz with widely ranging speakers from all over the world magazine in that time, of course. Publications Officers, who were It’s been a pleasure and a privilege to work the database system Filemaker Pro, has who are invited to deliver talks on their research, also the Editors of the magazine, have come and gone, and help on MT, seeing both it and the Society through benefited not only the meetings organization organizing their travel arrangements when asked, has also been provided by an editorial assistant (Janice Meekings for many changes and developments. With hardly any but also many other activities in the External providing reassurance and quietly but firmly 2010

2010 many years, now Yvonne Taylor). An editorial board of ‘volunteers’ exceptions (!), the authors have been a delight Relations Office.

nagging the recalcitrant ones into providing their Y from among the Council membership was set up in 1999, and to interact with and all seemed to have been Josiane is not totally unflappable, of MA Y AV requirements and abstracts as near to time as MA has since provided essential help in finding authors for articles as pleased to make contributions. In all the time we course, she has been seen running out of the 70 possible. 71 themed issues of the magazine developed. SGM staff also provide have been commissioning pieces, only one article office screaming at the sight of a wasp. She In addition to her work in securing venues copy for their area of responsibility, not always willingly it has to has failed to materialize at all, which says a lot Josiane unwraps also does not like chilli, which cuts down on DA Y and organizing the infrastructure of the meetings, DA Y a leaving present O be said! It’s a great team effort and we think, a great members’ about the dedication of our contributors. That the choice of restaurants when staff have O s, microbiolo T at her farewell ensuring that lecture theatres are ready and not T

magazine! one omission meant I had to write four pages e to eat out! Nevertheless, she will be sorely lunch. Laura only are we fed, but that the food and drink turns The production process has changed hugely over the past just before going to press, but it just added to the Udakis missed at the SGM and everyone wishes her up at the right time in the programme, Josiane two decades. When we started, the typesetting was outsourced frisson of the job. Perhaps one thing that most a very happy retirement. has also processed thousands and thousands and great long galley proofs had to be checked. All I remember is readers don’t know is that if no-one’s name is As anyone who has spoken to Josiane of bookings from delegates. Whatever their MicroBiology MicroBiology a preponderance of mis-keyed letter ‘j’s throughout the text that attached to a piece of text, it’s written by me. knows, she is French by birth and plans to MicroBiology Janet and Josiane requirements for meals, had to be corrected. The proofs were cut up and stuck on a spend a lot more time with her large family in their office, accommodation and other template, which was then sent to the printers. Images were supplied April 2010. Laura in France, as well as achieving various other

activities, these have to activiti in the form of hard copy photographs or even 35 mm slides and Udakis ambitions to visit destinations such as Peru be logged and turned into y

the magazine was mono throughout. August 1992 marked a big t and Nepal. As a recent proud ‘Mamie’, she a format that results in change – along with a new design, we were allowed to have a e will also be helping to look after her baby what is wanted on the day colour picture on the cover! grand-daughter Matilda. at the meeting. Offered

I am not sure of the date of the eventful day when Sylvia, Ian oci It has been a great pleasure to me papers, posters and abstract and I headed off to a trading estate in High Wycombe, the location S personally to work closely with Josiane books do not appear by of the only Apple suppliers in the area, but we bought a Mac there, over the past 11 years and I wish her the themselves either, and much ordered QuarkXpress and started to do our own typesetting. The fulfilment of all her dreams in retirement. work is involved in handling era of DTP (and Ian’s career in design) at SGM had begun! these, obtaining decisions janet Hurst In 1995, as part of the SGM Golden Jubilee celebrations, a from session organizers, professional redesign of the Quarterly was commissioned. We st on

disseminating these to the e And a note from Josiane… became two-colour (black and blue) and were soon including a submitters and cleaning up the Josiane would like to express her few pages with full-colour illustrations. To mark the millennium, in abstracts so that the text is fit heartfelt thanks to all the colleagues both 2000 the Quarterly was completely redesigned again and, after much in and out of the SGM office who

for publication. lat internal debate, given a new name. The full-colour Microbiology Publicizing the meetings contributed to her retirement gifts and Today came into being. The design was refreshed in 2005 and again and keeping the website up- he sent good wishes.

more recently. t Feedback on february Council meeting highlights the new-look New Council structure time last year. Concerns were expressed about a Implementation of the revised, smaller Council small downturn in membership, but Council has MT structure is now well underway. The new sub- already set up a small working party to address Very few comments were committees had either met or were about to hold this issue. On a more positive note, Council received on the new design, their first meetings. President Hilary Lappin- approved the transfer of £500k cash that will not from which the editorial team Scott welcomed 11 elected members and be needed until later in 2010 to a fund yielding a deduce that most members officers to the meeting. She proposed to change higher return. either never read the magazine Join the SGM online global community the format of Council meetings to include an or were happy with the Social networking is great for connecting people around the world who item where a member of staff at Marlborough Scientific meetings changes. Our authors were all are interested in microbiology. House gives a presentation on the activities of In the absence of the Scientific Meetings Officer, pleased with the stunning way Follow us on Facebook (nearly 600 followers, help us make it to 1,000!) their department, so that Council more fully his Deputy Evelyn Doyle reported that a in which their pearls of wisdom www.facebook.com. understands the detailed running of the Society. good number of registrations had been received were set out. Adverse remarks Tweet with us on Twitter http://twitter.com/SocGenMicro She also hoped that it would foster closer links for the spring meeting in Edinburgh. She also all referred to the small point with staff. Suggestions for future topics would be noted that the spring meeting in 2012 would size of the sans serif text and in Hayes-Burnet Award 2010 AGM welcome. be taking place at the new conference centre particular, the inability to read This scheme, run jointly with the Australian Society for 2010 in her home city of Dublin, coinciding with the Succession planning European City of Science event being hosted in it when reversed out from pale Microbiology (ASM), supports the reciprocal exchange of one The AGM Changes are also taking place within the Society’s Dublin. Council heard that a full review of the orange. Design Manager Ian postgraduate student member to present their research at the of the Society professional staff. Three senior managers are new meetings structure will take place after the Atherton is at pains to point out other society’s main conference and to visit a research laboratory in will be held retiring in the first half of 2010 and the Chief Edinburgh meeting. Opinions of past delegates that the colour in print was not that country. The award was developed to strengthen a long lasting on Tuesday, Executive is due to retire in 2011. Members would be sought by an online survey to inform as it appeared on screen and 2010 2010 bond between the SGM and the ASM. It is designed to benefit 7 September heard that thanks to careful succession planning, Y he will make sure never to use PhD students in both countries by giving them the opportunity the evaluation.

MA Y 2010 at the MA the new staff taking over running the meetings that colour combination again! to present their work overseas and experience the best of Society Meeting 72 office and the finance office were already in Publications 73 If you still find some microbiology in the partner country. at Nottingham sections hard to read in this place and functioning well. Council welcomed Howard Jenkinson, the Publications Officer, Amanda Rossiter of the University of Birmingham is the latest University. ss DA Y the General Secretary’s proposal that the two reassured Council that he will relay the activities DA Y O issue, do let Ian know, so that recipient of the Hayes-Burnet award and will visit Australia in July O T Agenda papers, T he can make any necessary new posts created to cover the duties of the and fortunes of the Society’s journals to them this year to attend the ASM Annual Scientific Meeting and also including reports e Deputy Chief Executive following Janet Hurst’s regularly, on behalf of the editorial boards. The changes (i.atherton@sgm. spend time in the laboratory of Dr Mark Shembri at the University from Officers retirement in May should be filled by temporarily new Publications Committee will meet twice a ac.uk). of Queensland. and Division promoting Jane Westwell to Head of Meetings year, in spring and autumn. Chairs and the New SGM web page for members’ reports and Membership Services and Dariel Burdass MicroBiology MicroBiology Accounts of MicroBiology to Head of Education and Public Affairs. This Education Members often send us reports of SGM-funded events and meetings for which the Society arrangement will be subject to a review of The presentation on the widely varying and there is no space in Microbiology Today, or when the timing does not fit in with the for 2009 will management structure when the new CEO is extensive activities of SGM to promote

magazine’s deadlines. So that these can still be shared with other people, a web page be circulated usin appointed. New support staff will be recruited for microbiology education, delivered by Education has been created where these can be posted. Go to the Newsdesk at http://www. with the these two areas of work. Manager Dariel Burdass, was much enjoyed.

sgm.ac.uk/news/ and click on Members’ News. The first post is by David Lloyd of August issue B Council members’ interest was revealed by the Cardiff University and covers the 50th Annual Conference of the Association of of Microbiology Finances large number of questions that were raised. jo Microbiologists of India. Send your news to Jane Westwell ([email protected]) Today. Council was pleased to accept verran, the Education and Public Affairs Officer, the Treasurer’s Financial Report Bergey’s Organizes New Society y also remarked on the Society’s work in increasing for the year ended 31 December public engagement with microbiology.

Bergey’s Manual Trust has formed a new society for microbial taxonomists. The major goals of Bergey’s International t 2009. A small surplus had been Society for Microbial Systematics (BISMiS) are to comprehend the vast, undiscovered diversity of microbial life and to achieved in line with Council’s Taxonomy and culture collections

cultivate, describe, name and classify novel bacteria and archaea. The society will promote the discipline of microbial e policy to break even each year. A detailed discussion took place about the issues A study of the monthly figures systematics by enhancing communication among the worldwide community of microbial systematists. BISMiS will begin raised by Dr Brian Tindall in a letter to an online publication Bergey’s International Society for Microbial Systematics Bulletin (Bergey’s Bulletin for short), the first issue for January, which were the first Council about fundamental aspects of prokaryotic of which is scheduled for autumn this year. BISMiS will also organize meetings, the first of which will take place in Beijing, available to reveal the impact research relating to the availability of taxonomic China, in 2011. Anyone joining in 2010 will be considered Charter Members and be eligible for a special certificate. To of the new tiered pricing for data on micro-organisms. It was agreed to set up

join or learn more about it, see www.bergeys.org. The Board of Trustees comprises James Staley (Emeritus Chair), oci commercial journal subscriptions, a working group to take the matter forward. Michael Goodfellow (Chair), William Whitman (Director of the Editorial Office), Peter Kämpfer (Vice-Chair), Fred Rainey showed an encouraging outcome. (Secretary), Jongsik Chun and Paul De Vos. S Income was up 14% on the same David Blackbourn, General Secretary SGM staff Royal Society 350th Anniversary PeoplE Welcome to Suzanne Beaumont (right), who has http://seefurther.org taken over the role of Finance In November 1660, a group of young men Manager from Richard Noble. gathered to hear a young Christopher Wren Scottish Science Advisory Council (SSAC) Suzanne is a chartered certified give a lecture on astronomy. They decided to Two SGM members have been invited to join the panel of experts accountant with over 20 form a ‘Colledge for the Promoting of Physico- from the science and business community who provide the Scottish years’ experience in financial Mathematical Experimental Learning’ which 2 Government with independent advice on a range of science-related management and most recently years later Charles II made his Royal Society. topics. Professor Nigel Brown, University of Edinburgh and worked at Jacobs Engineering 350 years on, the Society is still flourishing and Professor George Salmond, University of Cambridge attended in Reading. Although Richard many celebrations to mark the anniversary are the first meeting of the panel in March. Former SGM Council has handed over his financial planned for 2010. Events, in the form of lectures, Member Professor Anne Glover is Chief Scientific Adviser responsibilities to Suzanne, exhibitions, discussions and outings, are taking for Scotland and Co-Chair of SSAC. he will continue to work on place throughout the UK. the journal commercial sales The renowned Royal Society Summer Congratulations to… marketing project until retiring Exhibition this year will be part of See Further: Nobel Laureate and Honorary SGM member at the end of June. Laura Udakis Sir Paul Nurse who has been nominated to be the Festival of Science and Arts, a 10-day event at the Southbank Centre in London. Several of the next President of the Royal Society Congratulations to Laura exhibits feature microbiology: Peter Borriello (on right), Chief Executive of the Udakis, External Relations Journey to the centre of the Earth: the first 23 cm Veterinary Laboratories Agency, who was presented Administrator, on the 2010

2010 (Rothamsted Research and John Innes Centre)

with the Society for Applied Microbiology/Proctor & award of an MSc in Science Y explores the mysteries of life in the topsoil. MA Y Gamble Applied Health Care Microbiology award on Communication from the MA Emerging infections: viruses that come in from the 74 16 April 2010. The award is made for a distinguished University of the West of 75 individual who has used microbiology research to England. Laura acts as SGM wild (University of Oxford) uses rabies, influenza and HIV as examples to show how ‘wild’ viruses DA Y gain a better understanding of human health. press officer amongst many and DA Y O O T varied other duties to promote cross the species barrier to transform into T Stewart Cole, Director of the Global Health microbiology. emerging infections in humans. Institute, Lausanne, Switzerland, who was one of

Society for Applied Microbiology Leishmania: lessons from a parasite (Imperial two recipients of the Kochon Prize for 2009. Each Faye Stokes, who has been College London and University of Addis Adaba, winner received a Medal and half the prize money of Public Affairs Administrator Ethiopia) shows how scientists are working to Never too late for $65,000. The Prize is awarded annually to persons, MicroBiology MicroBiology since 2003, has decided not understand and treat this most neglected tropical MicroBiology institutions or organizations that have made a highly success in microbiology to return to the SGM at the disease which is the second biggest cause of death significant contribution to combating tuberculosis. Aberdeen microbiologist Alex Brand, was end of her maternity leave. due to parasitic infections after malaria. Professor Cole directed the team that sequenced the profiled inMRCNetwork following her success In particular Faye did sterling genome of Mycobacterium tuberculosis in 1998 and is Meet the algae: diversity, biology and energy in receiving not only a Royal Society University work on the Microbiology currently working on new drugs to treat TB. (University of Cambridge) explores these beautiful Research Fellowship, but also an MRC New Awareness Campaign after it and diverse organisms. Not only are they found in Charles Dorman, former Editor-in-Chief of Investigator Grant. Alex only started her career was initiated, helping to raise glaciers as well as hot springs, oceans as well as in Microbiology, who has not only been elected a Fellow in microbiology at the age of 40 by completing the profile of microbiology to moist soil, but scientists can exploit their powers of the American Academy of Microbiology, but is an access course in science that led to a first politicians and opinion-formers, to produce green energy. also to become ASM International Ambassador for class honours degree in biochemistry at the and was also heavily involved Western Europe from 1 July. Running from 25 June–4 July, the Festival also University of Aberdeen. She then studied for in the organization of the highly explores links between the sciences and arts and a PhD with Neil Gow in microbiology and the Colin Hill, University College Cork, Ireland who successful SGM stands at the features a host of cross-disciplinary collaborations, rest is history. Alex is now setting up her own has been elected a Fellow of the American Academy Chelsea Flower Show. scientific and artistic events. research team to work on Candida albicans. of Microbiology. Royal Society special stamps Deaths It is with great sadness that we have to report the death of a member of the SGM staff, Royal Mail have launched a set of special stamps to celebrate this anniversary. They feature Dr Duncan McGarva. An obituary of Duncan appears on p. 133. 10 iconic Fellows, two of whom are famous in the annals of the history of microbiology: Edward The Society also notes with regret the deaths of Dr Milan V. Nermut, formerly of NIMR, Mill Jenner (vaccination) and Joseph Lister (antiseptics). Each stamp (see above – images courtesy Royal Hill (member since 1972), and Dr harry A. painter, formerly of the Water Pollution Research Mail) pairs the famous scientist’s portrait with dramatic and colourful imagery representing their Laboratory, Stevenage who joined SGM in 1954. achievements. A range of prestigious awards is made by Fleming Award Undergraduate Microbiology SGM Undergraduate Microbiology nts Scientific Meetings the Society in recognition of distinguished This is awarded annually for Prizes Prize. Submissions can only be contributions to microbiology. Nominations are accepted on the form which has Travel Grants outstanding research in any The prizes aim to encourage now sought for the 2011 prize lectures. The branch of microbiology by a been sent to all institutions. The Support for early-career microbiologists wishing excellence in the study of RA award panel will consider the submissions in young microbiologist in the full rules and further copies of the to present work at a scientific meeting in the UK microbiology by undergraduate the autumn and take their recommendations to early stages of his/her career. form may be downloaded from or overseas. Graduate research assistants and students and to promote G lecturers (within three years of first appointment November Council for approval. The outcome The winner receives £1,000 and the SGM website or obtained scholarship in, and awareness of, in both cases), postdoctoral researchers will be announced in the February 2011 issue gives a lecture based on his/ from the Grants Office at microbiology in universities. The SGM has a wide range of grant (within three years of first appointment) and of Microbiology Today. Prize lecture rules and a her work to a Society meeting. Marlborough House. The closing prizes are awarded annually to schemes to support microbiology. nomination form are on the SGM website: The text is usually published in a postgraduate students are eligible to apply. the undergraduate student in date for nominations is 27 August See www.sgm.ac.uk for details. www.sgm.ac.uk/about/prize_lectures.cfm Society journal. Retrospective applications are not considered. each qualifying institution who 2010. Any enquiries should be made performs best in microbiology in A 2009 undergraduate prize international schemes Colworth Prize Lecture to the: their penultimate year of study recipient found the award to be of International Development Fund This is awarded biennially for an more than monetary value. Santa Grants Office for a Bachelor’s degree. Each The fund exists to provide training courses, outstanding contribution in an Kumari Gurung of London SGM winning student will be awarded publications and other assistance to area of applied microbiology. It Marlborough House £150, a certificate and a free year’s Metropolitan University wrote to microbiologists in developing countries. is sponsored by the Colworth Basingstoke Road SGM undergraduate membership of the the Society, ‘I am very honoured Laboratory of Unilever Spencers Wood President’s Fund for Research Visits SGM. and surprised to be the recipient Research. The winner receives Reading RG7 1AG Up to £3,000 is available to support early- One prize is available to of such a prestigious award. I am £1,000 and gives a lecture based tel. 0118 988 1821 career microbiologists who are planning a short each university in the UK and originally from Nepal. I spent 19 on his/her work to a Society fax 0118 988 5656 research visit to another laboratory (minimum PRIZE Republic of Ireland offering a years there. I was always interested meeting. The text is usually email [email protected] visit 4 weeks, maximum visit 3 months). 2010 2010 degree course with a significant in science during my school years and published in a Society journal. Y wanted to make career in science Check out the current schemes,

MA Y content of microbiology. The The Watanabe Book Fund MA so I joined London Metropolitan to ensure that you don’t miss any 76 Fred Griffith Review university chooses the assessed Members who are permanently resident in a 77 LECTURES Lecture microbiological work for which the University to study for a bachelor’s deadlines. developing country may apply for funding to prize is awarded. The submission degree in biomedical science. The DA Y This is awarded biennially acquire microbiology books for their libraries. DA Y O O T free undergraduate membership of T in recognition of long and should be supported by formal These annual awards are available as a result distinguished service to marks, not an informal assessment. the Society for a year will be of great of a generous donation from Professor AND Winning students should have help for my future as I will be able to Student schemes T. Watanabe of Japan. microbiology. The winner attained at least 2(I) overall in their learn about careers in microbiology Postgraduate Student receives £1,000 and gives a The closing date for applications to these schemes degree examinations at the stage and make up my mind in time about Meeting Grants personal overview of an area is 24 September 2010. MicroBiology MicroBiology MicroBiology MicroBiology of microbiology to a Society at which the award is made. it. This award has encouraged me Grants cover travel and AWARDS Universities are now invited to work harder and do better in my meeting. The text is usually accommodation expenses published in a Society journal. to nominate a student for a 2010 studies.’ for attendance at ONE SGM Medical meeting each year. Applications Microbiology Peter Wildy Prize for for a grant to attend the Microbiology Education Nottingham meeting (6–9 Support Grants This is awarded annually for an September 2010) must be Elective Grants outstanding contribution to any submitted by 3 September Funding for medical/dental/veterinary students to area of microbiology education. 2010. work on microbiological projects in their elective The winner receives £1,000 and GRADschool Grants periods. gives a lecture on a topic of his/ Postgraduate Student members Trainee Support Grants her choice at a Society meeting. who are not eligible for a free Funding for SGM members carrying out small Completed nomination forms, place on a Vitae (www.vitae. lab-based microbiology projects during either together with the supporting ac.uk) personal development foundation or specialty postgraduate medical documents, should be sent course (National GRADSchool) training. Up to £3,000 is available towards the to Dr David Blackbourn, c/o may now apply for a grant from consumables costs of a project. SGM HQ. Closing date for all SGM to cover full course fees. nominations: 30 September Retrospective applications are The closing date for both these schemes is

2010. Laura Udakis not considered. 24 September 2010. Sushi. Digital Vision / Thinkstock s s

Dolphin Sushi feast for bacteria e Metabolic minimalism model for Genes from marine bacteria that live on the Less is more for one atypical member of the Porphyra seaweed that’s used to wrap sushi have Glowing squid shed marine cyanobacteria family that has streamlined

cervical cancer ORTS also been found in gut bacteria isolated from its metabolic network to such an extent that it Aquatic animal health scientists light on symbiosis Japanese people, but not in similar gut flora from has ditched several major pathways. The stripped- H Trillions and trillions of bacteria live inside from the University of Florida, North Americans. Scientists from the University down genome of UCYN-A, found in tropical the human gut, providing us with numerous stori testing samples from dozens of Pierre and Marie Curie in Paris, who reported waters worldwide, has left it uniquely suited to of marine mammals, have beneficial biochemical services, in exchange

their work in Nature, sequenced the genetic gy perform a single important function: nitrogen for room and board. The details of how this concluded that dolphins may makeup of Zobellia galactanivorans bacteria taken fixation. Nitrogen fixation fertilizes the oceans, happy symbiosis plays out and the nature of be an ideal model for cervical from the seaweed and searched DNA databases controlling overall biological productivity and the interaction between the host cells and the cancer in humans. Dolphins can thereby affecting how much carbon dioxide the

for matches. They analysed the 11 genes also MICROS bacteria are largely unknown. Now, researchers become infected with multiple present in the Japanese gut microbe Bacteroides oceans absorb from the atmosphere. Scientists at are using bioluminescent bacteria to, quite strains of papillomaviruses that plebius and found them to be responsible for the University of California found that UCYN-A literally, shed light on the matter. Researchers are responsible for causing breaking down carbohydrates in the seaweed. lacks genes essential for a key component of from the University of Wisconsin-Madison cervical cancer in women, yet These genes enable the Bacteroides in the the photosynthetic machinery that splits water have spent 20 years studying the interaction do not develop the disease intestines to help digest sushi when it is eaten. molecules and also the Krebs cycle. The absence between the Hawaiian bobtail squid that lives in themselves. Figuring out why Japan has a long history of eating seaweed and the of the Krebs cycle, central to normal energy- the warm waters of the Pacific and the glowing humans develop cervical cancer researchers believe that over the centuries, the generating pathways, represents an evolutionary bacterium, Vibrio fischeri. The bacterium powers and dolphins don’t could lead marine microbes have swapped genes with and ecological paradox. The finding suggests that the squid’s light organ that is used to confuse to a strategy for preventing the gut organisms. the organism must have found an alternative the disease. There are around nt microbiolo www.nature.com/nature/journal/v464/n7290/ e route of providing energy for nitrogen fixation, 100 different strains of human 2010 c 2010 edsumm/e100408-14.html probably relying on an external source. papilloma viruses and cases Y e

MA Y doi:10.1038/nature08786 MA of individuals being infected 78 with up to eight of these have 79 been reported in humans. Bacterial power grids DA Y Co-infection is thought to be Building batteries DA Y O Microbes that live on the ocean floor appear O T one of the biggest risk factors to have developed a novel way of looking after from GM viruses T for development of cervical each other using electrical communication on a Genetically modified viruses capable of splitting cancer. Dolphins are the only microscopic ‘power grid’, according to scientists water molecules into oxygen and hydrogen atoms animal apart from humans that from Aarhus University in Denmark. If the findings using sunlight could be used to produce unlimited

can harbour co-infections in the are confirmed, the work could revolutionize our ts somE r amounts of ‘green’ energy, according to a new MicroBiology MicroBiology MicroBiology MicroBiology genital mucosa. understanding of how the tiniest ecosystems study. Researchers from Massachusetts have

http://news.ufl.edu/2010/02/18/ operate. Aerobic bacteria that inhabit the seabed gh replicated the first step of the method that plants dolphin/ must live either on top of the sediment and use to photosynthesize, in the hope of producing li compromise their access to the mineral nutrients Bobtail squid. high quantities of hydrogen fuel from water and below, or live below the ocean floor which Matthew Oldfield / Science Photo Library sunlight alone. The scientists genetically engineered a gh

restricts their supply of oxygen. Researchers now i harmless bacteriophage to bind to a catalyst (iridium

think that both populations manage to survive predators that might be lurking in the ocean’s h oxide) and a biological pigment (zinc porphyrin). by communicating electrically through electron depths at night – when the squid is most active. The viruses spontaneously arranged themselves into

transfer. The details of this exchange are unclear, Using microarray technology, the scientists have wire-like structures around these molecules, allowing although it is suggested that the bacteria may charted daily patterns of gene expression in both the catalyst and pigment to harvest sunlight to split be connected to each other on an electric grid, the bacterial and squid cells. They found that water molecules. So far, the team has managed to possibly via tiny metal particles in the sediment, the bacteria seemed to cycle through different use the viruses to split off oxygen; the next stage is

such as iron or manganese. If this theory is proved metabolic states in response to the different food to bring the hydrogen atoms together to form H2 correct, bacteria under the surface would be able sources provided by the host. The researchers UDAKIS gas. Professor Angela Belcher, who led the research, to obtain their energy in the form of electrons say it is quite likely that many of these details are said that although there was much work to do, a and could send nutrients back up to the surface applicable to many animal–microbial associations prototype of a commercial product that carries out Dolphin. via chemical migration. and may provide insight into how pathogenic gut the water-splitting reaction could be developed Stockbyte / Thinkstock http://news.sciencemag.org/sciencenow/ bacteria cause disease. within the next 2 years.

2010/02/-deep-on-the-ocean.html?sms_ss=email Stockbyte / iStockphoto / doi:10.1073/pnas.090971210 LAURA doi:10.1038/nnano.2010.57 Sunlight on the ocean Thinkstock Comstock / Thinkstock

delivering modern microbial science e

Spring 2011 s

r Harrogate International Centre

www.sgm.ac.uk/meetings e u 11–14 April 2011 t Intracellular Life nc

Fu www.sgmharrogate2011.org.uk e

Autumn 2010 r

University of Maynooth e Mo–Fe nitrogenase protein. Laguna Design/SPL; Geobacter metallireducens digesting uranium waste. Eye of Science/SPL 2–3 September 2010 – Scientific Meetings Officer University of Nottingham Jubilee Campus Special Lectures Insect-mediated microbial diseases of ivision ee Peter Wildy Prize Lecture: Dr Sue Assinder Professor Chris Hewitt humans and animals: current problems 6–9 September 2010 Hot Topic Lecture D and future threats tt

email [email protected] conf 2010 Outreach Prize Lecture Organizer: Kevin Kavanagh (email kevin. – Deputy Scientific Meetings Officer www.sgmnottingham2010.org.uk

ish [email protected]; www.sgm.ac.uk/ Dr Evelyn Doyle Also featuring meetings/MTGPAGES/IrdSept10.cfm Ir

UMN Metals and Microbes email [email protected] Sir Howard Dalton Young Microbiologist of the Year Finals T Poster sessions with drinks Spring 2011 – Education Division Microbes have evolved elaborate mechanisms to

AU Queen’s University Belfast scavenge for the metals essential for many metabolic Conference Dinner Dr Sue Assinder 19–20 April 2011 functions. Top international speakers will focus on the Trade Exhibition

ings Commi email [email protected] Microbial viruses: genomics, diversity of microbial metal homeostatic systems and t evolution and applications in ecology, – Eukaryotic Microbiology Division also consider the importance of metals in microbial Grants

ee biotechnology and medicine Professor Neil Gow adaptation and in pathogenicity. Conference grants are available to SGM Associate Members who 2010 2010

M Organizer: Dr Leonid Kulakov

are Postgraduate Students or Technicians. Y email [email protected] MA Y MA c Complementary sessions will cover: i – Irish Division Autumn 2011 80 f Bioremediation of metals CPD 81 i University of Cork Dr John McGrath t Bioleaching of metals – new technologies Approved by the Royal College of Pathologists and the Institute of Marine biotechnology DA Y email [email protected] Biomedical Science. Up to 27 points available. DA Y O O T For details of all Irish Division activities, T ien – Prokaryotic Microbiology Division Other sessions

c contact John McGrath ([email protected]) Who should attend? s Dr Ian Henderson Systems & Cells Anyone who wants to keep up to date with modern microbial

email [email protected] s SGM is supporting the following meetings: Microbial death | Acid stress: surviving and responding | science, no matter what their field or stage of their career. The t – Virology Division Bacterial vesicles | New insights into secondary metabolism | conference will also provide a great opportunity for networking. 4th Annual Irish Fungal Meeting MicroBiology MicroBiology MicroBiology MicroBiology Professor Mark Harris Protein folding and misfolding 24–25 June 2010 ven email [email protected] University College Cork, Ireland Accommodation E

Contact: [email protected] Medical & Clinical Microbiology Dinner, bed and breakfast is available in en-suite accommodation

– Meetings Manager r Respiratory and septic infections | Microbial models of on site. Book through the SGM meetings office. Sub-nuclear Structure and Disease Susan Leonard human disease | Streptococci he 27–30 July 2010 tel. 0118 988 1832 Deadlines Wellcome Trust Conference Centre, Environment Ot fax 0118 988 5656 Abstract submission: 11 June 2010 Hinxton, Cambridge, UK Extremophiles | Microbiology in the indoor environment email [email protected] Earlybird registration: 6 August 2010 https://registration.hinxton.wellcome. ac.uk/display_info.asp?id=193 Suggestions for topics for future Industry symposia are always welcome. Industrial Biotechnology 2025 Federation of Infection Societies 17–19 November 2010 Abstracts Learning & Teaching Edinburgh International Conference Titles and abstracts for all presentations Centre Learning from the evidence: improving microbiology Edinburgh Meeting Abstracts must be submitted through the SGM www.fis2010.co.uk teaching through educational research 29 March – 1 April 2010 website by the advertised deadlines. European Society of Clinical Virology Systems, Mechanisms and Micro-organisms Workshops society for general microbiology 13–15 January 2011 Prokaryotic taxonomy The full text of the abstracts is available online at: www.sgm. Institute for Child Health, London sgmconferenceswww.sgm.ac.uk/meetings Personal development for early-career microbiologists ac.uk/meetings/pdfabstracts/edinburgh2010abs.pdf www.escv.org/meetings/meetings.asp Beyond

the infinite – Winter sun over a Norwegian Metatranscriptomics fjord. iStockphoto/Thinkstock tracking enable us to study whole bacterial communities of bacteria. Observing gene how microbial 2010

marine ecosystems 2010 Y MAY MA expression respond to external 82 83

DA Y stimuli could ODAY O T T lead to a greater iology understanding of B icro MicroBiology MicroBiology Jack A. Gilbert climate change. M If the number of known stars in the Milky Way cell is capable of, it doesn’t tell us whether that cell ever colossal number of interactions within their diet from fine French cuisine to Ocean acidification and is multiplied by the number of known galaxies in the takes advantage of this capability. Transcriptomics gives us a system as complex as even one tea- fast food? The technique of meta- the metatranscriptome universe the result is a huge number, a septillion (11024). a snapshot of which genes are expressed (transcription – spoon of seawater. Hence, enter ‘meta- transcriptomics is analogous to using Ocean acidification is currently Yet, large as this is, it pales in comparison to the number of see Fig. 1) and by comparing the transcriptomic profile transcriptomics’ – meta is taken from a satellite to examine how a city occurring in our seas and oceans as

microbial cells found in the world oceans, estimated to be of a cell as it moves between different environments, we the Greek for beyond, and the term works; we can see trains and cars a result of the CO2 we emit into the 1 nonillion (11030). When we start to include soil, air and can start to understand how an organism will respond to describes our observations of the trans- moving around, rush hour, lunch atmosphere being absorbed into organism-associated environments, this number becomes changes within its ecosystem. But bacteria do not live by cription of a whole community at once. hour, etc. When we unsettle the city, the seawater that covers 70% of our unimaginable. Traditional microbiology is our gold stand- themselves. Invariably they live in communities made of for example with a bomb threat, a planet, where it converts into car- ard for understanding how these trillions and trillions of polymerized sugars stuck to a solid surface. Those that Metatranscriptomics – sudden change in how it functions bonic acid, thus reducing the pH. In bacteria function. Basically, we grow the bugs in a labora- are free-living, generally still require interactions between asking the big questions can be spotted. Some processes, such 2006, we performed a large-scale tory, one species at a time, and test how they respond to themselves and other bacteria, archaea and eukarya in their Treating the community as if as taxi journeys, will keep ticking experiment where six plastic bags, chemical stimuli. Ultimately, we sequence their genome ecosystem, from which they will receive nutrients, chemi- it was a single cell when searching along, while others, such as security, each containing 11,000 litres of and try to map their genes to particular functions. To help cals and communications, much like a human community. for big changes in it, has many will suddenly increase, and some, such water, were suspended in a fjord off

make this link we can observe the expression of these genes When we include viruses, which will kill some organisms, advantages. This is ideal when we as deliveries, will suddenly reduce. the coast of Norway. CO2 was bub-

in response to certain stimuli, so called transcriptomics. prolong the life of others, and move genetic material ask big questions, such as how does Seeing how a community responds to bled through the water in three of between different species (even different kingdoms), the an ecosystem respond to climate a change in the environment enables these bags, while air was bubbled Beyond the Transcriptome complexity increases further still. It quickly becomes change or pollution, or what hap- us to identify specific questions or through the others. We wanted to While looking at the genome of an organism and apparent that understanding how one organism responds to pens to the bacterial community in hypotheses which we need to exam- know how the microbial community classifying the function of its genes can tell us what that specific stimuli, while important, will fail to encompass the someone’s intestine when they change ine with more detailed analysis. would respond to the increased Plymouth

25m

L4 15ʹ 50m Trawling area mRNA responds to change. In addition, meta- Gene transcriptomics is only one power tool Eddystone in the toolbox. To fully understand Protein the community dynamics we need L5 A 10ʹ to perform multi-’omic observations using metagenomics, metaproteomics Genome Fig. 1. Transcription is the action of a gene being transcribed into Zooplankton series messenger (m)RNA, which is also called a transcript. The transcript and metametabolomics to determine Ribosome then binds to a ribosome which translates it into a protein. J.A. Gilbert changes in the genomic potential, protein inventory or metabolite L6 5ʹ profile. When combined with meta- acidity which has been predicted for the sea by the year Metatranscriptomics transcriptomics we have information 2100. and fundamental Fig. 2. The from the four key areas of cellular To determine how the gene expression profile of the microbial ecology Western Channel information storage (Fig. 1). community changed in response to the acidification, we Observatory Understanding how microbes E1 extracted mRNA from an acidified bag and an air-bubbled function and interact in an ecosystem network of observation sites. A word on bag and used the technique of pyrosequencing to read mil- is vital if we are to act as responsible 0ʹ N Hydrographical series We primarily focus environmental data lions of the mRNA fragments from each. We found that stewards of the Earth’s natural re- on the L4 site, One thing to always consider in the acidified bag there was an increase in the expression sources. As with ocean acidification, which we sample is that without information about of bacterial proton pumps, which was expected, because we need to know how our actions 75m weekly. www. the environment from which these greater acidity results from an increase in hydrogen ions will affect the functioning of an westernchannel 25ʹ 20ʹ 15ʹ 4°10ʹ W observatory.org meta-’omic observations are made, (H+) or protons in the environment. This suggested that ecosystem so that we can protect it; if the community was responding to this potential threat by you were asked to drive your friend’s we can reach no meaningful conclu- removing the excess protons from their cells to maintain Ferrari, you would want to make sure Over the last 7 years we have been During the summer we also sions regarding the relationship of their own internal pH at a comfortable level. you knew how to drive and how the expanding our understanding of the see transcriptional responses to the these observations to the ecosystem.

2010 Contextual information such as 2010 Another interesting finding was that in acidified water car worked before you did so, or they diversity and function of the micro- reduced availability of nutrients 2010 Y the community expressed far more chaperone proteins. These might not be your friend for long! bial community in this ecosystem, with a considerable increase in the temperature, rainfall, pH, nitrate MAY MA are proteins which help other proteins to function under Similarly, it is vital we understand and we now track the ebb and flow abundance of transcripts that encode concentration, salinity, etc. help us MA Y 84 stressful conditions by helping to maintain their structure how microbes drive an ecosystem, of more than 10,000 bacterial species nutrient transport proteins that act to to build up a picture of the condi- 85 or facilitate access to the substrate they are acting on. how they recycle nutrients and the air as the community changes within and move phosphorus and nitrogen across tions which have acted to create the DA Y What we found from looking at the metatranscriptome we breathe, how they produce food; between years. the cell membrane. When there is not metatranscriptome in the first place. DA Y ODAY O O T T T

was that the community was adapting to the increased for example, for fish to maintain our Recently, we started to use meta- a lot of this about, the microbes start When comparing studies, it is even acidity of the water. It was not apparently under any con- fish stocks, and what environmental transcriptomics to explore how the to scavenge and hoover-up all they more essential to have a minimal set siderable stress, but it was responding to it. conditions most affect how they can communities at this site change their find. Again, these studies provide of data to determine the main key iology

We are getting ready to perform this same experiment perform these tasks. gene expression between day and us with information about how the differences between the environments. B in the Arctic this June (www.epoca-project.eu/). The night in different seasons (winter, community is responding to natural The Genomic Standards Consortium icro MicroBiology MicroBiology M Arctic Ocean has been chosen because its communities, Western spring and summer). Strikingly, we changes, which helps us to predict (www.gensc.org) is a non-profit org- MicroBiology potentially, are more fragile than those in the coastal North English Channel: found that microbial communities how they will change when they anization which aims to coordinate Sea; so we expect to see a more severe response to the L4 – a model showed a significant increase in the experience man-made stresses, such as the community to produce a list of acidified conditions. By comparing these two experiments ecosystem expression of genes involved in pollution and climate variability. essential data which must be recorded we will be able to determine what cellular functions are at In Plymouth, we have been explor- photosynthesis during the winter to provide context for these studies. compared to the spring or summer. most risk, and therefore if the impact of ocean acidification ing, cataloguing and experimenting Metatranscriptomics – Without this effort, most studies will will actually threaten the function of these communities. As Obviously, the expression of photo- the future in the L4 sampling site (www.western exist in isolation and reduce the value they are responsible for the vast majority of the recycling channelobservatory.org.uk – Fig. 2) synthetic genes, which require light, Using pyrosequencing to explore of these expensive and time-consum- of the world’s gases and nutrients and approximately half of for more than 100 years. For the last always occurred during the day, but the unknown transcriptome of a ing datasets for future researchers. the world primary productivity, it is extremely important 20 years we have sampled this site the seasonal trend supports previous community has provided us with a that we know this. every week using our research vessels. findings that have shown that, despite valuable tool with which to compare the reduced light availability in the and contrast communities exposed Dr Jack A. Gilbert is a Senior winter, microbial photosynthesis is to different conditions. However, Molecular Ecologist at Plymouth Marine Laboratory, “Understanding how one organism responds far more important in that season, new sequencing platforms, such as Prospect Place, The Hoe, Plymouth PL1 3DH whereas it is larger algae which domi- third-generation Illumina and SOLiD (email [email protected]) to specific stimuli, while important, will fail to nate during the spring and summer. systems, will be able to characterize Additionally, we see very specific a metatranscriptome to greater effect Further reading encompass the colossal number of interactions patterns in the metatranscriptome so that we can start to look deep into Gilbert, J.A., Field, D., Huang, Y., Edwards, R., Li, within a system as complex as even one between day and night with a lot the less abundant transcripts and W. & others (2008). Detection of large numbers of of cell division processes occurring understand how the subtle changes novel sequences in the metatranscriptomes of complex teaspoon of seawater.” during the night, and a lot of meta- in community gene expression may marine microbial communities. PLoS ONE 3(8), bolic activity during the day. be influencing how the community e3042. doi:10.1371/journal.pone.0003042 Background Prochlorococcus cells. Claire Ting / Science Photo Library David G. Adams Cyanobacteria are the most environmentally significant group of bacteria on Earth. What is it that makes them so important?

Stromatolites at Hamelin Pool Marine Nature Reserve, Shark Bay, Western Australia. Stromatolites are formed by the trapping of sediments and calcium carbonate in a biofilm dominated by cyanobacteria. Georgette Douwma / Science Photo Library Cyanobacteria 2010 2010 Y MA MA Y 86 87

Cyanobacteria are a huge which are organosedimentary structures formed in tidal Fluorescence micrograph of Trichodesmium DA Y group of photosynthetic bacteria zones by the trapping of sediment and calcium carbon- IMS 101 showing the localization of the DA Y O O T found in almost every environment ate in microbial biofilms dominated by cyanobacteria. nitrogenase enzyme detected with a specific T on Earth, including many of those Stromatolites are still forming today, but fossil forms antibody (blue fluorescence). The nitrogenase most inhospitable to life, such as hot have been found in rocks dating back at least 2.7 and protein is restricted to a subset of cells in the filament. Reproduced with permission from Díez springs, deserts and the Antarctic. possibly as much as 3.5 billion years, although their heyday et al. (2008) They are also enormously abundant, was probably around 1.25 billion years ago. Cyanobacteria MicroBiology MicroBiology particularly in the oceans, and are may have made their first appearance as much as 3.5 billion MicroBiology primary producers, meaning that they years ago, although this date has been questioned. Certainly

fix CO2 and in many cases also N2; as they were present by the time of the massive oxygenation a consequence they have an immense of the atmosphere which occurred around 2.4 billion influence on the planet’s nutrient years ago. cycles and even its weather. Life on The evolution of oxygenic photosynthesis created a

Earth owes a further great debt to problem for N2-fixing cyanobacteria because nitrogenase,

this group of bacteria because their the enzyme responsible for the fixation of 2N , is evolution of oxygenic photosynthesis, irreversibly inhibited by oxygen. As a consequence, in which oxygen is released from cyanobacteria have evolved a number of strategies to the splitting of water, resulted in the protect nitrogenase from oxygen inactivation, including

eventual oxygenation of the atmos- the temporal separation of N2 fixation (at night) and phere, providing the stimulus for the oxygen-evolving photosynthesis (in the day). However, evolution of complex life forms. In the most complex strategy is the development of a special- addition, cyanobacteria are the ances- ized cell, the heterocyst, which maintains a microaerobic tors of plastids, the photosynthetic interior ideal for nitrogenase to function. Heterocystous organelles of today’s algae and plants. cyanobacteria are some of the most complex of all Cyanobacteria are an ancient bacteria, capable of differentiating not only the heterocyst, group, but when did they evolve? but also the spore-like akinete (which is resistant to cold Answering this question has proved and desiccation), and in many genera, specialized motile controversial. The best fossil record of filaments known as hormogonia which are a means of cyanobacteria is found in stromatolites, dispersal. MARINE CYANOBACTERIA by animals and humans. Baltic Sea Vast areas of the oceans are blooms tend to be dominated by

dominated by the picophytoplank- the N2-fixing heterocystous cyano- ton, consisting of photosynthetic bacteria Nodularia spumigena and organisms in the 0.2–2 µm size range. Aphanizomenon, whereas in the open

The picophytoplankton is in turn ocean, blooms of N2-fixing but dominated by two genera of unicel- non-heterocystous Trichodesmium are lular cyanobacteria, Prochlorococcus and common. Synechococcus, the remainder being

a diverse mix of eukaryotic algae. N2 FIXATION

Approximately half of all CO2 fixa- Approximately half of global N2 tion occurs in the oceans, where the fixation occurs in the oceans and picocyanobacteria are the dominant almost all of this is attributable to primary producers and, along with cyanobacteria, the most important the eukaryotic phytoplankton, sit at of which is probably Trichodesmium, the base of the food chain, support- although the heterocystous Richelia ing the immense food webs in the (an endosymbiont in several species oceans. Prochlorococcus strains can be of large diatom, such as Rhizosolenia divided into two ecotypes, one adap- and Hemiaulus), and even unicellular ted to high light and the other to low cyanobacteria, make important con-

light, the latter being found in large tributions. Cyanobacterial N2 fixation numbers only in deeper water to a is the dominant source of nitrogen in depth of 200 m where the light the open ocean, whereas inputs of N irradiance is a mere 0.1% of that at from rivers and from the atmosphere

2010 the surface. These picocyanobacteria have their greatest effect in the coastal 2010 Y are the smallest and most abundant regions and the continental shelf. MA MA Y photosynthetic organisms in the Although N2-fixing cyanobacteria are 88 oceans. At the other end of the size found worldwide in freshwater and 89

scale is the filamentous, 2N -fixing terrestrial environments where temp- DA Y cyanobacterium Trichodesmium, which eratures seldom reach 25 °C, in the DA Y O O T is also enormously abundant and can oceans cyanobacterial N2 fixation is T form immense surface accumulations restricted to the tropics and subtropics known as blooms. where the temperature exceeds 25 °C. The reason for the discrepancy re- BLOOMS AND TOXINS mains unclear. Another surprise is that MicroBiology MicroBiology Cyanobacterial populations in the only heterocystous cyanobacteria MicroBiology freshwater lakes, brackish water bodies in the oceans are the symbiotic forms such as the Baltic Sea and in the found in some diatoms. Why is this? oceans can at times grow to such great One possibility is that the relatively size and density that they can be low oxygen concentrations in warm seen from space. For example, in seawater, together with elevated res- the Baltic Sea such blooms can piration rates at higher temperatures, cover an area of up to 200,000 km2. enable non-heterocystous cyano- Many bloom-forming cyanobacteria, bacteria to maintain sufficiently low particularly in fresh and brackish water, intracellular oxygen levels for efficient

produce a range of potent toxins N2 fixation. These conditions may that can be lethal when ingested actually disadvantage heterocystous “Free-living cyanobacteria, especially marine strains, produce an enormous range of unusual and potentially useful metabolites.”

A summer phytoplankton bloom, approximately 200 km in length, filling much of the Baltic Sea in 2005. European Space Agency/Envisat “In many ways life on Earth owes its very existence to the A cyanobacteria and they continue to have an enormous influence

Phase contrast micrograph of the filamentous cyanobacterium A on the Earth’s nutrient cycles on Anabaena cylindrica. Some of the vegetative cells in each filament have differentiated into either nitrogen-fixing heterocysts (arrows) which all life depends.” or the cold- and desiccation-resistant cells known as akinetes (A). D.G. Adams

strains which must make energetically sometimes fixed carbon from photo- reefs. Interest in sponges has increased important roles in reef ecology as nutrient cyclers and way because recent experiments with Nodularia spumigena

expensive heterocysts to fix N2. synthesis. In the oceans, in addition rapidly in the last decade or so, largely primary producers, and they provide food and a habitat for from the brackish Baltic Sea have shown that it responds to

to the cyanobacterium Richelia, N2- because they produce a wide array a wide range of organisms. Their cyanobacterial symbionts elevated CO2 with a decrease in both N2 fixation and cell SYMBIOSES AND fixing cyanobacteria can be found as of biologically active secondary meta- confer several advantages over the algal symbionts in other division. An additional complicating factor is iron; this is SECONDARY METABOLITES symbionts in at least one coral and a bolites with antiviral and anticancer photosynthetic sponges because they have a wider tempera- an essential part of the nitrogenase enzyme, and its avail-

Cyanobacteria form symbiotic dinoflagellate. There are also approxi- activity, some of which derive from ture tolerance, produce sunscreens and can photosynthesize ability may constrain any future increases in N2 fixation.

2010 In many ways life on Earth owes its very existence to associations with a wide variety of mately 100 species of cyanosponge the cyanobacterial symbionts. Indeed, at very low light, enabling their hosts to grow in full sun in 2010 Y hosts including many plant groups, hosting unicellular and filamentous free-living cyanobacteria, especially intertidal zones and at low light in shaded areas, even in caves. the cyanobacteria and they continue to have an enormous MA fungi and animals such as marine cyanobacteria, and they typically marine strains, produce an enormous influence on the Earth’s nutrient cycles on which all life MA Y 90 worms and sponges. The cyanobacteria constitute 30–50%, but sometimes range of unusual and potentially use- GLOBAL WARMING depends. Their massive abundance in the oceans means 91

provide the host with fixed 2N and up to 90% of the sponges on tropical ful metabolites. Cyanosponges play Global temperature increases and an elevation in CO2 that the health of the marine cyanobacterial population is DA Y in the atmosphere will have impacts on the phytoplankton of crucial importance to the health of the planet, empha- DA Y O O T in the oceans, which may in turn have consequences for sizing the importance of understanding the impacts that T global nutrient cycles and even the weather. Recent obser- continuing climate change will have on this remarkable vations that the cell abundance of phytoplankton increases group of bacteria. with temperature appear to be at odds with the measured 60 decrease in total phytoplankton biomass due to continuing Dr David G. Adams is Senior Lecturer in the Institute of Integrative MicroBiology MicroBiology global warming. How can this be? The answer may be and Comparative Biology, University of Leeds, Leeds LS2 9JT (email d.g.adams@ MicroBiology that warming of the oceans is resulting in a decrease in the leeds.ac.uk) size of individual phytoplankton cells. If true, this will have impacts on the biogeochemistry of the oceans, including FURTHER READING a reduced potential for carbon sequestration, because the Bracher, A., Vountas, M., Dinter, T., Burrows, J.P., Rottgers, R. & Peeken, I. (2009). sinking velocity of phytoplankton is inversely dependent Quantitative observation of cyanobacteria and diatoms from space using PhytoDOAS 0 on cell size, so a shift to higher populations of picophyo- on SCIAMACHY data. Biogeosciences 6, 751–764. plankton will reduce sinking. Díez, B., Bergman, B. & El-Shehawy, R. (2008). Marine diazotrophic cyanobacteria:

Enrichment of the oceans with anthropogenic CO2 out of the blue. Plant Biotechnol 25, 221–225. helps mitigate global warming, but the cost is a reduction Hutchins, D.A., Mulholland, M.R. & Fu, F. (2009). Nutrient cycles and marine

in pH, which in turn has consequences, some of which are microbes in a CO2-enriched ocean. Oceanography 22, 128–145. already apparent. For example, calcifying organisms, Morán, X.A.G., López-Urrutia, A. Calvo-Díaz, A. & Li, W.K.W. (2010). Increasing such as corals, are being damaged by reduced rates of importance of small phytoplankton in a warmer ocean. Global Change Biology 16, –60 calcification and increased dissolution of calcium carbon- 1137–1144. ate. However, predicting likely outcomes is never easy, Scanlan, D.J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W.R., Cyanobacteria as demonstrated by experiments with the N2-fixing Post, A.F., Hagemann, M., Paulsen, I. & Partensky, F. (2009). Ecological genomics absorption (15 cyanobacteria Trichodesmium and Nodularia. Evidence from of marine picocyanobacteria. Microbiol Mol Biol Rev 73, 249–299. October to 14 –180 –120 –60 0 60 120 180 laboratory experiments with Trichodesmium, which is Stal, L.J. (2009). Is the distribution of nitrogen-fixing cyanobacteria in the oceans November 2005). Reproduced with thought to be responsible for half of all marine N2 fix- related to temperature? Environ Microbiol 11, 1632–1645. ation, suggests that higher CO availability in the oceans Whitton, B. & Potts, M. (editors) (2000). The Ecology of Cyanobacteria: Their 0.00 0.25 0.50 0.75 1.00 1.25 1.50 1.75 2.00 2.25 permission from 2 Bracher et al. may lead to an increase in N2 fixation. However, it seems Diversity in Time and Space. Dordrecht: Kluwer. (A new version of this book is due Absorption strength (2009) that not all N2-fixing cyanobacteria behave in the same to be published in late 2010 or early 2011.) Parasites are typically small organisms that exploit 18S ribosomal RNA gene). All investi- occurrence of such parasites in range of hosts such as dinoflagellates, their host both as a food source and as a habitat. Although gations performed so far have shown the As global warming marine waters. Interestingly, recent ciliates, cnidarians, crustaceans (like well-studied as human pathogens and organisms prejudicial overwhelming occurrences of environ- studies performed with the smallest copepods and crabs), chaetognaths, to human interests, they have been persistently ignored mental DNA sequences affiliated to planktonic fraction taken from lakes radiolarians and fish eggs. Indeed, in microbial aquatic ecology. Increased awareness of the novel eukaryotic lineages that have been takes hold, research also revealed a high proportion of these parasites potentially affect most important role of viruses in marine aquatic ecosystems in grouped under the term of MALV (for environmental sequences belonging marine planktonic organisms. In processes as diverse as species competition, carbon cycling, MArine ALVeolate). These enigmatic to putative parasites (mainly chytrids, particular, Syndiniales includes the and gene transfers has recently changed our overall view of new lineages represent up to 50% shows that a group Cercozoa, Perkinsozoa and Colpo- widespread genus Amoebophrya, aquatic parasites. Recent evidence of the widespread occur- of sequences retrieved in all marine dellids). Although different lineages known to infect a large number of (if rence of small eukaryotic parasites, requiring eukaryotic environments, from coastal waters to have been retrieved from marine and not all) dinoflagellate species, includ- hosts, has highlighted the existence of another kind of deep hydrothermal vents. They are of eukaryotic marine freshwater ecosystems, these converg- ing several responsible for toxic ‘red pathogen which potentially has specific ecological roles. everywhere. ing observations show the ecological tides’ (Fig. 1). The Amoebophrya vege- Today, MALV sequences are parasites could have significance of small eukaryotic para- tative life-cycle takes about 2–3 days The (re-)discovery of the existence of believed to belong to Syndiniales, a sites in aquatic environments. and is characterized by alternation eukaryotic parasites among plankton group of species composed to date between a small, free-living stage 2010 2010 Y During the last decade, novel eukaryotic lineages have exclusively of marine parasites, which a far-reaching impact Ecological significance (the dinospore) and an endoparasitic MA been discovered within the smallest fraction of marine have been known for more than a of Syndiniales growing stage (the trophont) (Fig. MA Y 92 eukaryotic plankton using culture-independent methods century! Indeed, molecular techniques Described Syndiniales species are 2). The life-cycle starts when a dino- 93 (mainly by the analysis of the genetic diversity of the have clearly revealed the widespread on marine ecology. all obligate parasites, and infect a wide spore, a biflagellate cell 2–10 µm in DA Y DA Y O O T T The ecological MicroBiology MicroBiology significance of MicroBiology small, eukaryotic Laure Guillou

Fig. 1. Red tide produced by dinoflagellates in the Bountiful Islands, parasites in Gulf of Carpentaria in Queensland, Australia, potentially resulting Catharina Alves-de-Souza from the displacement of populations induced by the global warming and the absence of natural pathogens in the area of introduction. Bill Raffaele Siano Bachmann / Science Photo Library marine Background. Sun glinting off sea surface. AbleStock.com / Thinkstock Humberto González ecosystems “Although different lineages have been retrieved from marine and freshwater ecosystems, these converging observations show diameter, invades a host cell. The Dinoflagellate trophont grows inside the host until it nucleus the ecological significance of small eukaryotic breaks the host cell wall. At this stage, Initial it may produce a synchronous swim- infection parasites in aquatic environments.” ming colony (a sort of long filament Dinospores of cells), called the vermiform stage. first introduced in terrestrial ecology, but can be adapted population regulation and microbial communities. This To complete the cycle, each cell of to planktonic organisms. In our case, this is an interesting could be particularly relevant at the surface of all oceans, the vermiform stage differentiates into explanation for the general increase of blooms in the con- where microbial food webs usually dominate the transfer of many dinospores, which are released text of global warming and an illustration of the ecological carbon through complex trophic interactions. They may rapidly. Considering that one infec- role of eukaryotic parasites. also have a key role in the regulation of invasive species tion eventually produces hundreds of in the context of the recent global warming and host Mature dinospores, each one able to infect a Implications of Syndiniales for food migrations. However, more quantitative studies are required trophont new host, these parasites are likely to webs and carbon flow to better evaluate the functional role of these parasites have the capacity to control their host Considering the wide host range of Syndiniales, these and their contribution to carbon flow in marine food webs. population. This hypothesis is in fact parasites could have a key role in marine planktonic food In comparison, major differences exist between the Vermiform supported by numerous field observa- webs and fisheries. However, the ecological impact of regulation of viruses and parasitic eukaryotes. Dinospores tions reporting episodic outbreaks such eukaryotic parasites remains to be conceptualized and are known to be actively grazed by microzooplankton, of hosts infected by Syndiniales, considered by biogeochemical models. All species known whereas viruses are not consumed. Also, viral infections sometimes with significant loss to to date are highly virulent, as infection generally voids host seem to be particularly relevant for very small organisms, metazoan fisheries (for example Hematodinium, cell replication and results irremediably in death of the like bacteria and nanoflagellates, while the ecological roles food web a virulent parasite of crustaceans such host. Estimates based on culture experiments using dino- of eukaryotic parasites are directed towards larger hosts. as crabs and lobsters). However, the flagellate hosts suggest that almost half of the host biomass Thus the ‘dino loop’ could constitute an important trophic Fish ecological role of Syndiniales has been is transformed into dinospores; the rest is rapidly incor- pathway in the recycling of carbon through different particularly well-studied in the case of porated into the pool of particulate and dissolved organic compartments of marine trophic webs.

2010 Amoebophrya species infecting noxious

matter (POM and DOM) and used as substrates by marine 2010

Y Tunicates Dr Laure Guillou works at CNRS (Centre National de Recherche dinoflagellate species able to produce Jellyfish bacteria. Syndiniales dinospores can be very abundant

MA Scientifique), UMR 7144, Station Biologique of Roscoff, Place Georges Teissier, MA Y ‘red tides’. within the smallest size fractions of marine eukaryotic BP 74, 29682 Roscoff Cedex, France (email [email protected]). 94 Dinoflagellates are important pri- plankton. Sometimes they can account for an impor- 95 Meso- Catharina Alves-de-Souza is a PhD student at the University mary producers in coastal areas. Some tant proportion (>25%) of nanoplanktonic (2–20 µm) zooplankton of Paris 6 and University Austral of Chile (email [email protected]). DA Y species may proliferate and change the DA Y microbial organisms and can constitute a suitable food source for O Dr Raffaele Siano works at the Taxonomy and Identification of O T colour of seawater, forming blooms microzooplankton (the heterotrophic protists between T food web Marine Phytoplankton (TIMP) facility of the Stazione Zoologica A. Dohrn Villa known as ‘red tides’. Dinoflagellates 20–200 µm). Like viruses, these parasites reroute a sub- Nano- Comunale, 80121 Naples, Italy (email [email protected]). like warm and stratified waters. Thus, Micro- stantial proportion of the carbon invested in the general phytoplankton Dr Humberto González is a researcher at the University Austral global warming favours this group Micro- phytoplankton food webs, and interfere in the competition between of Chile, Institute of Marine Biology, Campus Isla Teja, PO Box 567, Valdivia, of microalgae. The increasing occur- zooplankton species by preferentially infecting the most actively growing Chile (email [email protected]) MicroBiology MicroBiology rence and geographical expansion of species. This process is called the viral loop (or viral shunt) MicroBiology red tides is consequently a worldwide Pico- for viruses. The myco loop describes a similar pathway FURTHER READING phenomenon. In addition, such phytoplankton for chytrids infecting freshwater diatoms. Additionally, Chambouvet, A., Morin, P., Marie, D. & Guillou, L. (2008). Control of toxic marine Nano- Dino proliferations are often recurrent zooplankton eukaryotic parasites are particularly efficient infective dinoflagellate blooms by serial parasitic killers.S cience 322, 1254–1257. because many dinoflagellates can Loop agents of large, inedible dinoflagellates, releasing carbon viral Montagnes, D.J.S., Chambouvet, A., Guillou, L. & Fenton, A. (2008). Can produce resistant stages, or cysts, that biomass potentially refractory to microbial grazing activity. microzooplankton and parasite pressure be responsible for the demise of toxic loop contaminate sediments for a long The myco loop describes a similar pathway for chytrids dinoflagellate blooms? Aquat Microb Ecol 53, 201–210. time. It has been suggested that these Viruses Bacteria/ infecting freshwater diatoms.. By homology, Syndiniales Guillou, L., Viprey, M., Chambouvet, A., Welsh, R.M., Massana, R., Scanlan, D.J. archaea Dinospores proliferations are favoured by the produce a ‘dino loop’ within marine food webs, from & Worden, A.Z. (2008). Widespread occurrence and genetic diversity of marine absence of efficient pathogens in new microalgae to large metazoans. parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10, 3349–3365. areas they colonize. Thus, a blooming Park, M.G., Yih, W. & Coats, D.W. (2004). Parasites and phytoplankton, with species is in fact one species escap- DOM Conclusion special emphasis on dinoflagellate infections.J Euk Microbiol 51, 145–155. ing its natural enemies for a period POM That fact that Syndiniales parasites constitute a very Kagami, M., de Bruin, A., Ibelings, B.W. & Van Donk, E. (2007). Parasitic chytrids: of time. This hypothesis, also called diverse and widely distributed parasitic group suggests their effects on phytoplankton communities and food-web dynamics. Hydrobiologia the ‘Enemy Release Hypothesis’, was that they could play an important role both in host 578, 113–129.

Fig. 2 (top). Life cycle of Amoebophrya sp. infecting Neoceratium minutum. Red, nucleus of the host and the parasite; green, cytoplasm of the parasite detected by fluorescent in situ Hybridization. Samples taken from the Mediterranean Sea, collected during the BOUM cruise. C. Alves-de-Souza

Fig. 3 (bottom). Parasitic loops in marine food webs. A potential role for eukaryotic parasites is highlighted by the dino loop pathway that parallels the viral loop for smaller organisms. DOM, Dissolved organic matter; POM, particulate organic matter. L. Guillou & C. Alves-de-Souza all the phage on earth “Assuming an average length of 100 nm, lined end-to-end, all the phages on the earth would extend a distance10 of million10 million light light years.” years.

K. Eric WommacK Far left. TEM image of viruses from a Delaware soil sample. Reproduced with permission from Williamson et al. (2003)

Left and background. TEM image of viruses from a Chesapeake water sample. Reproduced with permission from Wommack & Colwell (2000)

Metagenomics is now revealing the amazing diversity and abundance of viruses in the biosphere…

Although it happened just over 20 years ago, the we still find ourselves pondering the memory of leafing through the 10 August 1989 issue of same essential ecological questions: 2010

Nature on a bright morning in the tea room of the Gatty how abundant and how diverse are 2010 Y Marine Lab remains fresh in my mind. I had come across natural viral assemblages? MA the now infamous paper by Øivind Bergh, Knut Børsheim, MA Y 96 Gunnar Bratbak and Mikal Heldal, a group of marine How abundant? We 97 microbiologists from the University of Bergen, that really don’t know DA Y reported the initial discovery that free virus particles are Although the throughput and DA Y O O T typically 10-fold more abundant than bacterial cells in accuracy of methods for viral direct T aquatic environments. That paper ultimately set the counting has improved since the 1989 philosophic course of my career, but I never could have report based on transmission electron predicted that this humble discovery in marine micro- microscopy, the ‘factor of 10’ ratio of bial ecology would forever change our perceptions of the viral to bacterial abundance within MicroBiology MicroBiology influence of viruses on the biosphere. aquatic environments has remained MicroBiology Prior to this discovery, fundamental research on viruses, a surprisingly common observation. and especially bacteriophages, had largely focused on the Extrapolating the ‘factor of 10’ rule Viral use of viruses as model systems in molecular genetics to the biosphere has lead to estimates research. In the late 1980s, molecular geneticists began that global viral abundance is in the moving towards more complex model systems and the little order of 1031 individuals. Assuming an we knew of viruses within natural microbial ecosystems average length dimension of 100 nm, ecology: seemed to indicate that viruses were rare in the ocean. Much Curtis Suttle has proposed that, lined of this thinking was probably shaped by the long-held end-to-end, all the phages on earth dogmatic belief that pathogenesis is typically not an import- would extend a distance equivalent ant mechanism of mortality within stable, undisturbed eco- to that of the nearest 60 galaxies (10 old questions, systems. Thus despite the long track record of discoveries million light years, 1024 m). How- from bacteriophage research such as: defining DNA as the ever, there are reasons to think that molecule encoding genetic information; characterization these astronomical numbers may of the first gene; uncovering the fundamental mechanisms actually underestimate global viral new challenges of gene regulation; and the first completely sequenced abundance. Lagging more than a genome, research interest in non-pathogenic viruses was decade behind studies in aquatic fading. As fortune and serendipity would have it, ecological environments, recent work in soils investigations of viruses stemming from the modest 1989 has shown that viral abundance can Nature paper has ushered in two decades of discovery and exceed bacterial abundance by more scientific advancement, a time that Nick Mann has adeptly than 1,000-fold, with the highest termed the third age of phage. Yet, today, two decades on, ratios occurring in agricultural and desert soils. The highest ratios have new picornaviral families is probably warranted; however, virioplankton is one of episodic and dramatic bursts in the reports using contig spectral analysis of viral metagenomes been seen in the Antarctic Dry Valleys, only one new virus family – Marnaviridae – has been abundance of a subset of viral genotypes corresponding tends to show that virioplankton assemblages are best suggesting that the relatively high created, since none of the other potential families contains with infection events of one or a few protistan host strains. modelled by a highly even power-law distribution with abundance of viruses may be related a cultivated representative. The late winter and spring seasonality in the occurrence the most abundant single genotype comprising less than to slow loss rates from these cold, In contrast to the more directed search for picorna- of viruses infecting the cosmopolitan diatom Chaetocerous a few percent of the entire assemblage. Total genotype sandy soils. Indeed, the only locations like RNA viruses, our first clues to the abundant presence gracilis, in the Chesapeake lends support to this idea. richness varies widely with location, single libraries from showing ‘factor of 10’ ratios are well- of ssDNA viruses within the virioplankton came more the Sargasso Sea, Chesapeake Bay and Yellowstone hot saturated forest and wetland soils, eco- through chance. Metagenomic sequence libraries of marine How diverse? Anyone’s guess springs were estimated to contain thousands of genotypes, systems that comprise only a fraction virioplankton from the Sargasso Sea, and to a lesser extent While we are only beginning to grapple with the whereas Peru rainforest soils contained over a million. of soil ecosystems in the biosphere. coastal environments of British Columbia and the Gulf ecology of ssDNA and RNA viruses in microbial envi- However, models of viral community composition by The most commonly used viral of Mexico, contained highly frequent sequences which ronments, the ubiquity and abundance of dsDNA viruses contig spectra are only as good as the quality of input direct counting techniques rely on showed strong homology to ssDNA bacteriophages within in the biosphere is unmistakable. Through the dedicated assumptions of viral genome size and the parameters used fluorescent stains that most strongly the Microviridae. Although the prevalence of microviruses efforts of a number of research teams we now appreciate in sequence assembly. For the Chesapeake library, a 2.5- fluoresce when bound to double- was probably overestimated due to the use of multiple that dsDNA viral assemblages within coastal waters show fold increase in assumed average genome size resulted in stranded DNA (dsDNA). Hence, displacement amplification (MDA) of virioplankton DNA high production rates with turnover times of a day or less. an equal fold decrease in genotype richness. Similarly,

“Ultimately, the best answer to the possible limits of viral diversity will come through greater understanding of viral biology.”

the natural abundance of RNA and prior to sequencing, follow-up data-mining analysis Moreover, viral production shows diel periodicity with reducing the percentage identity cutoff within sequence single-stranded DNA (ssDNA) viruses selectively targeted towards detecting ssDNA genes found peak rates occurring at 12- to 18-h intervals. The question assemblies from 95 to 50% for viral metagenomes from is largely unknown, yet there are that virioplankton libraries also contain a diverse range of remains, however, are the high production rates of dsDNA Yellowstone hot springs dropped genotype richness 2.5- indications that aquatic environments plant and animal ssDNA viral families, including circo- viral assemblages due to modest production of a diverse to nearly 5-fold, decreasing average richness estimates can contain diverse populations of viruses, geminiviruses and parvoviruses. The bias of MDA collection of viral populations, or high production of only from ~1,400 to ~400 genotypes.

2010 these viruses. All nucleic acid classifica- towards amplification of circular ssDNA was exploited to a few populations? By extension, the modest production Ultimately, the best answer to the possible limits of viral 2010 Y tions of RNA viruses have been shown enrich a rice paddy soil viral metagenome for sequences scenario would mean that viral infection has a similar im- diversity will come through greater understanding of MA to exist within marine ecosystems from ssDNA viruses. Along a theme similar to that of RNA pact on a diverse collection of microbial host populations; viral biology. Although, the pool of genes within natural MA Y 98 and recent work shows that marine viruses, sequences with homology to ssDNA Rep proteins, whereas, the high production scenario would mean a small viral assemblages is vast, there must exist a finite number 99 protists may host highly diverse col- a phylogenetically diagnostic gene of many ssDNA viruses, collection of host populations are subject to high levels of of gene combinations that form the genomes of evolution- DA Y lections of RNA viruses within the were sufficiently divergent to warrant family-level taxo- viral mortality. Answering this question continues to be arily successful viruses. Thus, the grand challenge for DA Y O O T order Picornavirales. Molecular phylo- nomic designation for these unknown ssDNA viruses. highly challenging for the simple reason that it is difficult to the third (and fourth) age of phage, will be to constrain T genetic analysis of RNA-dependent Although information on the activity and absolute measure viral diversity. Unlike the small subunit ribosomal the combined biological functions and associated genes RNA polymerase genes amplified abundance of RNA and ssDNA viruses within the virio- RNA gene for cellular life, there is no universal genetic which lead to the planet’s most ecologically successful from a variety of coastal environments plankton has been elusive, it is likely that these viruses marker capable of dissecting phylogenetic relationships viruses. indicates that the creation of several will show a markedly different ecology to their dsDNA and building a universal taxonomy for all viruses. More- K. Eric Wommack MicroBiology MicroBiology brethren. The few protistan RNA over, the high genetic exchange rates between dsDNA is Associate Professor at the University of MicroBiology and ssDNA viruses characterized to viruses is likely to cloud assumptions of shared phenotyes Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, 7 1.2x10 date, show that these tiny viruses can among viruses based on the phylogeny of a single universal DE 19711, USA (email [email protected]) quickly lyse dense cultures of phyto- gene. 1.0x107 plankton host cells and produce tens Only recently has a potential solution to the conun- Further reading of thousands of progeny viruses within drum of estimating viral diversity become available. Viral Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A. & others (2006). a 1- to 2-day incubation period. metagenomics – high-throughput sequencing of DNA The marine viromes of four oceanic regions. PLoS Biol 4, e368. 8.0x106 High burst sizes and rapid lysis cycles from entire viral assemblages – provides a means to sample Bench, S.R., Hanson, T.E., Williamson, K.E., Ghosh, D., Radosovich, M. & others would predict that assemblages of the genetic composition of a whole viral assemblage. A (2007). Metagenomic characterization of Chesapeake Bay virioplankton. Appl –1 6

h 6.0x10

–1 ssDNA and RNA viruses might show strong consensus of results from viral metagenomic studies Environ Microbiol 73, 7629–7641. marked dynamic swings in genotype shows that the function and taxonomic origin of most viral Culley, A.I., Lang, A.S. & Suttle, C.A. (2003). High diversity of unknown picorna-like 6 iruses ml 4.0x10 V composition with a predominance genes is unknown, making natural assemblages of dsDNA viruses in the sea. Nature 424, 1054–1057. of just a few strains at any given mo- viruses among the largest reservoir of uncharacterized Lang, A.S., Rise, M.L., Culley, A.I. & Steward, G.F. (2009). RNA viruses in the sea. 2.0x106 ment in time. Indeed, the behaviour genes on earth. Besides the utility of viral metagenomics FEMS Microbiol Rev 33, 295–323. of two small metagenome libraries data for exploring the universe of viral genes, these data Mann, N.H. (2005). The third age of phage. PLoS Biol 3, e182. of uncultivated RNA viruses indi- offer a means to estimate the possible genotypic diversity Williamson, K.E., Radosevich, M., Smith, D.W. & Wommack, K.E. (2007). Incidence 0 cated that just a few distantly related of a viral assemblage through sequence assembly of of lysogeny within temperate and extreme soil environments. Environ Microbiol 9, viral genotypes dominated RNA viral metagenome libraries. The central assumption 2563–2574. 6 –2.0x10 viral assemblages within British behind this approach is that assemblages containing a lower Winget, D.M. & Wommack, K.E. (2009). Diel and daily fluctuations in virioplankton 2 pm 6pm 10 pm 2 am 6 am 10 am 2 pm Columbia coastal waters. Although diversity of viral genotypes should show greater levels production in coastal ecosystems. Environ Microbiol 11, 2904–2914. Time of day it is early days, an emerging picture of sequence assembly, i.e. longer contiguous stretches of Wommack, K.E. & Colwell, R.R. (2000). Virioplankton: viruses in aquatic Graph showing diel changes in viral production for a single of the ecology of ssDNA and RNA assembled sequences (contigs). To date, the handful of ecosystems. Microbiol Mol Biol Rev 64, 69–114. experiment in the Chesapeake Bay. D.M. Winget & K.E. Wommack Thermotoga is a and organic nitrogen, like yeast extract or peptone, in source of thermophilic order to grow in the laboratory. Very little growth is enzymes observed if the carbohydrates are omitted. Sugars are either Thermotoga first attracted the atten- fermented into lactic acid or oxidized to carbon dioxide tion of biotechnologists because of and acetic acid with sulfur or protons as electron acceptor. the variety of thermophilic enzymes The protons are reduced to hydrogen. When glucose is found in the genus. These bacteria metabolized through glycolysis, the yield of hydrogen from Fig. 1. T. maritima cells. Bob Kelly, reproduced with permission from Johnson et al. (2005) grow on different carbohydrates that glucose often approaches the theoretical maximal value of are degraded into their sugar mono- 4 mol hydrogen (mol glucose)–1. In most other bacterial mers before they are taken up and hydrogen producers, the yield of hydrogen is only half as metabolized. It has therefore been great. Glucose is oxidized twice to form carbon dioxide possible to isolate, characterize and and acetic acid. The two oxidations lead to the forma- use a number of highly thermostable tion of NADH and reduced ferredoxin. While reduced hydrolytic and other enzymes from ferredoxin is a strong enough reducing agent to effectively –1 Thermotoga. reduce protons to hydrogen (∆G0ʹ = –6.4 kJ mol ), NADH –1 is not (∆G0ʹ = 19.3 kJ mol ). The secret behind the high Thermotoga includes yield of hydrogen in Thermotoga seems related to a special some of the most bifurcating hydrogenase that needs NADH as well as Thermotoga is a small genus that contains some promising microbial reduced ferredoxin to function, and the hydrogenase of the most hyperthermophilic bacteria. Some grow at A marine hydrogen producers therefore uses the excess reduction potential of reduced temperatures above 90°C, and the temperature optima The second great biotechnological ferredoxin to run the more unfavourable re-oxidation for most of them are between 70 and 80°C. The genus is thermophile shows potential of Thermotoga relates to their of NADH. Thermotoga can use all reducing equivalents named after the characteristic outer membrane, also known exceptional ability to form hydrogen. generated from glucose to produce hydrogen. as the toga, which encapsulates the rod-shaped cells (Figs All members of Thermotoga are 1 & 2). Thermotoga maritima was the first member of the promise as a anaerobes, and growth and hydrogen Growth and hydrogen synthesis 2010 2010

Y genus to be described in marine geothermic locations. production have been investigated in under microaerobic conditions

MA More species have since been isolated from similar environ- new source of cultures grown in closed serum flasks Experimental results published in 2002 indicated that MA Y 100 ments and from marine oil wells, and a few species have or in laboratory scale bioreactors (Fig. one species, Thermotoga neapolitana, was able to produce 101 also been found in non-marine environments. biofuels 3). The bacteria need carbohydrates hydrogen under microaerobic conditions with a yield of DA Y DA Y O O T Thermotoga, T MicroBiology MicroBiology a small genus MicroBiology with a large

Niels Thomas Eriksen potential in

Thomas Marius Nielsen Fig. 2. (Left) T. neapolitana cells showing the outer membrane, or toga, exceeding the length of the cell. biohydrogen Exponentially growing cells (in this case 3) often stay Nikolaj Kyndby Holm connected by their togas. (Right) Typical morphologies. The upper, rod-shaped cell is from an exponentially growing culture. When cultures go into stationary phase the cells become coccoid (lower cell), and Martin Leegaard Riis GIPhotosrock / Scoemce Photo Library synthesis they may lose their toga. Cells are 1–2 µm long. N.T. Eriksen those found in Thermotoga but productivity, process stabil- ity, and substrate availability still pose unsolved challenges to the implementation of all of these bacteria at a large scale: productivity is a function of biomass concentration, “Thermotoga first attracted which at the moment does not even reach 1 g l–1. We do Fig. 3. Bioreactor used for continuous cultivation of T. neapolitana. Sensors for not know what restricts the biomass concentration, but it measurement of exit gas flow, hydrogen and carbon dioxide are collected in the the attention of biotechnologists may be related to the formation of free-floating biofilms. box with a transparent lid. The reactor is wrapped in isolating tin foil to maintain It is therefore possible that more productive cultures can temperature inside at 80°C. The inset shows serum flasks used for batch cultivation of T. neapolitana. The reddish colour of the medium in flasks 1 and 3 because of the variety of be established in fluidized beds or membrane reactors (from the left) is caused by resazurin, which in its oxidized state is pink and is where the cells grow attached to particles or surfaces, and added to the medium as redox indicator. Flasks 2 and 4 have been sparged with thermophilic enzymes found where metabolic products are not allowed to accumulate as nitrogen to remove oxygen and the resazurin has been reduced. N.T. Eriksen they do in batch cultures. Large-scale axenic cultures will in the genus.” probably not be economically viable, and stable processes will depend on culture conditions that give Thermotoga an hydrogen that exceeded not only that advantage in competition with other microbes and elimi- Fig. 4. Closed –1 nate hydrogen-consuming methanotrophs. The extremely under anaerobic conditions, but also serum flasks used only 2.6 mol (mol glucose) , while the maximal theoretical yield. It was for cultivation cultures producing lower amounts of high temperature in Thermotoga cultures is an advantage also observed that cultures consumed of T. neapolitana lactic acid reached 4 mol hydrogen in both respects, and long-term, non-axenic hydrogen Medium with cysteine Medium without cysteine oxygen, but the responsible metabolic containing 50 ml (mol glucose)–1. We therefore need production at high temperature has been documented, pathways were not identified. Yields growth medium to focus on how to control the form- although not yet in Thermotoga. Studies on hydrogen pro- with cysteine (two duction based on agricultural products are beginning to exceeding 4 mol hydrogen (mol glu- left flasks) and ation of lactic acid. Fortunately, –1 cose) might theoretically be possible without cysteine maximal hydrogen yields concorded emerge, and have been promising, as different Thermotoga if the cells were able to oxidize (two right flasks). with maximal yields of ATP. Both species seem to metabolize the dominant carbohydrates a small fraction of the glucose aero- The top panel people and these bacteria therefore in plant materials as efficiently as they metabolize glucose. shows flasks 2010 The coming years will hopefully show if processes depend-

bically, gain energy from this process, share a common interest in the same 2010

Y after the medium ent on these hyperthermophilic bacteria grown in novel and use the energy to ensure that was flushed with metabolic processes. Accumulation of MA MA Y the remaining glucose is oxidized via nitrogen gas to hydrogen inhibits its own synthesis. bioreactors and on non-food substrates can be made 102 other hydrogen-generating pathways. remove oxygen. Despite the efficiency of the bifurcat- sufficiently productive and stable to enable a sustainable 103 These results led a number of research The centre panel ing hydrogenase, hydrogen formation production method for hydrogen. Despite the fact that they shows the flasks DA Y groups, including ours, to study the is still associated with a positive have not fulfilled all our expectations, these bacteria are still DA Y O approximately 10 O T production of hydrogen in micro- ∆G value. NADH and ferredoxin the most efficient producers of biohydrogen known to us. T min after oxygen 0ʹ aerobic T. neapolitana. Our results con- was added to the become increasingly reduced as the firmed that these bacteria do tolerate headspace, and the hydrogen concentration rises and Niels Thomas Eriksen is an Associate Professor, and Thomas oxygen and maintain hydrogen flasks were shaken. lactic acid formation becomes increas- Marius Nielsen, Nikolaj Kyndby Holm and Martin production under microaerobic con- While the redox ingly favourable. This is probably why Leegaard Riis are MSc students in the Department of Biotechnology, indicator resazurin MicroBiology MicroBiology ditions. Unfortunately, our results became oxidized cultures begin to form lactic acid Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej MicroBiology also indicated that energy metabolism in the flasks with later than acetic acid, and only after 49, DK-9000 Aalborg, Denmark (email [email protected]) and hydrogen formation in T. neapoli- no cysteine, some hydrogen has accumulated, but tana depend exclusively on anaerobic flasks with into the reduced zone, anaerobic hydrogen production otherwise there does not appear to Further reading processes. Gas transfer studies in the cysteine became continues despite oxygen from the headspace continuously be a clear relationship between lactic Eriksen, N.T., Nielsen, T.M. & Iversen, N. (2008). Hydrogen production in anaerobic stratified and serum flasks and growth media that the bottom part diffusing into the upper phase. Neither oxygen consump- acid formation and hydrogen pressure, and microaerobic Thermotoga neapolitana. Biotechnol Lett 30, 103–109. we and others use for growing these of the medium tion, nor oxygen contents of 10% or more in the head- even in batch cultures where final Huber, R., Langworthy, T.A., König, H., Thomm, M., Woese, C.R., Sleytr, U.B. & bacteria (Fig. 3, right) showed that stayed reduced. space can therefore be taken as evidence for microaerobic hydrogen contents may constitute Stetter, K.O. (1986). Thermotoga maritima sp. nov. represents a new genus of unique the oxygen consumption previously After 2 h with conditions in the vicinity of the cells. When cysteine was more than 50% of the headspace gas. extremely thermophilic eubacteria growing up to 90°C. Arch Microbiol 144, 324–333. observed in T. neapolitana cultures an oxygenated omitted from the medium, the cultures became much Lactic acid formation has actually Johnson, M.R., Montero, C.I., Conners, S.B., Shockley, K.R., Bridger, S.L. & Kelly, atmosphere (lower can be explained by non-biological panel), the medium more oxygen-sensitive, and addition of more than 1% been at least as hydrogen-sensitive as R.M. (2005). Population density-dependent regulation of exopolysaccharide oxidation of medium components, with no cysteine oxygen to the headspace of stirred cultures was completely acetic acid formation in later stages of formation in the hyperthermophilic bacterium Thermotoga maritima. Mol Microbiol especially oxidation of the amino acid was still oxidized inhibitory while lower oxygen concentrations were not. our cultures. 55, 664–674. cysteine, which is added to keep the while only the We therefore believe that Thermotoga sees oxygen solely as Nelson, K.E., Clayton, R.A., Gill, S.R. & others (1999). Evidence for lateral gene redox potential low. If the cultures are surface layer of a toxin and not a substrate. The future for transfer between Archaea and Bacteria from genome sequence of Thermotoga the medium with not stirred, addition of oxygen to the cysteine remained hydrogen production maritima. Nature 399, 323–329. headspace results in stratification of oxidized. Maximizing hydrogen yields in in Thermotoga Schut, G.J. & Adams, M.W.W. (2009). The iron-hydrogenase of Thermotoga the medium, with an upper oxidized N.T. Eriksen Thermotoga The majority of the research into maritima utilizes ferredoxin and NADH synergistically: a new perspective on zone and a lower reduced zone (Fig. The key to maximizing the hydrogen yield is to hydrogen production in Thermotoga anaerobic hydrogen production. J Bacteriol 191, 4451–4457. 4), even in serum flasks containing minimize the formation of lactic acid. In T. neapolitana has focussed on yield. A few other Van Ooteghem, S.A., Beer, S.K. & Yue, P.C. (2002). Hydrogen production by the as little as 50 ml of medium. Since cultures where the ratio between acetic acid and lactic acid hyperthermophilic bacteria show thermophilic bacterium Thermotoga neapolitana. Appl Biochem Biotechnol 98, the cells in non-stirred cultures settle production was roughly 2:1, the yields of hydrogen were hydrogen yields that are comparable to 177–189. For most, the search for sunken reduced, resulting in increases in life Jem Stach treasure evokes images of glistening expectancy. gold discovered when a diver’s hand The majority of compounds that wafts away the sand. However, for were discovered during this period another kind of treasure hunter, the were isolated from soil bacteria, most bioprospector, the sand itself is the notably the filamentous Actinobacteria target, brought from the depths of the (actinomycetes). The emergence of sea, to the laboratory bench. In this antibiotic resistance in the 1970s co- case, the bioprospector is interested in incided with a high rediscovery rate of marine microbes and their potential the major antimicrobial classes; the to produce antimicrobial compounds. low-hanging fruit had apparently With global sales of these life-saving all been picked. Antimicrobial products set to exceed $100 billion by development after the Golden Age 2015, such micro-organisms could be was characterized by semi-synthetic worth more than their weight in gold. modifications of compounds that were already clinically proven. Antimicrobials The poor antimicrobial discovery from microbes, rate from microbes, coupled with the a brief history availability of chemically synthesized The period of antimicrobial drug small molecule libraries, led to the discovery from the early 1940s to the abandonment of microbial screen- 1960s is referred to as the Golden ing programmes in the majority of Age. During this time, the industrial- pharmaceutical companies. To date, ization of penicillin production creat- small chemical libraries have failed

2010 ed the expertise and facilities to make to deliver a new antimicrobial com- 2010 Y significant quantities of antimicrobial pound to the clinic, prompting many MA compounds by fermentation. The to speculate that the withdrawal of MA Y 104 clinical use of antibiotics heralded microbial screening was premature, 105 a health care miracle; deaths due to exacerbating the threat of antibiotic- DA Y bacterial infections were significantly resistant bacteria. DA Y O O T T

Photodisc / Thinkstock MicroBiology MicroBiology Bioprospecting for novel actinomycetes on the seabed could MicroBiology be the source of much-needed new antimicrobial drugs

Antimicrobials: treasures from the oceans Why the high rate of are distributed among the actinomycetes at varying Marine poorly explored. It has been known rediscovery? frequencies, such that a single compound may be found Streptomyces. for at least 40 years that actino- Before considering why the in 1 in 10 strains screened, whereas thousands of H.-P. Fiedler mycetes could be recovered from the marine environment is of interest in compounds will be found in 1 in 107. sea. However, as actinomycetes are the search for novel antimicrobial It is therefore not difficult to envisage that previous able to produce spores, the presence compounds, it is important to screening activities were focused on limited species of these actinomycetes was explained speculate on the reasons for the diversity, and that those species produced a number of com- by terrestrial run-off. high rate of rediscovery in previous mon compounds (rediscovered antimicrobials) that would Questions as to whether truly screening programmes. These are obscure the detection of novel antimicrobials in the lower marine actinomycetes exist have been likely to include bias in the screen- frequency ranges. Richard Baltz of Cubist Pharmaceuticals addressed in the past two decades; ing programmes and limitations in defined the challenge as finding the resources necessary to technological improvements and avail- analytical technology, but more discover new antibiotics at frequencies of <1 in 107 within ability of submersibles to academics, importantly in the organisms being a background noise of 2,000 known antibiotics. along with SCUBA diving, have over- screened themselves. First, over half Understanding the reasons for rediscovery, coupled come previous sampling limitations. of the antimicrobial compounds with disappointing returns from small molecule libraries, The first seawater-obligate marine isolated and developed during the has led to a revival of interest in microbes as sources of anti- genus of actinomycetes, Salinispora, Golden Age were isolated from a microbial compounds. Proponents of this renaissance have was reported in 2002 and this discovery single genus – Streptomyces. The distri- suggested focusing on rare actinomycetes, the assumption was followed by other genera such as bution of microbial species probably being that species novelty will lead to chemical novelty. In Demequina, ‘Marinispora’, ‘Solwaraspora’ follows that of other organisms, so this instance, rare actinomycetes are not necessarily those and ‘Lamerjespora’ that so far appear that there are small numbers of highly that are scarce in nature, but those that are rarely brought to be exclusively marine. The divers- abundant species and if these species into culture. Thus, it is reasonable to predict that focusing ity of actinomycetes in marine are also those that are readily cultured on environments that have been underexplored will lead to environments has also been surveyed (as is the case for Streptomyces), then the the isolation of novel genera and species of actinomycetes by DNA-based methods that do not

2010 species that were present in screening and thence new antimicrobial compounds. require isolation and culture of the 2010 Y programmes would have represented a microbes. Indications are that there MA small fraction of the diversity present. The marine environment as are thousands of novel species and MA Y 106 Second, as recent genomic studies a source of rare actinomycetes genera awaiting isolation. 107 have demonstrated, actinomycetes are Earth is a blue planet, oceans cover 70% of its surface, DA Y capable of producing more antimicro- and in terms of phyla, the diversity of the oceans is about Antimicrobial DA Y O O T bial compounds than are revealed in double that of the land. Environments such as the deep sea “Renewed interest in marine actinomycetes compounds from T fermentation studies. Third, the floor, once thought barren, are now known to be equally or marine actinomycetes biosynthetic gene pathways used to more biologically diverse than tropical rainforests. In terms and their ability to produce antimicrobials It has been argued that because of make the antimicrobial compounds of microbial sampling, these marine environments are the high dilution effect of seawater, has resulted in numerous reports of novel marine-derived bioactive compounds MicroBiology MicroBiology may have evolved great potency. This MicroBiology Dermacozines antibacterial compounds.” theory was supported in 2003 with produced by the report of salinisporamide A, a Dermacoccus abyssi, potent anticancer agent that provided an actinomycete isolated from the compelling evidence for the ability Mariana Trench, of marine actinomycetes to produce the deepest point novel bioactive substances. This of world’s oceans compound holds the record for fastest (10,898 m). discovery-to-clinical trials in cancer W. Mostafa research. The following year, abyss- omicin, a first-in-class antimicrobial compound, was described from a marine isolate of the rare actino- mycete genus Verrucosispora. Renewed interest in marine actinomycetes and their ability to produce antimicrobials has resulted in numerous reports of novel anti- bacterial compounds. Whole-genome sequencing has provided genetic evidence for continued screening of marine actinomycetes: those species are antimicrobial compounds unique to marine species. applying marine actinomycetes to target-specific, whole-cell screens Whole-genome analysis of the genus Salinispora indicates in order to discover novel antimicrobial compounds’, says Jeff that differences in secondary metabolite biosynthetic genes Errington, Chairman of Demuris. Hopefully, the successes may be a driver of speciation, supporting the hypothesis of such companies will attract the attention of big pharma that new species will produce new compounds. Further and the resources they offer for antibiotic development. analysis is needed to determine whether this property will hold as more species are described, or whether genetic Jem Stach is a lecturer in the School of Biology, Newcastle exchange results in a shared pool of genes among all marine University, Newcastle-upon-Tyne NE3 7RU, UK (tel. +44 191 222 7709; actinomycetes species, i.e. it is the different combinations email [email protected]). of these genes that enable speciation. Genome analysis is also vital in order to understand the The author wishes to thank Paul Jensen for valuable discussions molecular adaptations that have led to seawater-obligate during the writing of this article, and Hans-Peter Fiedler, Marcel species. This may enable genetic modification of strains Jaspars and Wael Mostafa for supplying images. so that they are able to grow under standard fermentation conditions, something that would be of use for large-scale Further reading fermentation production of antimicrobial compounds. Bull, A.T. & Stach, J.E.M. (2007). Marine actinobacteria: new opportunities for Finally, if antimicrobial compounds are to make it from natural product search and discovery. Trends Microbiol 15, 491–499. the ocean to the clinic, big pharma must re-engage in Fenical, W. & Jensen, P.R. (2006). Developing a new resource for drug discovery: drug discovery from microbes. Currently, small pharma- marine actinomycete bacteria. Nat Chem Biol 2, 666–673. ceutical and biotechnology companies such as Aquapharm Jensen, P.R., Mincer, T.J., Williams, P.G. & others (2005). Marine actinomycete Biodiscovery, Cubist Pharmaceuticals, Demuris, Nereus diversity and natural product discovery. Antonie Van Leeuwenhoek 87, 43–48. Pharmaceuticals, PharmaMar and Thallion Pharma- Penn, K., Jenkins, C., Nett, M. & others (2009). Genomic islands link ceuticals, have been, or are currently engaged in anti- secondary metabolism to functional adaptation in marine actinobacteria. ISME J microbial discovery from marine actinomycetes. ‘We are 3, 1193–1203. 2010 2010

Y A false-colour electron micrograph of the abyssomicin-producing

MA Verrucosispora sp. strain AB-18-032. J. Stach MA Y 108 109 DA Y so far investigated dedicate about 10% compounds has been well demonstrated, and clearly they DA Y O (a) (b) O T of all their genes to the biosynthesis have a future role in the fight against antibiotic-resistant T of secondary metabolites (the group pathogens. Ongoing research efforts to isolate and screen of metabolites to which most anti- new marine actinomycete species should be accompanied bacterial compounds belong). This by efforts to understand their ecology. Extensive culture- figure is roughly twice that of related dependent and -independent surveys of terrestrial and MicroBiology MicroBiology organisms isolated from soils. Further- marine actinomycetes should be prioritized to determine MicroBiology more, comparing the genomes of the extent to which marine and terrestrial diversity differs, marine actinomycetes with their e.g. is the isolation of rare actinomycete genera from the terrestrial counterparts has enabled sea merely due to the fact that terrestrial-to-sea input Paul Jensen and colleagues at the skews the species distribution, i.e. are the ‘weed’ species University of California to begin less abundant? The isolation of seawater-obligate actino- identifying genes that may be mycetes has proved that marine adaptation has occurred responsible for specific adaptation to in this lineage, but so far this property has only been Antimicrobial (d) marine environments. Studies by this identified at the genus and species level, an indication that compounds isolated group have shown that an obligate marine adaptation is a comparatively recent evolutionary from marine (c) requirement for salt is present in about event. If such adaptation is rare within the actinomycetes, actinomycetes, 6% of actinomycetes isolated from it is reasonable to expect that seawater-obligate strains will all of which show marine sediments, thus it is likely represent species that have no terrestrial counterparts, and activity against that the majority of marine-derived thus they are unlikely to have been previously screened for antibiotic- resistant bacteria, actinomycetes are not restricted to antimicrobial compounds. e.g. meticillin- the sea, a finding that may enable Genomic analysis of marine actinomycetes is needed resistant prioritization of marine-adapted to determine what barriers, if any, exist to the exchange Staphylococcus species for screening. of genes between marine and terrestrial species; many of aureus (MRSA). (a) the compounds identified in marine actinomycetes are also Salinisporamycin, (b) abyssomicin, Future perspectives found in terrestrial species. However, compounds such as (c) diazepinomicin The ability of marine actinomy- salinisporamide, as yet, have not been identified in terres- and (d) lynamicin. cetes to produce novel antimicrobial trial species. This raises the intriguing possibility that there J. Stach Yvonne w Taylor helps In February, Dariel Burdass e children at St Trea’s School. St Trea’s School and Yvonne Taylor from SGM on the External Relations

Office crossed the Irish Sea the road in oolzon h to promote microbiology Northern sc to primary school children around Belfast. Ireland

The SGM and Queen’s University Belfast and tomorro Active participation maintained the students’ Children at Waringstown joined together in February this year to run two y attention throughout the session and lots of Primary School one-day workshops at Waringstown Primary interesting questions were raised because they Banbridge School and St Trea’s Ballymaguigan in Northern could relate to the range of topics covered. Chronicle Ireland, enabling around 100 enthusiastic 11-year- The students took their role as ‘microbiologists’ 2010 2010 olds and their teachers to explore the fascinating seriously and completely engaged with the Y roles that both beneficial and harmful microbes MA Y subject, drawing on knowledge and skills they had MA play in our daily lives. 110 developed from previous science lessons. 111 The workshops began with a discussion on what the children understood by the word ‘micro- It’s all glow! acting yeast or fresh yeast and DA Y DA Y O organism’. Sickness, disease, and germs were the O T The students were fascinated to learn that while tested which grew the fastest T commonest answers. They were surprised to not all infections can be avoided, simple hand by measuring which gave off learn that we couldn’t survive without microbes, washing is one of the best methods of prevention the most carbon dioxide in how special fungi and soil bacteria play an essential and it is easy to do. Through a simulation activity a set amount of time. The role in breaking down waste and that green using a hand cream containing a harmless dye that students did this by measuring MicroBiology MicroBiology algae, like green plants, are primary producers glows green in ultraviolet light, poor hand washing the circumference of the MicroBiology at the bottom of the food chain. Using contexts was highlighted by the glowing dye that remained balloon and the class results

that were familiar to the children, the students ducation toda on the fingers of the students. It was explained were collated and the mean

went on to discover in greater detail the role e that if the dye had been a nasty microbe such as value for each type of yeast was of different micro-organisms in their home and one that caused a cold or the flu, then those with calculated. A warm classroom garden. the green fingers would stand a good chance of gave impressive results. There

Volunteers were asked to become specific infecting themselves and passing the virus on to was much excitement as the microbes. If they were a good microbe they other people. The students were then shown balloons inflated. The students wore a T-shirt with a large, green, smiling gy how to wash their hands correctly, concentrating were keen to carry out further microbe on the front; if bad they wore a T-shirt on the areas around the nails and between the investigations, testing their own with a large, red, sad microbe. T-shirts were highly fingers. They also consolidated their knowledge ideas such as ‘if we add twice as coveted and there was no shortage of willing on when it was important to wash their hands much yeast will the balloons be models especially for the red ones! In fact at the properly. twice as big?’ end of the session we had to prise the T-shirts Children at off the children as most wanted to keep them. Yeast power! But is it art? Waringstown Primary School They thought they were really cool! Equally A simple scientific experiment followed to Through microbial art with John popular were the very cute giant microbes, stuffed demonstrate that yeast is a living micro-organism. activities some of the children McGrath toys that look like tiny microbes – only a million Balloons were used to collect the carbon dioxide consolidated what they had and Dariel Burdass. times actual size! The Rhinovirus was particularly produced when yeast is grown in sugar solution learnt. Paperweight Petri dishes Banbridge

popular. microbiolo in a plastic tube. The students chose either fast- containing 3D models of Chronicle microbes were made. A hushed Quotes from children at The Nuffield Foundation Science atmosphere descended as the Waringstown: Bursary Programme gives students a chance to children became absorbed work alongside practising scientists and engineers, Nuffield in their creative work. They – The experiment was very contributing to research or development projects carefully observed the shape, good and enjoyable. I learnt a in universities, industry, field centres and research surface detail and texture of lot more about microbes and I institutions. The scheme is open to anyone in their chosen subjects, producing never knew that bacteria could a school or college who is halfway through an Bursaries outstanding models that were Children be good for you! advanced level STEM programme, which may be academic or vocational. Projects so realistic identification proved measuring PS I am the one who last from 4–6 weeks and are carried out during the summer holidays. Unlike work inflated wanted a T-shirt. ethan easy. Quotes from children at St Trea’s: balloons at St experience schemes, the students carry out defined projects that have clear scientific The workshops closed with Trea’s School. or technological purpose, contribute to the work of the host organization and allow The day when the microbiologist came in we – It was the best science a quick round robin activity. – St Trea’s School scope for initiative. Students receive a weekly bursary (increased from £75 to £80 learnt that a sneeze goes faster than a jet taking lesson I have ever had! It was The children were asked to per week in 2009) to help them participate in the programme during their summer off and goes up to 30m long! daniel very interesting and exciting come up with one interesting holidays. There is a network of 22 co-ordinators across 12 regions that help to match learning about microbes. fact that they had learnt during – On our microbiology day we learnt about good students up with suitable project providers (host organizations) and ensure that the Thank you. victoria the session. They were eager germs and bad germs. If you sneeze without using programme runs smoothly at a local level. a tissue it spreads germs everywhere! CATCH it, to contribute to this activity A cuddly bug – Thank you for teaching The SGM has provided bursaries for microbiology projects for several years. In to show their newly gained KILL it, BIN it! bronagh and a ‘bad bug me about some of the most 2009 we funded 10 bursaries, which took place in a range of institutions and on a knowledge. Most contributions T-shirt’ at broad variety of topics, as shown in the table below. – Today was a great day, we did fun Waringstown interesting things in science were original and all came away experiments, learnt interesting facts and found Primary (micro-organisms) hopefully Project provider Title Supervisor with a much more positive view out that one germ on your hand can multiply up School. I will be able to remember of the role that microbes play in Banbridge NovaBiotics Ltd Effect of Candida albicans morphology on the Dr Derry to 16 billion germs if you don’t wash your hands Chronicle these in my next school. PS I antimicrobial activity of novabiotics compounds Mercer 2010

2010 our daily lives. properly! padraig was the one who was swine University of Glasgow, Production of biofuels by microbial fermentation: a Dr Robert MAY MAY MA Y flu and held the little green Glasgow Biomedical comparative study of ethanol production from the Davies Dariel Burdass is – I never realized how fun and interesting LETTER FROM Research Centre fermentation of glucose by Saccharomyces cerevisiae 112 thing. Thanks a lot for coming 113 microbiology can be. I can’t believe microbes can WARINGSTOWN SCHOOL: and Zymomonas mobilis Education Manager at SGM in. zach (email [email protected]) blow up to balloons. caitlin Green Biologics A comprehensive screen of anaerobic and/or Dr Renia DA Y thermophilic bacteria for the utilization of a range Gemmell ODAY O Dear Mr McGrath, I learned a lot more T As a result of this fact-filled day we now know – T – of feedstocks The SGM would like to thank both Thank you very much for about germs and bacteria that 95% of germs are good! Microbiology is a Royal Holloway, How endophytic fungi Cladosporium and Prof. Alan John McGrath and John Quinn coming to our school and WOW! Ryan and will think more carefully University of London, Trichoderma affect the creeping thistle Gange from Queen’s University Belfast teaching us all so many iology about hygiene, I never thought School of Biological B We learnt some interesting facts when who co-ordinated the organization – interesting things in a very fun bacteria could be so good for Sciences

microbiologys came to our school. We learnt that icro MicroBiology MicroBiology of these workshops and also for way. We all enjoyed it very you and I have really took on Plymouth Marine An investigation of antimicrobial activity amongst Dr Karen Tait M only a small 5% of germs are bad. From this visit Laboratory coral-associated microbes their very kind hospitality during much and I’m sure everybody board what you have said. we learnt that some germs are very dangerous Feedwater Ltd The relative efficiency of growth media in the Gary Hogben our stay. will certainly wash more PS I would have been a better detection and counting of pathogenic Legionella spp. like samonella which you find in chicken. Kirsten carefully from now on after bad germ than everyone else, in water samples seeing all those germs on our my soap smells really nice! John Innes Centre Anti-adhesive carbohydrates as inhibitors of bacterial Rob Field hands! We have taken our Thanks! alana Norwich adhesion and Sergey yeast experiment home and Nepogodiev most of us have repeated – Thank you very much University of Cloning a gene from a food associated bacterium, Dr Gary the experiment again. Our for the lesson about colds, East Anglia Salmonella Rowley largest balloon was 32 cm at germs and microbes. It was Agri-Food & To detect, using molecular microbiological Mrs C. Biosciences Institute techniques, bacterial populations in digesta of Nicholson great! I really enjoyed learning its widest point which we all pigs involved in feeding trials thought was pretty impressive about what you do. It was University of Ulster, Investigation of the clinically relevant antibiotic Prof. Geoff as some were only 19 cm at great fun seeing all the School of Biomedical resistance profile of 25 strains of P. aeruginosa McMullan their widest point. We would germs on my hands. I had Sciences isolated from hospital environments be very grateful if you could fun doing the experiment The Nuffield Foundation offers over 1,000 bursaries for enthusiastic students pass this on to the two ladies. about the balloon and the each year and they are always looking for more project providers. If you are sugar and yeast. Thank you interested in hosting a student, please contact Sarah Saunders at The Nuffield Yours sincerely for the little soap and the Foundation (email [email protected];tel. 020 7681 9626) who will cute monkey. It was cool! primary 7 mrs sloane put you in touch with your local Co-ordinator. For more information, see also the courtney SGM’s Yvonne Taylor with children at Waringstown Primary School. Banbridge Chronicle 2010 is a Microbiologyonline Everyone needs to take on board the landmark year goes live 2010 MiSAC message that illness caused by microbes such as for Society The SGM microbiology Salmonella and Campylobacter can be avoided by educational education website has been Competition correctly storing food, cooking it properly and resources completely redesigned. The new preventing cross-contamination from uncooked to as not only site is an important resource Food cooked foods. This is never more important than does the for budding microbiologists, at barbecues on a warm day where raw meat is new website but its broader purpose is to safety and being handled alongside salads and hungry people go live, but inspire widespread interest can be too eager to take food off the griddle the fantastic in the subject and reflect the barbecues which is raw on the inside, though charred round Key Stage needs of both teachers and the edges! 5 pack on students. Through clever design Microbiology – The 22nd Microbiology in Schools Advisory microbiology, and the use of high quality A resource for kS5 Committee (MiSAC) competition for UK and compiled images, the subject is brought This resource contains up-to- Ireland secondary schools aimed to reinforce by Gemma to life, prompting curiosity and date information relevant to this message. The focus was on preventing food Sims, edited interaction. the AS and A2 specifications, poisoning and students (in two age groups) were by Dariel Visitors to the site will be including contemporary topics asked to design a storyboard for a television Burdass and struck by the bold use of colour, such as hospital-acquired advertisement to promote food safety at designed by vivid imagery and large-scale infections, biotechnology and barbecues. The students took to the theme Gary the Killer Sausage! A competition Ian Atherton, graphics to encourage instinctive the role of microbes in climate with enthusiasm and more than 400 entered entry. Lucy Harper is now the competition, some collaboratively. Nearly 50 available. Janet Hurst (SGM) and Martin schools participated.

Adams (SfAM) judge the entries in 2010 2010 The judging took place at SGM headquarters the 2010 MiSAC competition. Lucy Y New, new, new from SGM and the panel had a hard time deciding on the MA Y Harper MA winners. The Society for Applied Microbiology 114 115 exploration; the interface change. It reflects How Science sponsored the competition and were represented is populated by a series of Works and has relevance to on the panel by Professor Martin Adams of DA Y DA Y O modules that guide users to the wider curriculum, including Surrey University, Lucy Harper, the society’s O T T specific topics and themes. ethical and moral issues and the Communications Manager, and Dr Anthony Microbe Passport, a novel implications of science in society. Hilton of Aston University, alongside the interactive feature populated Illustrated in full colour, it covers Chairman and other members of MiSAC. The by cartoon microbes, has been four aspects of microbiology in high quality and creative approach of the entries MicroBiology MicroBiology included to highlight the diverse the curriculum: in both age groups was very impressive, and MicroBiology nature of these organisms. – Microbiology basics many entrants clearly enjoyed expressing their By clicking on the revolving – Making use of microbes artistic talents. The judges looked particularly microscope visitors can zoom – Microbes and disease for originality, eye-catching design, a title that in and explore the secret – Microbes and the immediately indicated the purpose of the world of microbes and find out environment storyboard, a clear sequence to the panels that more about these mysterious A CD-ROM accompanies maintained viewers’ attention, sound factual microscopic organisms. this book, which provides a and scientific content, including mention of The new site provides an comprehensive, full-colour specific microbes involved in food poisoning, an engaging channel into many PowerPoint presentation and appropriate approach to communicating science layers of factual content, for a range of innovative student to a television audience, and use of the entrant’s both students and teachers. activities. own words. But, it is further enriched, and For further information on The winners received cash prizes and a brought right up-to-date by the pack, email education@ memory stick loaded with Micropod podcasts an interactive quiz, access to sgm.ac.uk from SfAM. All students who participated were podcasts, a noticeboard, topical Price to non-members: £20. given a certificate of entry and their school news items and a series of School members of the SGM received some microbiology teaching resources. downloadable resources. There will receive a free copy of Next year’s competition will be on ‘famous is also an online order form for the pack with this issue of fungi’ sponsored by the British Mycological SGM’s printed resources. Microbiology Today. Society. A job as: university lecturer cycles in Petri dishes, and I was but often read or do work at home in the evenings If you enjoy research but also want to communicate the hooked! too, but I enjoy what I do so it doesn’t really seem E excitement of science to others, then a career as a university Why did you decide to like work. The great thing about academic life is Q ists lecturer allows you to do both. Jane Westwell finds become a lecturer? that every day is different, so there’s no chance g out how SGM Council member Paul Hoskisson got to do a A I realized pretty quickly in to get bored. The only drawback now is I get less fulfilling job that he loves. my PhD that I wanted to run hands-on time in the lab. my own research group. There Q What do you love about your job? RADLIN are two routes really, become A I love the intellectual freedom, the ability to a project leader at a research follow areas of research that really interest me, G institute, or become a university and also being able to make a contribution to lecturer. I wasn’t fussed which I microbiology. got, but I have always enjoyed Q What opportunities are there to travel? the teaching side of my work, A One of the great perks of science is being able trying to enthuse students about to travel to conferences and on research visits. I science and microbiology, so have been lucky and been to meetings in most of when I got a university lecturer r microbiolo Europe and North America over the years. position, I was quite happy, especially as the university is Q Do you have time for outside interests / a ee keen to support my research social life? too. A Yeah, I still maintain my outside interests Q Describe a typical day. and have a social life. In fact over the years I have ended up with lots of friends who are also

It depends a lot if it’s 2010 A car 2010

scientists, so going to conferences often ends up Y

university term time or holidays. y MA Y But typically I get to work as a friends’ reunion. MA 116 around 8 am, and spend an Q When you were a researcher….. 117

hour or so checking emails and arl – What were the working hours like? DA Y DA Y e O doing administration. I try to A Like most things you only get out of it O T T get in to the laboratory outside what you put in, so you have to work hard, and Did you always want to be – Present occupation Lecturer at Strathclyde University Q of term time and still do some I normally worked about 8 am–6 pm, sometimes a microbiologist? If not, what – Education experiments, and check if the later, sometimes earlier, often your day is dictated guided your university choices? PhD: Liverpool John Moores University (2001) students in the lab need any by your bugs! help or advice. I spend a lot MicroBiology MicroBiology BSc Applied Microbiology: Liverpool John Moores University A I have always been fascinated – Did you work with other people? MicroBiology of time keeping up-to-date for (1997) with all living things, and I was A Most modern research is done as part of a with current research in my e especially interested in life team, I have worked in small research groups of – Work history field, looking for new areas of cycles, but I began to realize that 3–4 and also large ones of around 30 doing similar Between graduating and beginning my PhD, I worked in the potential interest and also doing studying them in big organisms research. Each has its challenges and benefits. pharmaceutical industry on the development of production bioinformatics. Another large takes a long time. I knew that These have been in bigger departments, so there processes for live vaccines. I realized pretty quickly that industry part of my job is trying to obtain there were always going to are always people around to chat to and socialize wasn’t for me and craved the intellectual freedom of academia. be jobs for microbiologists research funding, by writing with after work. In October 2001, I moved to the John Innes Centre (JIC) in because the subject covers grant proposals. Communication – What were the challenges? Norwich as a postdoctoral researcher on a 3-year contract, to virtually every aspect of human of science to the academic A The main challenge of being a researcher is continue working in the same field as my PhD – sporulation in life, so I chose to study for a community is important so getting data, if you get data, you will get papers, Streptomyces. After JIC I took another 3-year postdoc position microbiology degree. I reckoned writing papers is vital. I also do in the University of Aberdeen, staying in the same field. that if I wasn’t successful in editorial work for a journal, and and publishing papers gets you jobs and respect

– Paul Hoskisson within your field. The other challenges are no After about 18 months, I realized that I was in a position to getting into research, then the referee grants and papers for s and advic e different to those in other jobs, but you do need begin looking at lecturer jobs, and applied to the University of training would open the door other journals and grant-funding e Strathclyde for a post in Microbiology. Although it was my first to lots of job opportunities in bodies. to be quite self-motivated, often there is nobody attempt, I was lucky and was offered the position, and was also different areas. Whilst I was an In term time I give a few lectures, breathing down your neck waiting for results, so it is up to you to work hard without being told. able to defer my start date by 6 months to finish my project undergraduate, I discovered as well as being a personal tutor dat p rofil in Aberdeen. I have now been a lecturer at the University of Actinomycetes and realized to some students. I normally jane westwell is SGM External Relations & Grants

p Strathclyde for 3 years. that I could study complex life leave the office or lab at 6 pm, u Manager (email [email protected]) Whether or not it is the media’s role to educate, a poll to mark the opening of the Science Media Centre in 2002 found that ‘90% of the general public get most of their information about science from the media’. This means that we, as scientists, have a responsibility that the science we convey in the media is well explained and clear. Journalists want to write good, accurate stories media workshop Participants at the Manchester VoYS meeting. Sense About Science but, in many cases, they can Engaging only be as accurate as their What would entice In March, Sense about Science’s Voice of Young the interest of potential source. tomorrow’s a microbiologist, an Science programme (VoYS) ran a ‘Standing up for collaborators from a variety of Ultimately, we should feel aerospace engineer, a Science’ media workshop in Manchester. Sense fields more than a paper in a very pleased that science is talent today health psychologist and about Science is a small charity that works with dedicated academic journal. The reported in the media at all and a mathematician (amongst researchers to equip people to make sense of simplification and sensationalism that the vast majority of it is AEA has taken over running others) to spend a day science and evidence. Their VoYS programme needed for a news story may be reported well. Scientists should the Researchers in Residence together? answer: a shared helps early career researchers to get involved the price to pay for reaching a take every opportunity to (RinR) scheme, which is funded 2010 2010 interest in how science is in public debates about science. The aim of the large audience. present their research and their by RCUK with support from the Y workshop was to provide early-career researchers There was a thought- methods to a wider audience. I Wellcome Trust. RinR brings Standing up for Science MA Y portrayed in the media. MA with an opportunity to form views on how provoking debate on whether came away from the workshop together researchers, young 118 119 science is portrayed and communicated and to it is the role of the media to with a fresh perspective on people and teachers via exciting Alison Graham. Sense About Science question people directly involved in the media. educate the public about the science in the media; we may and innovative placements in DA Y DA Y O The day was divided into three sessions scientific process, the inherent work in different ways, but there secondary schools across the O T T with scientists and journalists talking about uncertainty scientists themselves is a lot to be gained by working UK. their experiences and work. Among others the are familiar with and the caveats together and workshops like RinR enriches the speakers included Trevor Cox, Professor of always attached to any data. these are invaluable for fostering classroom experience, engages Acoustic Engineering at the University of Salford The journalists at the meeting links between young scientists young people with real-life MicroBiology MicroBiology and resident scientist on BBC Radio Manchester; sold a convincing argument and journalists. research and gives researchers MicroBiology Raymond Tallis, an Emeritus Professor of Geriatric that this is not actually the Members of the Society the opportunity to gain new Medicine from the University of Manchester who role of a newspaper. The for General Microbiology skills. RinR benefits everyone has published extensively outside of medicine; dictionary definition of ‘news’ have priority places on these involved. Richard Van Noorden from Nature and Kevin is ‘information on recent workshops. For further RinR has been running Fitzpatrick from BBC Radio Manchester. Each events or happenings’. The information about Voice of since 1994 and it provides a speaker introduced themselves and gave a short story needs to be relevant Young Science (VoYS) and great opportunity for early talk on their opinions and experience of science and affect the audience. future workshops please career scientists to develop in the media and then the session was open to There is minimal space in a visit the website www. transferable skills, as well as questions from the floor. This led to an informal newspaper for a story that is senseaboutscience.org/VoYS communicate the excitement of environment where everyone felt able just ‘interesting’. Discussing or contact Julia Wilson at their subject to young people. to contribute. how science is carried out is jwilson@senseaboutscience. The scheme is open to all PhD A few interesting points came out of these undoubtedly interesting but org and postdoctoral researchers discussions. It was felt that academics are not is it ‘newsworthy’? Possibly, if funded directly or indirectly by necessarily comfortable with the sensationalism it is linked directly to a recent ALISON GRAHAM is a Postdoctoral one of the seven UK Research required of a news story, but increasingly some scientific finding or in a longer Researcher in the Department Councils or the Wellcome are viewing it as a ‘necessary evil’ to get their ‘features’ article, but perhaps of Molecular Biology and Trust. research into the public eye. If your research is there are better places to teach Biotechnology, University of accessible and has wide-reaching applications, about scientific methodology Sheffield, Sheffield S10 2TN Tel. 0845 365 7470 an article in a national newspaper may pique and critical thinking. (email [email protected]) www.researchersinresidence.ac.uk/cms/ gy UBLIC

SGM shines brightly at the Big BanG G P Enthusiastic children, glow gel, plastic food and Laura (left) from SGM at the Big Bang. All images courtesy Big OIN Bang except bottom far left and bottom centre (L. Udakis) G

Two industrial-sized boxes of paper towels, 3 rolls of blue kitchen roll, 2,000 giveaway boxes of soap leaves, 5 bottles of glow gel, 3 stained 2010 2010

tablecloths and approx. 68 cups of Y of microbiolo of MA Y coffee was the consumable count for MA

120 e 121 the SGM’s recent trip to North West DA Y DA Y O England. Laura Udakis tells you why. O T T

The Big Bang exploded into action for 3 days in March at Manchester Central – a huge converted railway station the size of 20 football rofil MicroBiology MicroBiology pitches. The main arena had been split into four MicroBiology zones featuring some impressive interactive p exhibits designed to take you on a journey display posters – in addition to onslaught of over-excited school children. And it

through science, engineering, technology and some top quality educational was busy indeed. We had divided our stand into maths, and the impact they have on the world. resources – the stand was 3 different stations, each with different activities. At this enormous science fair, some excellent looking very attractive. We had All of these involved the use of UV glow gel

school projects that were competing in the finals he some initial teething problems (or spray, or powder) that was invisible to the of the CREST awards and the Young Engineer for trying to get a fully functioning naked eye, but glowed fluorescent under UV Britain award were also displayed, interspersed sink incorporated into our light and served as a good model for microbial

with the exhibits. Stand-out offerings included a t exhibit, as well as a power transmission. The children, as predicted, did arrive coffee-powered car, a giant DNA model built point in each corner, but this in their hordes and practically fell over themselves out of Coca Cola™ bottles and a display of g was quickly resolved leaving us queuing up to have a go. carnivorous plants. enthusiastic and ready to go. Dariel, Janet, Yvonne and I however, had Knowing that 20,000 Lending hygiene a hand our own exciting activities that we were sure people – school groups and the To demonstrate why good hand-washing skills would easily compete with a coffee-powered general public – had booked are important, we got the children (and adults) to car. As well as sponsoring the event, SGM was for the fair over the 3 days was rub the gel all over their hands. After reassuring promoting the importance of good hand hygiene, a little intimidating. The doors the children that we were NOT covering them and after unpacking boxes and boxes of UV opened on Thursday morning with some kind of strange bioluminescent

lamps, glow gel, plastic food (read on!), soap and raisin and we braced ourselves for an bacteria, amid cries of ‘Ugh! That’s minging!’ we Students enjoying the activities. Nottingham University Hospitals NHS Trust Most young people national pathology week 2009 don’t understand the Recruitment into microbiology- true importance of related professions in the UK has been in decline. There microbiology in our daily appears to be a general lack of lives. Vanessa Wong knowledge of the career paths that involve microbiology and and her colleagues this in turn has led to a deficit at the Nottingham in people applying for degrees in microbiology. I believe the University Hospitals key to reversing this trend is to NHS Trust put on an raise the profile of the practical applications of microbiology Dariel from SGM spraying glow gel onto a student’s hand. Courtesy Big Bang exciting lab event that in everyday life as well as of opened their minds. the jobs that are available with a microbiology degree. encouraged them to wash their hosting with each group of school children. The Organized by the Royal College hands in the sink with plenty of excitement induced by plates of plastic food was of Pathologists, National soap and water. Those guilty of quite amazing! They picked up the meat and put Pathology Week was held for less-than-desirable hand washing it on the grill and squealed with delight at the the second year running on were quickly shamed under the very authentic sizzling noises and fat (water) that Can 2–8 November 2009 and was 2010 2010 UV lamp, where fluorescent dripped from the grill. After their plastic food had the perfect opportunity to Y nails and wrists were abundant. been sizzled enough times, the children picked it MA Y encourage school students to MA I am delighted to report that up and chose their accompaniments. I reminded gain first hand insight into the 122 123 the model proved robust, after them that they had failed to wash their hands I bug work microbiologists do and one man completed the activity after handling the ‘raw’ meat and most were allow them to get involved in DA Y DA Y O and presented hands that, horrified to see fluorescent spots on their hands O T the ‘World of Microbiology’. T after careful examination, were and the plastic vegetables under the UV lamp. A We hoped that the event entirely fluorescence-free. ‘You brief discussion of the types of harmful bacteria you? would inspire them to pursue obviously have a very effective that raw meat and poultry can harbour, combined careers in microbiology. hand-washing technique,’ I told with the evidence of how easily they can spread Vanessa Wong. Dariel Burdass MicroBiology MicroBiology him. ‘I should hope I do,’ he made most of them think twice about food MicroBiology replied, ‘I’m an infection control contamination, I’m sure. ‘Is that really Staphylococcus aureus?’ a student enthusiastically nurse!’ exclaimed as she peered wide-eyed at colonies of the organism A STAR PERFORMANCE on a blood agar plate. This was one of many activities organized by BUGS GET A GRILLING The 3 days whizzed by and we were left totally our microbiology department for school pupils during National The aforementioned drained at the end of each one. We perked up Pathology Week. The Pathology Department of Nottingham plastic food was a useful considerably one evening after Janet and Dariel University Hospitals NHS Trust invited two groups of 15 GCSE-level tool to demonstrate cross- excitedly reported spotting celebrity Peter Andre students from a local secondary school to spend a day learning about contamination, aided by some and his entourage entering the hotel where we the different pathology specialties – Microbiology, Histopathology, very life-like George Foreman were staying! Alas, he didn’t appear at the stand Immunology, Haematology and Clinical Chemistry. The day started toy grills that went down a next day to learn about hand hygiene and, sadly, with the students watching a short film that we made and released storm (with SGM staff as well that was the last we saw of him. on YouTube explaining the role of pathologists (see www.youtube. as the children). After fashioning Celebrities aside, we were convinced that com/watch?v=yYCnwjs1qUs). some rather realistic ‘chicken several thousand children (and at least a few more Our aim was to raise the profile of microbiology as a clinico- drumsticks’ from play dough adults) would be washing their hands properly in pathological specialty, focusing on its crucial part it plays in diagnosing impregnated with UV glow future. Happy with our success, we went home disease and managing patients, and to explain the role of the powder and ‘contaminating’ completely shattered but glowing – in every sense. biomedical scientist and microbiologist to pupils who are considering some plastic burgers in a options for their future career. Building upon our experience of last similar way, we prepared the laura udakis is External Relations Administrator at year’s event, we felt that an interactive ‘hands-on’ session would be ‘dinner party’ that we’d be SGM (email [email protected]) the most effective way to engage young people with microbiology. workshop activities making and in the environment as nitrogen-fixing The SGM press office, headed up by Laura Udakis, uses the media to promote Our microbiology workshop lasted 1 hour and bacteria for plant growth. There was also an microbiology to a wide audience. This means regularly scanning papers in SGM 15 minutes and was held in one of the teaching exploration of various illnesses which illustrated to journals and the abstracts of papers and posters to be presented at Society the students where and how bad microbes may laboratories of the University of Nottingham. We conferences for potential ‘stories’ to write up as press releases and circulate to had groups of three to four students rotating cause disease. journalists. Sometimes the authors need convincing this is a good thing! One around five stations. Each station lasted 10 Station Four was the ever popular, but minutes and was run either by a medical student, gruesome parasitology demonstration, where initially rather doubtful researcher describes how he was won round and Laura biomedical scientist or microbiologist. a range of different parasitology specimens in gives her take on the process from the press officer’s perspective. Station One involved three clinical cases of formalin were displayed and supplemented with common infections and their corresponding pictures of their corresponding life cycles and causative organisms: Escherichia coli causing a clinical conditions. Working with the media urinary tract infection; Staphylococcus aureus The last station, Station Five, was a poster causing cellulitis; Streptococcus pyogenes causing display introducing the students to microbiology Dr Gerard Fleming information form dealing with following the progress of the release around tonsillitis. Students examined pre-prepared Gram and more specifically to meticillin-resistant the summary of findings and the the world. Self-satisfied, smug, haughty and 24- films under microscopes. They learnt about Staphylococcus aureus (MRSA), Clostridium difficile, I had extremely mixed feelings significance of the results. This hour Google alert junkie would accurately have colonies of organisms on a variety of different and sexually transmitted infections. The set-up at the thought of my work going information must be written described my demeanour. These emotions were solid growth media and the treatment choice allowed the students to freely ask questions about out to the press – the main one in ‘layman’s’ language and rapidly replaced by pure panic when journalists any infection-related topic. In addition, they were being trepidation. Recalling how was one of the most difficult given SGM leaflets on various diseases including the press had been less than pieces of writing I have ever norovirus, C. difficile, MRSA and Mexican swine forthright with their coverage attempted. I was acutely aware flu as well as career information in the form of of topics such as global warming that if it was not accurate, the two leaflets; ‘Microbiologists make a difference’ and and bird flu, as well as the science could be seriously 2010

2010 ‘Microbiology, your career questions answered’. predictions that the Earth misrepresented. I was also Y would be ‘gobbled up’ by a conscious that this document MA Y MA mini black hole created by would act as a template for 124 feedback 125 It was clear that many of the students were CERN’s Large Hadron Collider, Laura (in conjunction with the unaware of microbiology as a subject to study in I was concerned at what original paper) to formulate DA Y DA Y O sensational headlines OUR the press release. After she O T its own right and that others had not considered T it as a potential career path. They felt that talking work might go under. Did the had got back to me with a to people who worked in microbiology was the press officer (Laura) handling couple of very good questions best way to better understand the subject. The the story even have a science and sent me a draft, we were students were asked to complete an evaluation background, let alone know both happy with the contents MicroBiology MicroBiology form at the end of the day and the feedback was anything about microbiology? I of the release. Laura suggested MicroBiology overwhelmingly positive, ranging from ‘I learned was also a little surprised that the final title: ‘Disinfectants may a lot about things like MRSA that I had heard being our paper had been chosen promote growth of superbugs’. I for promotion. I felt honoured was hesitant about the use of Nottingham University Hospitals NHS Trust mentioned in the news, but never fully understood what it was’ to ‘I want to be a microbiologist when I to be asked, although slightly the word ‘superbugs’ but by for each condition, explained by demonstrating grow up’! The majority of students said they would uncomfortable in that many of this stage a trust had developed and radio correspondents antibiotic susceptibility testing. recommend the day to their peers. my colleagues have published between Laura and myself. She started to request interviews. Station Two was a demonstration of the excellent and highly significant clearly knew her science but While stagefright and self-doubt importance of hand-washing using the ‘wash and vanessa wong is a Specialist Registrar in Medical papers over the years without was also very press-savvy and abounded, a rapid re-read of glow’ ultraviolet machine. The large number of Microbiology at the Queen’s Medical Centre, Nottingham their work being selected for knew how to draw journalists in. the paper proofs and I was microbes that was revealed on their hands by the (email [email protected]) public scrutiny. Would they The embargo was lifted on ready to go, or so I thought. device shocked the students. Infection control feel a sense of injustice? After 28 December, the morning of The first interview was a issues in a hospital setting were also addressed Acknowledgements consultation with my co-authors which I received a text message disaster. A live radio interview and leaflets were handed out to the students. Paul and Alain we decided to from a senior colleague at NUI: lasts about 4 minutes and is I wish to thank the SGM for supporting this event with an At Station Three, the students participated in a Education Development Grant (see www.sgm.ac.uk/PA_forms/ seize the opportunity. Of course ‘You’re on the BBC website’. A very different to a 50 minute short quiz on ‘good microbes’ and ‘bad microbes’. PEM10.doc), the University of Nottingham Medical School I had a safety blanket – I believed quick Google search revealed undergraduate lecture. I was Prizes were awarded to students who scored the for all their help in organizing the event and providing the that the press would not have we were also on the Times of well-versed regarding the highest mark on the quiz. This was followed by a equipment and laboratory facilities, and the Microbiology the slightest interest in the story! India, LA Times, CBC, CNN purity of our scientific findings, discussion on how microbes can be beneficial in Department at Queen’s Medical Centre, Nottingham University The first challenge was trying and Fox news websites. It experimental design, controls, the food industry for processes such as yoghurt- Hospital NHS Trust for their support. to complete the press release was completely mesmerizing, etc., but this was not what the listener wanted to hear. I returned to Laura’s well-honed pointing out what it costs to run a PhD student for a in the media is often a question Officers press release and condensed the data to four or five points year! Alas, that’s the last I hear from them! Despite initial of luck and is not a reflection on – President – Prof. Hilary M. Lappin-Scott that I needed to get across and used everyday scenarios to concerns about the reaction of my peers, they have all the newsworthiness of the research – email [email protected] illustrate these. The narrative was practiced and practiced been incredibly supportive and delighted at the increased or indeed the quality of the writing! – Treasurer – Prof. Colin R. Harwood School of Cell and Molecular Biosciences, University until I was comfortable with the content. I made it a point recognition our institution has received. It was a positive General elections, erupting volcanoes of Newcastle Medical School, Framlington Place, to respond to and accommodate media queries and and enriching experience and has certainly allayed my initial and the suchlike are unpredictable and Newcastle upon Tyne NE2 4HH requests as rapidly as possible and after a few interviews it fears about dealing with the press. will immediately quash all hope tel. 0191 222 7708; fax 0191 222 7736 was like wearing an old and very comfortable pair of shoes. of getting any coverage. email [email protected] General Secretary – Dr David J. Blackbourn I quickly learnt that I had to take control in interviews so gerard fleming is at the National University of Ireland, Galway I sometimes field concerns from – University of Birmingham, Cancer Research UK Institute that the conversation did not stray far outside my area of (email [email protected]) scientists about inaccuracies in the for Cancer Studies, Edgbaston, Birmingham B15 2TT expertise. I knew that statements made in haste often have reporting of their work in the press. tel. 0121 415 8804; fax 0121 414 4486 a habit of coming back to haunt you in the future!! Dr Gerard Fleming’s paper ‘The effect of sub-inhibitory Inaccurate reporting is often beyond email [email protected] Was it a good experience? I am happy that the concentrations of benzalkonium chloride on the the scientist’s or my control, but can – Scientific Meetings Officer – Prof. Chris J. Hewitt Department of Chemical Engineering, Loughborough press attention appears to have raised the profile of competitiveness of Pseudomonas aeruginosa grown in be minimized by responding to media University, Loughborough LE11 3TU

microbiology at NUI, Galway. It has also increased the continuous culture’ was published in the January 2010 issue enquiries as quickly as possible to tel. 01509 222506; email [email protected] council 09–10 pressure and expectations for ‘follow-up’ publications in of Microbiology (vol. 156, part 1, pp. 30–38) ensure reporters have their stories – Education and Public Affairs Officer – Prof. Joanna Verran the field, but it should also help with sourcing additional straight. In the majority of cases, Department of Biology, Chemistry and Health Science, Manchester Metropolitan University, Chester Street, funding. There are many emails in my in box on foot of The press release ‘Disinfectants may promote growth of although frustrating for both the Manchester M1 5GD the release which request the team to test some new superbugs’ released on 29 December 2009 is available under scientist and myself, minor inaccuracies tel. 0161 247 1206; fax 0161 247 6325 disinfectant or other. I respond to these with some gusto, ‘media releases’ at www.sgm.ac.uk/news can be overlooked in view of the email [email protected] Duncan McGarva ‘greater good’ achieved by press – Publications Officer – Prof. Howard Jenkinson Department of Oral and Dental Science, University of Spotting a bit of research that will interest Joe Public coverage, e.g. highlighting particular laura Bristol, Lower Maudlin Street, Bristol BS1 2LY 2010 can be tricky. It has nothing to do with the complexity fields of research whose existence tel. 0117 928 4358; email [email protected] 2010 Y of the work, but instead has everything to do with its the public may be completely MA udakis MA Y ‘newsworthiness.’ The research must be relevant, e.g. it unaware of. Members 126 127 impacts on daily life; something people can relate to, e.g. The repercussions of wide press – Prof. Mike R. Barer Infection, Immunity and Inflammation, household cleaners; and it must be timely, e.g. influenza coverage can be unexpected and University of Leicester, Medical Sciences Building, DA Y PO Box 138, University Road, Leicester LE1 9HN DA Y O research during a flu pandemic. significant. Researchers who have built O T tel. 0116 252 2933; fax 0116 252 5030 T From the initial request to the author of a paper until up a rapport with certain reporters email [email protected] several weeks after the release has gone out, the press gain a reputation for being ‘media- – Dr Richard M. Hall GlaxoSmithKline Biopharm R&D, release process is an equal partnership between the friendly’ and will find themselves Gunnels Wood Road, Stevenage SG1 2NY tel. 01438 762735; email [email protected] scientist and myself. After going through the research paper invited to provide their expert opinion – Dr Kim R. Hardie Centre for Biomolecular MicroBiology MicroBiology and the press release information form, I often return on future news stories and features. Sciences, University of Nottingham, University Park, MicroBiology to the scientist with clarifications and further questions. While this may sometimes feel Nottingham NG7 2RD This not only helps me to write accurately, but also gives cumbersome and time-consuming, tel. 0115 846 7958; fax 0115 586 7950 email [email protected] the scientist a first taste of having to explain his work to it is worth remembering that if you – Prof. Mark Harris Institute of Molecular & Cellular someone outside their field of research with a limited don’t comment, someone else who Microbiology, Faculty of Biological Sciences, University interest in the technicalities! As the release evolves, each is potentially much less qualified will. of Leeds, Leeds LS2 9JT draft is sent to the scientist to ensure they are 100% happy These opportunities give scientists a tel. 0113 343 5632; email [email protected] with what has been written and what they have been chance to take some responsibility in – Dr Paul A. Hoskisson (Editor Microbiology Today) Strathclyde Institute of Pharmacy & Biomedical Sciences, University of quoted on. Ultimately, the final say is theirs on any release way (although this is no easy feat!), fighting back against the inaccurate, Strathclyde, 204 George Street, Glasgow G1 1XW issued from SGM. but ‘selling’ the story. This is achieved sensationalist science reporting we tel. 0141 548 2819; email [email protected] Writing the press release is all about creating a ‘story’ by stressing the significance of the are all forever complaining about. – Dr Catherine O’Reilly Dept of Chemical and Life Sciences, that captures the reader’s (i.e. the journalist’s) attention, work and its future implications. From now on, if I get in Waterford Institute of Technology, Cork Road, Waterford, covers the 4 Ws (who, what, where and why) and also Scientists are often a bit nervous touch with you about producing a Ireland tel. +353 51 302858; fax +353 51 378292 passes the ‘so what?’ test. Journalists receive hundreds of about extrapolating many years ahead press release from your research, I email [email protected] press releases everyday, of which maybe two or three get of time to talk about a potential new hope you will have no hesitation in – Dr Karen Robinson Centre for Biomolecular covered. A snappy headline and a concise first paragraph treatment or vaccine for an infectious agreeing! Sciences, University of Nottingham, University Park, containing just the right amount of intrigue is the best disease, but ultimately this is what nails Nottingham NG7 2RD tel. 0115 823 1094; email [email protected] strategy to ensure the release is not deleted after 3 seconds! the ‘so what?’ test. laura udakis is External Relations – Dr Gary Rowley School of Biological Sciences, University The biggest challenge in constructing the body of the After the press release is sent out, Administrator at SGM (email l.udakis@ of East Anglia, Norwich NR4 7TJ release is not explaining complex research in an accessible whether it gets picked up and covered sgm.ac.uk) tel. 01603 592889; email [email protected] Spicy supplements fight infection Bio- ss The advent of antibiotics has transformed the Bansal, S. & Chhibber, S. (2010). surgeons e outcome for anyone suffering from a bacterial

Curcumin alone and in combination r infection through providing a way to remove with augmentin protects against versus the bacteria and give a much greater chance of pulmonary inflammation and p

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combination therapies have this, while others received while secreting antimicrobial, pe 128 129 not been very effective, so curcumin in their food as well proteolytic and other a Once there are large numbers of P. aeruginosa, researchers continue to seek as the antibiotic therapy. The compounds that reduce the p signals are exchanged between the cells and they DA Y DA Y O new solutions. inflammation. The healthy tissue start to synthesize a range of toxic compounds O T result was that although the T Shruti Bansal and Sanjay antibiotic, and not the curcumin, is exposed, cleaned of many that might include ones toxic to maggots. Chhibber in the Department significantly decreased the infecting bacteria and it has a ot In tests where the maggots were given only media better chance of healing. h MIC of Microbiology at Panjab number of bacteria in the lungs colonized with different varieties of P. aeruginosa University in India have taken of the mice, the curcumin had Researchers have been keen to as food, it was very obvious that they did not like MicroBiology MicroBiology inspiration from the spice a very significant impact on work out the best method for the bacteria. The researchers could see that the MicroBiology ts turmeric, which contains several markers of inflammation. this treatment, now generally maggots kept away from the microbes, ate very the active herbal compound termed maggot debridement little, and most died. Strains of P. aeruginosa from These all indicated that there gh curcumin. Turmeric extracts was less inflammation and thus therapy (MDT). Occasional which some genes required for signalling had been have been used for centuries less damage to the lungs. As reports that the level of li removed were less toxic, but did not rescue the in the Indian subcontinent to the researchers point out, this infection increased as a result maggots completely. The obvious conclusion from treat illnesses such as coughs, of the maggots, or that the gh this is that a test for infection with P. aeruginosa

result is additional evidence i inflammatory bowel conditions maggots died in the wound, should be carried out before using maggots that a spice that is part of h and arthritis. Scientific research normal cookery can give extra spurred Danish researchers for therapy. If large numbers of this species are at the Copenhagen Wound has shown that curcumin really benefits during illness. It also s present, antibiotics or other treatments should

has anti-inflammatory properties provokes further thought about Healing Center and Statens e be used in addition, or as an Andersen, A.S., Joergensen, B., through reducing levels of the importance of the diet and Serum Institut AMOF to alternative, to maggot therapy. Bjarnsholt, T., Johansen, H., several cellular factors involved investigate the relationship Interestingly, the researchers also food consumption by hospital Karlsmark, T., Givskov, M. & Krogfelt, in inflammation. To find out patients. between the maggots and found that the maggots secreted K.A. (2010). Quorum-sensing- whether it could be effective wound bacteria further. In something that partially inhibited regulated virulence factors in countering cellular damage particular, they wanted to follow l jon bacterial signalling and they are in Pseudomonas aeruginosa are

Turmeric. iStockphoto / Thinkstock e during a bacterial infection, the up reports that Pseudomonas continuing to investigate exactly toxic to Lucilia sericata maggots.

researchers carried out a study aeruginosa, a frequent bacterial ri how this works to find out if Microbiology 156, 400–407.

over one week in mice suffering infection in chronic ulcers, was e it can be developed into

from bacterial pneumonia. problematic for the maggots. m something clinically useful. s

Jiang, J., Zhang, Q., Hu, X., Shao, C., Polar Microbiology: s

Spotted shrimp Sequencing e Al-Rasheid, K.A.S. & Song W. (2010). The Ecology, Biodiversity and White spot syndrome virus (WSSV) is a problem the unseen Two new marine ciliates, Euplotes Bioremediation Potential of

in shrimp farming, causing major economic losses. sinicus sp. nov. and Euplotes Microorganisms in Extremely ew parabalteatus sp. nov. with new Although wild shrimp can be infected with the Ciliates are microscopic Cold Environments small subunit rRNA gene sequence vi virus, it has never been reported to cause the unicellular protozoa found in Editors a.K. Bei, J. Aislabie & R.M. Atlas sourc of Euplotes rariseta (Ciliophora; e mass mortality seen in farmed shrimps. The marine and fresh waters around Publisher CRC Press / Taylor & Francis Group (2009) Spirotrichea; Euplotida). Int J Syst e the world, as well as within Details £99.00 | pp. 402 | ISBN 978-1-42008-384-2 r eponymous symptoms of white spots appear as Evol Microbiol 60, 1241–1251. the shrimps become lethargic and stop eating. the digestive tract of animals. Reviewer David Pearce, British Antarctic Survey They are named after the very Not only can it kill all the stock in a shrimp farm diversity of ciliates in the sea small hairs called cilia on their This book is about polar micro-organisms and, in particular, within days, but it is also highly contagious. First near Qingdao, focusing on the surfaces that are essential for their physiological potential to remove or degrade hydrocarbon discovered in China and Taiwan in 1992, it has the size of a deletion in one genus Euplotes. Members of both feeding and movement. contaminants from a diverse range of polar environments. It now spread around the world and affects other region of the viral genome this genus have a worldwide Over 10,000 species have is a timely and much needed contribution to the field of polar crustaceans like crabs and crayfish as well. tended to become larger distribution and have adapted been identified, mainly based microbiology. With a focus on biodegradation and a clear As with all diseases, one step towards control is from north to south along to many different habitats. More on appearance under the shift from purely descriptive taxonomy to a consideration of JGVto understand the epidemiology of where each the coast, making it a useful species of Euplotes have been functional diversity, the book compliments the more engineering infection originates and how readily each strain microscope, although molecular marker on a countrywide scale, identified than of any other and environmental science-based approach of Bioremediation of spreads. This requires ways of distinguishing genetics is now being used as while a second deletion might ciliate genus although their Petroleum Hydrocarbons in Cold Regions (Filler et al.). By considering individual WSSV isolates. Nowadays, researchers a further source of information be valuable at a global scale. phylogenetic relationships are books and r high latitude, low-temperature environments, the book begins immediately reach for molecular methods that in ciliate taxonomy. The gene However, a problem with still poorly understood. with the taxonomy, physiology and biochemistry of polar micro- allow them to detect differences between the for a component of the protein this sort of marker is that the On morphological grounds, gy organisms, followed by their potential for biotechnology and DNA sequences of virus strains. These are now synthetic machinery (18S rRNA) deleted region of the genome 2010 2010 the researchers identified bioremediation.

is commonly used in these Y at the stage of comparing the complete genome must be unnecessary, and the two new species, E. sinicus and

MA Y The authors have been drawn from a wide range of experts in MA sequence of several WSSV isolates to develop phylogenetic studies. researchers think that this can E. parabalteatus, and recorded the field, and provide clear coverage of the subject from a range 130 molecular tools for epidemiology. A difficulty with identifying 131 only happen while a virus is ijsem the sequence of their 18S rRNA of different perspectives. Specific strengths of the book include the ciliates is that many are virtually To apply these in the real world, staff at the adapting to a new environment. genes. When they checked range of different micro-organisms considered and habitat types DA Y transparent. Researchers DA Y O Laboratory of Virology and Quantitative To look at variation on the the sequences, they realized covered (including the aerial environment, ice as an environment O T addressed this problem in the T Veterinary Epidemiology at Wageningen in the smaller scale of individual that they had also appeared for microbial growth and the overall relevance to astrobiology). early 20th century using a silver Netherlands, and the Biotechnological Research shrimp farms, the researchers during an earlier survey but the In particular, there are several useful summary tables, for example impregnation technique akin to and Development Institute of Can Tho University, recommended markers that researchers had not been able bacteria isolated from the region, a list of relevant studies of the traditional photography. Some turned to the shrimp farms of Vietnam. Large- involve changes in repeated to identify the ciliates at the Archaea, and specific phylogenetic comparisons. It is also possible to viral DNA sequences that are ciliate organelles and structures MicroBiology MicroBiology scale shrimp farming has only been developed in time. This time, observations select areas of polar microbiology that have not received significant MicroBiology can adsorb silver ions from Vietnam since around 2000, and the country has like the ones used in DNA of the exact appearance of attention in this edition, such as the marine environment, emerging solutions to become visible as in an accurate WSSV reporting system. WSSV was fingerprinting in humans. the ciliates and the silverline environments such as subglacial ecosystems, the full range of a black and white photograph. first confirmed in 1997 and the researchers had With this better appreciation patterns had narrowed the microbial taxonomic groups, for example the pico- This is the so-called silverline isolates available from infections along the whole of the spatial information that identifications down to a small eukaryotes and the viruses (except in respect of system that taxonomists can use length of the 2,500 km coastline. This allowed can be gained from particular number of known species, or HGT), the stability of the ecosystems themselves as part of ciliate classification. them to test several molecular marker systems to genetic markers, the researchers proof that the ciliates were new and the identification of specific regional hot spots see whether any provided statistically significant are now in a position to Researchers in Qingdao, China, species if the matches to these for analysis, but this would be to detract unfairly information about WSSV spread. investigate the rapid emergence in collaboration with Khaled known species were poor. The from what actually has been achieved. Perhaps one

Their results indicated that WSSV arrived first and evolution of this lethal Al-Rasheid from Saudi Arabia, morphological assessment of raisals of microbiolo significant omission was an introductory chapter in central Vietnam and then spread both south virus. This will involve analysing have recently investigated the two new species was supported summarizing polar environments as habitats

and north with the development of shrimp these genetic markers in isolates by the dissimilarity of the 18S pp for microbial growth or one which specifically aquaculture. The researchers discovered that from further geographical rRNA gene sequences to considered the application of new methodologies. locations or collected from known species. The researchers However, in comparison with earlier texts Dieu, B.T.M., Marks, H., Zwart, M.P. & Vlak, J.M. the same site over many years. also collected a third species, which provided a polar synthesis, such as those

(2010). Evaluation of white spot syndrome virus variable The ultimate objective must E. rariseta, during the survey and st a of Vincent (1998), Friedmann (1993) and Wynn-

DNA loci as molecular markers of virus spread at e be to determine what would were able to sequence its 18S Williams (1990), it is clear that the subject has intermediate spatiotemporal scales. be effective measures to stop rRNA gene for the first time to J Gen Virol 91, 1164–1172. grown significantly in recent years and is a still a this economically important give more information about its rapidly expanding topic, and so this work makes a

veterinary disease epidemic. phylogenetic position. Hon welcome and significant contribution.

Euplotes sinicus. X. Hu, Ocean University of China, Qingdao  

Reviews on the web Dr Duncan McGarva (24.3.55–19.4.10) s

Reviews of the following books e out misplaced apostrophes or spelling are available on the website at Members of SGM staff were greatly saddened to hear the news of Duncan’s death on 19 April. He had been mistakes wherever they occurred, be www.sgm.ac.uk/pubs/micro_ diagnosed with cancer and had spent the last few months it on a pub menu or the side of a lorry. today/reviews.cfm in hospital receiving treatment. Several of the fitter members of Biofilms in the Food and Beverage Duncan did his BSc in Microbiology and Cell Biology staff have organized a sponsored bike Industries (Fratamico et al.) at the then Plymouth Polytechnic. This was followed by a ride in Duncan’s memory, and will cover the 100 miles from Bristol to Pili and Flagella: Current Research and PhD at the University of Sussex, and two years as a Senior Reading, on the Kennet and Avon Future Trends (Jarrell) Research Assistant at the University of Liverpool, working

on DNA repair in Escherichia coli. canal towpath. The donations will obituari Antimicrobial Drug Resistance Vol. 2. He came to SGM in 1982, as Assistant Editorial go to the Duchess of Kent Hospice, Clinical and Epidemiological Aspects Secretary on the Society’s journals, becoming Editorial where the staff took excellent care of (Mayers) Secretary (Managing Editor) for Journal of General Virology Duncan in the last stages of his illness. Frontiers in Dengue Virus Research in 1986. He took the first cautious steps to introduction (Hanley & Weaver) of computers in the editorial process in 1989, using a Ron Fraser, SGM Chief Executive  Aspergillus Molecular Biology and machine he had bought with his own funds.  Genomics (Machida & Gomi) In 1994 he was appointed as Systems Manager, Micro and Nano Technologies in with the remit to introduce ‘on-screen edit-  Bioanalysis Methods and Protocols (Lee ing’ for the journals, and to become aware of  & Foote) developments in online publication. This led to Legume Nodulation: a Global Perspective the appearance of the journals on HighWire in the late 1990s. Duncan was also involved in the (Sprent) The Scourging Angel: development of the ESPERE system for online 2010

Neisseria: Molecular Mechanisms of 2010

Y submission and peer review, which served us The Black Death in the British Isles Pathogenesis (Genco & Wetzler) MA Author b. Gummer well for five years, until replaced by the current MA Y Recombinant Antibodies for Bench>Press system. In later years he was very 132 Publisher The Book Service (2009) 133 Immunotherapy (Little) much involved with maintaining the Society’s Details £25.00 | pp. 512 | ISBN 978-0-22407-767-5 Incredible Anaerobes: From Physiology to websites and IT systems development. DA Y Reviewer Steve Diggle, University of Nottingham DA Y O Genomics to Fuels (Wiegel et al.) However, he never lost his interest in the O T T The history of plague, and the Black Death in particular, has been one of my interests Applied Mycology (Rai & Bridge) production quality of the journals, and was quick to point out the (very occasional) error. for as long as I can remember. I was therefore keen to read Benedict Gummer’s new Campylobacter: A Practical Approach to Duncan in May 2008. Karen Rowlett His eagle eye, and defence of high standards in offering on the subject. the Organism and its Control in Foods written English, extended to gleefully pointing The aims of the book are simple: (a) to describe the British Isles on the eve of the (Bell & Kyriakides) MicroBiology MicroBiology Black Death; (b) to describe the progress of pestilence through the island and (c) to Microbial Safety of Fresh Produce (Fan MicroBiology assess the state of England, Ireland, Scotland and Wales after the disease had passed. et al.) Professor Patricia H. Clarke FRS (27.9.19–28.1.10) Whilst the aims might be simple, piecing together relevant information and joining RNA Interference and Viruses: Current Patricia née Green was born in Pontypridd, South S.T. Cowan she developed rapid them in a coherent and interesting way is not trivial. Because of this, Gummer has Innovations and Future Trends (Martinez) Wales, the daughter of a metal merchant. She won a Foun- enzyme tests to identify bacteria. In created an extraordinarily detailed book which is easy to read and brings the 14th Primate Parasite Ecology: The Dynamics dation Scholarship to Howells School in Llandaff, then in 1953 she was appointed as a lecturer and Study of Host–Parasite Relationships century to life. The book describes a level of sophistication in government, commerce, 1937 she read Natural Sciences at Girton College, Cam- in Biochemistry at University Col- (Huffman & Chapman) road networks and town and village life that I certainly didn’t know existed during this bridge, focusing on biochemistry in her final year. lege London (UCL), was promoted time. Applied Biomedical Microbiology: A Rather than continue with research at Cambridge she to Reader in 1966 and Professor Gummer does not discuss the biological agent of the Black Death, which is Biofilms Approach (Paulson) opted for war work. Until 1944 she did research on explo- of Microbial Biochemistry in 1974. currently a controversial subject as some researchers have suggested that the Black Microbiology: A Clinical Approach sives at Swansea and Woolwich Arsenal under the auspices Her research base was at UCL until Death was not Yersinia pestis but some other agent, possibly a virus. The book does (Strelkauskas et al.) of the Armament Research Group, Ministry of Supply. retirement in 1984. not really care (although it is discussed briefly in the appendix) which is a strength in Virology: Molecular Biology and From 1944 to 1947 she worked at Wellcome Research Patricia was interested in micro- my opinion. No time is wasted discussing the epidemiology of bubonic/pneumonic Pathogenesis (Norkin) Laboratories in Beckenham, Kent, in the research group bial biochemistry and decided to led by B.C.J.G. Knight. She worked mainly on toxins of investigate why on certain substrates plague and how 14th century Britain might have facilitated the spread of this particular Bioremediation: Methods and Protocols Clostridium oedematiens which causes gas gangrene. there was a lag before some bacteria disease. Indeed, Gummer’s descriptive account of the networks of trade existing (Cummings) She married Michael Clarke in 1940, a captain in the started to grow. She used Pseudomonas Biofuels: Methods and Protocols (Mielenz) between key market towns and villages and 14th century life in general, raises Tank Corps. After the war he was a documentary film aeruginosa and found that the delay significant doubts in my mind as to whether Y. pestis (at least as we know it today) Cellular and Molecular Biology of maker and was later Director of the University of London was because the bacteria first made was the culprit. At least we should keep an open mind to other possibilities. Filamentous Fungi (Borkovich & Ebbole) Audiovisual Centre. They had two sons, Francis and David. permeases, specific inducible systems An excellent book and worth a read if you are interested in plague, pandemics Lentiviruses and Macrophages: Molecular Patricia worked at the National Collection of Type allowing the uptake of nutrients. or history in general. and Cellular Interactions (Desport) Cultures at Colindale, London, from 1951 to 1953. With Pseudomonads can grow on a larger at the University of Wales to and co-edited text books relevant to her goat-adapted vaccine had been successful by 2001 when the last Plowright received numerous honours for his (1984–1987) and Professor at interests. widely available for decades and known case of rinderpest was work, including that of Commander of the Most the Chinese University of Hong Patricia had always believed that it was pos- had made a significant impact confirmed in Kenya. Distinguished Order of Saint Michael and Saint Kong. From 1990 to 1993 she sible for women to have fulfilling careers in on the circulation of rinderpest Kenyan independence saw George (CMG); fellowship of the Royal Society; was a member of the Advisory research and have a family. She was one of six virus, despite its drawbacks, but the demise of the CVS and fellowship of the Royal College of Veterinary Sur- Committee of the Palm Oil female members of the Committee on Women it was adoption of the new cul- Walter moved in 1964 to work geons; the Gold Medal of the Office International Research Institute of Malaysia. in Science, Technology, and Engineering set up ture techniques which enabled a for the Animal Virus Research des Epizooties (OIE); the Animal Health Trust’s Patricia Clarke She enjoyed microbiology by the Science Minister in 1993. Their report, novel vaccine to be developed. Institute at Pirbright, Surrey. Outstanding Scientific Achievement Award; and SGM range of organic compounds for several reasons, such as the The Rising Tide (1994), outlined the help needed Walter conceived that the Fortunately, he was able to con- the European Society of Veterinary Virology’s than most bacteria. Patricia fact that it required technical to encourage women back into scientific careers. tissue culture rinderpest vac- tinue his links with EAVRO, to Medal. Arguably the crowning accolade came in queried how this diversity had skills – she came from a long However, Patricia always admitted that she had cine (TCRV, generally referred which he was seconded from 1999 when, after nomination by FAO, he became originated. This led to work line of craftsmen. Microbiology been very fortunate in having excellent schools to as the ‘Plowright vaccine’) 1966 to 1971. Although rinder- that year’s World Food Prize Laureate, an award on the genetics of P. aerugi- was a developing area and there nearby and reliable after-school help. Her family would be cheaper, easier to pest ranked highly in his pro- given for contributions to advancing human de- nosa. She and her research group were always new puzzles and was the centre of her life, but having taken on a manufacture, easier to scale- fessional portfolio, he made velopment by increasing the quality, quantity or developed hundreds of mutants challenges. She enjoyed work- range of work commitments, she always gave of up and, above all else, easier significant contributions to the availability of food in the world. The Chairman of which had different inducer ing with research students and her best to these. to standardize to a high level understanding and control of the World Food Prize Foundation noted that ‘Dr and/or enzyme specificities. the demands of teaching. In 1970 she and Michael bought a house in of product safety. Through other livestock diseases, such as Plowright should be counted as one of the great heroes At UCL they were the first to She had a gift for writing Cirencester and lived there permanently when extensive laboratory and field malignant catarrhal fever and of the 20th century. His development of the rinderpest show that a single site mutation and speaking clearly, and they had both retired. There she was involved trials, he demonstrated that the African swine fever. vaccine nearly 40 years ago has helped save countless could result in an enzyme with thought carefully about what with local schools and colleges and also a keen attenuated vaccine was not only Returning finally to the lives, while ensuring that our global food supply remains a new activity. A family of new would interest her audience. She supporter of the Cirencester Science and Tech- highly efficacious, but was also UK, he resumed his academic abundant and safe for future generations.’ enzymes was evolved by com- was invited to give talks about nology Society and of the Cirencester Civic completely safe in all classes career at the RVC as Professor of All of Plowright’s considerable contributions bining mutations in the amidase her work worldwide – but also Society. of cattle and conferred a long Microbiology and Parasitology. to veterinary virology stemmed from his deep regulator with structural genes. enjoyed speaking to young She was appointed a Fellow of The Royal lasting immunity, subsequently During that time he continued appreciation of the way in which cell culturing

Patricia and her group devel- people and those without a sci- Society in 1976, and served on their Council and demonstrated to be lifelong. Its to conduct original research and techniques could be developed to yield a more 2010 2010 oped new enzymes which could entific background. Her 1979 was Vice-President in 1981–1982. She received availability ushered in a new era supervised the doctoral studies fundamental understanding of the nature of Y MA Y be used in biotechnology, ex- Leeuwenhoek Lecture, given at Honorary Doctorates from the University of Kent of rinderpest control which saw of several veterinary virologists veterinary viruses. It is to the unique benefit of MA 134 perimenting with the large-scale The Royal Society on Experi- (1988) and the Council for National Academic the disease progressively reduced who are well-known today. His mankind that, from the late 1950s to the early 135 production of enzymes, and ments in microbial evolution: new Awards (1990). Patricia was present at the inau- in Africa and Asia as a result of final full-time post (1978–1981), 1970s, he chose to work on a variety of tropical DA Y their purification. enzymes, new metabolic activities’ gural meeting of the SGM, a member of Council the near universal adoption of was Head of the Department of animal diseases and was supported by the British DA Y O O T On retirement she was was an example of her informa- 1960–1970, and Honorary General Secretary the new vaccine. Only with the Microbiology at the Institute for Government to do so. T awarded a Leverhulme Fellow- tive style. From 1989 to 1993 she 1965–1970. Michael predeceased her. She is perfecting of TCRV could in- Research on Animal Diseases in With his death the world has lost one of its ship so that she could continue was Biological Editor of Science survived by her two sons and her grandson Oliver. ternationally co-ordinated cam- Compton, Berkshire. most eminent veterinary virologists and authori- with her research, and was an Progress and enjoyed commis- paigns be considered. As a result After his formal retirement, ties on rinderpest. He was renowned as one who Honorary Professional Fellow sioning articles. She contributed Catharine Haines, Lancaster Joint Project 15 and the Pan- Plowright’s expertise continued did not suffer fools gladly, yet his clear and in- to be in demand as a consultant, MicroBiology MicroBiology African Rinderpest Campaign cisive intellect commanded respect and he could MicroBiology were mounted from the 1960s. visiting lecturer and professor. be a charming man. Many will remember him Walter Plowright CMG FRS FRCVS (1923–2010) It is impossible to conceive how In 1998 he gave the keynote as approachable, friendly, supportive, immensely the Global Rinderpest Eradica- address to the United Nations interesting and a stimulating source of advice. He Born into a farming family at Holbeach, He was appointed in 1956 as of the epidemiology of wildlife- tion Programme (GREP) could Food and Agriculture Organi- is survived by his wife Dorothy who he married Walter Plowright The World Food Lincolnshire, in 1923, Walter was educated in Head of the Division of Virus cattle rinderpest interactions, have reached its current status of zation’s (FAO) Technical Con- in 1959 and who supported him Prize Foundation Moulton and Spalding where he excelled at his Diseases at the East African Vet- but to the development of an putative global disease freedom sultation meeting on the GREP loyally for most of his African studies. Having early in his life decided he wanted erinary Research Organization’s attenuated tissue-culture-grown without the ‘Plowright vaccine’ in Rome, delivering a fascinat- and subsequent career. to be a veterinary surgeon, he studied veterinary (EAVRO) Muguga Laboratory vaccine. and its derivatives of improved ing and up-to-date account of Rinderpest is only the sec- medicine and surgery at the Royal Veterinary in Kenya. At the time rinder- He worked with a team of thermostability formulated in the science of rinderpest behav- ond disease in history to have College (RVC) in London during the war years, pest was continuously ravaging veterinary scientists in various the 1980s. Many millions of iour from a perspective covering been eradicated through human and after again distinguishing himself in his studies African cattle herds and wild disciplines who became distin- doses were used in campaigns virtually a century. In 2001, he efforts, the first being smallpox. he graduated as MRCVS in 1944. populations of buffalo, antelope guished in their own right for until, with improved epide- made a valued contribution to The formal announcement He was immediately commissioned into the and giraffe, not to mention the their work on a broad spectrum miological understanding and the Royal Society’s enquiry into by FAO and OIE, due immi- Royal Army Veterinary Corps and given post- lives of livestock-dependent of African livestock diseases. reduced disease incidence and infectious diseases in cattle fol- nently, that rinderpest has been ings in the Middle East, North Africa and Kenya, farmers. Walter is best known This was an exciting time to distribution, it became possible lowing that year’s outbreak of eradicated from the world will returning temporarily to the UK in 1948, as a for the seminal work on rinder- be a veterinary virologist as it for GREP progressively from foot-and-mouth disease in the confirm the achievement as a demonstrator in pathology at the RVC. How- pest that he conducted at Mu- was right at the beginning of 1994 to replace mass vaccination UK. Sadly, increasing health fitting and lasting memorial to ever, his love of Africa and infectious diseases guga. It set the foundation for the discipline when techniques with focused vaccination, using problems constrained his mobil- this remarkable scientist and soon lured him to Kenya in 1950 to work for the the eventual global eradication of in vitro virus cultivation were ‘Plowright’s vaccine’ targeted at ity in recent years and severely committed veterinary surgeon. Colonial Veterinary Service (CVS). He was to of the disease, as it led not only first becoming available. A eliminating residual reservoirs limited his acceptance of other spend 19 of the next 21 years working in Africa. to an improved understanding good vaccine in the form of a of infection. This tactic proved invitations. Peter Roeder oBE, Bordon ten years AGO I published a The Rosetta Stone. Brand X Pictures / Thinkstock satire in Microbiology Today about a momentous microbiological discovery in the year 2025. It was a critique aimed at the simple notion that 16S rRNA serves as a Rosetta Stone for tracing the evolution and relationships of bacterial species. The plot elaborated complex events which resulted in discovery of a unique ‘taxonomy gene’ which eventually could be deciphered to reveal the authentic names of all bacterial species. Thus, in Bergey’s Ultimate Manual of Definitive Bacteriology, The validity of using the 16S ribosomal Escherichia coli finally became known by RNA gene as the basis for bacterial its proper name Proteofermentoformicus lipocylindricus. taxonomy has been further called into The satire also considered an hypo- thesis explaining why the ‘taxonomy question following a recent evaluation gene’ was devised by a very advanced, of the complexities of evolution. ancient extraterrestrial civilization that according to Francis Crick (1981) howard gest might have seeded the primeval COMMENT gene’ ‘taxonomy The remarkable Earth with its first living organisms, My year 2000 satire in Microbiology Today can now be

2010 bacteria. readily accessed on the internet at https://scholarworks. Advances made during the past decade make it very iu.edu/dspace/handle/2022/3848. The internet version is MAY MAY unlikely that 16S RNA sequences are Rosetta Stones for identical with the original Microbiology Today paper, except 136 tracing bacterial evolution. In particular, increasing evidence that a photograph of the Rosetta Stone in the British for rampant gene exchange (‘lateral gene transfer’) among Museum is omitted, for copyright reasons. Poetic justice! microbial species argues against conventional ‘tree-of-life’ It is appropriate to quote a comment by the eminent ODAY T

representations. There are now good reasons to believe biogeochemist Preston Cloud (1977), that bacterial species evolved in the general form of a ‘Knowledge advances like the concentric ripples that complex ‘bush’, with numerous interconnections, which spread outward from a pebble tossed into a mill pond. iology

B Doolittle (2000) once described as a spaghetti-like web of Its expanding front is in contact with an ever-widening intermingled branches. periphery of ignorance as growing comprehension generates icro

M New evaluations of the evolutionary complexities are new and more subtle questions.’ discussed in ten articles in the 12 August 2009 issue of Philosophical Transactions of the Royal Society (Biological Sciences), Howard Gest is Distinguished Professor Emeritus of Microbiology and Adjunct on the theme ‘The network of life: genome beginnings and Professor History & Philosophy of Science at Indiana University, Bloomington, IN 47405, evolution’. In my opinion, this Royal Society issue will USA (email [email protected]) prove to be a landmark in redirecting our understanding of evolution in the microbial universe. Incidentally, it makes Further reading clear that the practice of changing the names of bacterial Cloud, P. (1977). The veils of Gaia. In The Encyclopaedia of Ignorance, pp. 387–390. genera and species based on irrelevant 16S RNA differences Edited by R. Duncan & M. Weston-Smith. Oxford: Pergamon Press. was a retrograde development. By 2003, it had become Crick, F. (1981). Life Itself – Its Origin and Nature. New York: Simon & Schuster. evident that the phenomenon of ‘16S name-changing’ had Doolittle, W.F. (2000). Uprooting the tree of life. Sci Amer 282, 90–95. several kinds of negative effects that were completely ignored Gest, H. (2000). Report from the year 2025 meeting of the American Microbiological by molecular biologists who had little or no interest in the Society: ‘Discovery of the bacterial ‘taxonomy gene’. Microbiol Today 27, 28–30. important practical aspects of determinative bacteriology. Gest, H. (2003). Names of bacteria and their evolutionary relationships. Microbiology 149, The great significance that attaches to a stable and generally 1956–1958. accepted nomenclature is discussed in Gest (2003), which Ragan, M.A., McInerney, J.O., & Lake, J.A. (editors) (2009). The network of life: genome cites articles critical of the name-changing epidemic and beginnings and evolution. Philos Trans R Soc (Biol Sci) 364, 2167–2289. noted that it must be confusing to younger investigators Van Niel, C.B. (1946). The classification and natural relationships of bacteria.I n Cold Spring when they explore the literature and encounter organism Harbor Symposia on Quantitative Biology, vol. XI, Heredity and Variation in Microorganisms, names that are unrecognizable and have no idea that many pp. 285–301. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory. of them are bacteria that have been previously studied for decades. Please note that views expressed in Comment do not necessarily reflect official policy of the SGM Council.