microbiologytoday
vol35|aug08 quarterly magazine of the society for general microbiology
life’s a gas microbes and oxygen
… and it’s hydrogen
methane: a natural gas
microbial genetics of seaside smells
toxic gases of the nitrogen cycle contents
vol35(3) regular features 106 News 138 Schoolzone 146 Hot off the Press 114 Microshorts 142 Gradline 150 Going Public 136 Meetings 145 Addresses 154 Reviews other items 141 Obituary – Professor Norbert Pfennig
articles 116 Microbes and oxygen 128 On the microbial genetics Martha Clokie of seaside smells A range of micro-organisms and even, Andy Johnston surprisingly, viruses are involved in oxygen DMS, responsible for the familiar aroma of the shore, is production on planet Earth. produced by complex microbial processes. 132 NO laughing matter: 120 Life’s a gas... and it’s the toxic gases of the hydrogen nitrogen cycle Mark D. Redwood & David J. Richardson, Lynne E. Macaskie Andrew J. Thomson & Some microbes gain energy by releasing hydrogen into the environment, a process which has many exciting Nicholas J. Watmough applications. Nitric oxide is an important part of the nitrogen cycle, but in some circumstances it can be a greenhouse gas.
124 Methane: a natural gas 156 Comment: Bad reporting in the media is hard to swallow James Chong Methane may be a greenhouse gas, but John Heritage conversely it also has great potential as a source Sometimes it can be a good thing that today’s newspaper is of green energy. tomorrow’s chip wrappings.
Cover image A natural-gas fireball. Photos.com / Jupiter Images The views expressed
Editor Dr Matt Hutchings––Editorial Board Dr Sue Assinder, Dr Paul Hoskisson, Professor Bert Rima––Managing Editor Janet Hurst––Assistant Editors Lucy Goodchild & Faye Stokes by contributors are not Editorial Assistant Yvonne Taylor––Design & Production Ian Atherton––Contributions are always welcome and should be addressed to the Editor c/o SGM HQ, Marlborough House, necessarily those of the Basingstoke Road, Spencers Wood, Reading RG7 1AG–Tel. 0118 988 1809–Fax 0118 988 5656–email [email protected]–web www.sgm.ac.uk Society; nor can the Advertising David Lancaster, Ten Alps Publishing, London Office, 10 Savoy Street, London WC2E 7HR–t 0207 878 2316–f 0207 379 7118–e [email protected] Regular feature images pp. 107 SGM; 137, 139, 155 Comstock / Jupiter Images; 143, 147 Stockbyte; 145 Digital Vision / Getty; 151 Ablestock / Jupiter Images claims of advertisers © 2008 The Society for General Microbiology––ISSN 1464-0570––Printed by Latimer Trend & Company Ltd, Plymouth, UK be guaranteed. news
SGM Council and sub-committees – changes proposed New members SGM Council News items in previous issues of Microbiology Today scientific learned societies have had recent experience of of Council February Meeting Highlights have mentioned that a small working party of Council downsizing their governing bodies to within this range. The following have been elected members and staff has been considering the optimum size unopposed to serve on Council for SGM Meeting, Edinburgh, Spring 2008 Accordingly, the working party and current Council and structure of Council and its various sub-committees, a period of 4 years from September The meeting took place in the Edinburgh International Conference Centre are recommending a move towards a smaller Council, to ensure continuing and effective good governance of 2008: and was attended by 1,318 participants. The quality of the science and the comprising the following appointed Officers: President, the Society, and reflect best modern practice. Council Professor Mark Harris, Institute organization were generally regarded as excellent. The SGM Prize Lectures General Secretary, Treasurer, Education and Public Affairs members are trustees of SGM as a charity and directors of Molecular and Cellular Biology, enjoyed a particularly large audience. Officer, Scientific Meetings Officer, and Publications Officer, of the company limited by guarantee. As such they University of Leeds together with six Elected Members. Council would also Planning for future SGM meetings have responsibility to ensure compliance with relevant Dr Gary Rowley, School of have the power to co-opt up to three additional members, The new meetings planning system has been approved by Council and will be legislation, and to ensure effective management of the Biological Sciences, University of to represent constituencies or areas of microbiological fully implemented from Spring 2009 onwards. Society in achieving its charitable objectives. They also science that were thought not to be adequately represented East Anglia have wider responsibilities to the members of the Society, European Society for Clinical Virology (ESCV) in the existing membership. One safeguard would be to Profiles of the new Council members and for the promotion of all aspects of microbiological ensure that the Society’s membership in Ireland is always will appear in a future issue of SGM is now providing administrative support (membership registration, science in the fields of education, research and public and adequately represented. Microbiology Today. subscription renewal and accounting) for the ESCV. political awareness. The working party is chaired by Petra Oyston and its members are Robin Weiss, Charles Penn, At present, the work of Council is expedited by three Nominations for SGM Prizes 2009 Neil Gow and Bert Rima, with Ron Fraser and Janet Hurst sub-committees: Treasurer’s, Scientific Meetings, and Nominations for the Colworth, Fleming, Fred Griffiths and Peter Wildy prizes from SGM headquarters in attendance. Publications, and these will continue. Publications Annual General for 2009 are requested (see the May issue of Microbiology Today and the SGM Committee will become the primary forum for the Editors- Meeting 2008 website for details). The working party has held several meetings since June in-Chief of the Society’s journals, and will be chaired by 2007, and has surveyed current governance arrangements The Annual General Meeting of The SGM Medal the new Publications Officer. In addition, an Education and the Society will be held on Tuesday, in similar organizations. The Society’s solicitors have also Council decided to create a new prize, called the SGM Medal. This prize will be Public Affairs Committee will be formed, chaired by the 9 September 2008 at the Society been consulted on the implications of any proposed bestowed annually on an individual from anywhere in the world whose research eponymous Officer. Meeting at Trinity College Dublin. changes for company and charity law, and for the is of internationally high reputation and has been of significance reaching beyond A Special Resolution to modify the Society’s Articles of mechanism for implementation of any proposed changes Agenda papers, including reports microbiology. The Prize comprises a Medal, a cheque for £1,000 and covers Association will be put to the Annual General Meeting on through re-wording of the Society’s governing documents. from Officers and Group Conveners, travel, accommodation and subsistence. Council approved the rules (see SGM 9 September, and is printed in the Annual Report and AGM An early conclusion of the working party was that at 24 the Accounts of the Society for website), and it is intended to bestow the first medal in 2009. A sub-committee booklet circulated with this issue of Microbiology Today. The members – 12 Officers with specific job titles and 12 2007 and a Special Resolution to will prepare recommendations for the July Council meeting. proposed timetable is that the changes to the Officers and Elected Members – SGM Council had grown over the years amend the Articles of Association sub-committees will be effective from September 2009, Review of Council composition and functions to a much larger size than is consistent with best modern are circulated with this issue of and that the elected Members will reach their new ‘steady practice for an effective decision-making and governing Microbiology Today. Council received the recommendations of the working group, chaired by state’ number in September 2011. body. The large number tended to make discussions Professor Petra Oyston, that had been set up to review its structure and function. protracted and decision-making more difficult. It was also SGM Council has over many years steered the Society Wide-ranging discussions ensued on the responsibilities of Elected Members, felt that the functions of some of the officer posts had been in many successful directions, including a vibrant and Virology at the roles of SGM officers, and the optimum size of such a body. As described increasingly overtaken by the employment of professional developing programme of scientific meetings, taking Warwick on p. 106, the group proposed reducing Council members to 6 Officers and 6 staff at the Society’s headquarters, and that there were on publication of two additional journals, and greatly Elected Members. Much of the business would be done in sub-committees, Sincere apologies are due to the opportunities to re-define and consolidate duties. In increasing its activities in education and public awareness of the chairs of which would report to Council. During its sessions Council would Department of Biological Sciences at addition, some of the Elected Members felt that they were microbiology. In all this time the Society has been efficiently concentrate on policy and strategic matters and on difficult/controversial issues. the University of Warwick for implying not being asked to contribute enough in specific ways to managed and has remained financially robust. The proposed Council approved these proposals and a Special Resolution to authorise the in the May issue that the only available Council, and that their range of responsibilities should be changes to a leaner and fitter Council with more focused changes to the Articles of Association will be put to the Annual General stand-alone virology degree courses enhanced and more clearly defined. responsibilities for individual members aim to build on this Meeting in September 2008. in the UK are at Glasgow University. and continue to deliver the best service to the membership, The survey of similar bodies and of the literature on the The notice published on behalf of the SGM Finances the general public and microbiological science. theory and practice of governance and decision-making latter was accepted in good faith. An Council approved the financial statements for 2007. suggested that around 8–15 members was optimal. Some Petra Oyston and Robin Weiss undergraduate degree in virology has, Retiring member of Council of course, been available at Warwick The President Robin Weiss thanked retiring member Professor Rick Randall for for many years. Details of the course his valuable contributions to the activities of Council. may be found at: www2.warwick. ac.uk/study/undergraduate/courses/ Ulrich Desselberger depta2z/biology/c520/#virology General Secretary
106 microbiology today aug 08 microbiology today aug 08 107 New Oxoid Precis™ Culture Methods
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Oxoid Precis culture methods allow isolation, detection and confirmed identification of foodborne pathogens in just 2 days without the need for specialist equipment or training. People Just follow these 3 simple steps: Queen’s Birthday Floral tribute 1. Enrichment – a single broth combining resuscitation and growth in overnight incubation Honours Well done to Tim Wreghitt, former SGM Clinical Virology Group Convener and Honorary Consultant in 2. Plating – a single medium incorporating enzyme specific inhibition and differentiation. Congratulations to Professor Brian I. Duerden, Professor Microbiology at Addenbrookes Hospital, Cambridge on Coloured colonies clearly indicate presumptive positive results of Medical Microbiology, yet again winning a gold medal at the RHS Chelsea Flower 3. Confirmation – confirmed test result available in less than 10 minutes, direct from plate* Cardiff University School Show. He organized an exhibit on behalf of the Royal of Medicine, Inspector of College of Pathologists and Health Protection Agency. Precis methods for Salmonella and Listeria monocytogenes, validated by AFNOR to ISO 16140, are Microbiology and Infection The display featured ‘malaria and treatment plants’ in the now available. Contact us to find out more. Control at the Department Continuous Learning section of the Show.
*ISO standard tests for confirmation have also been validated and approved by AFNOR, offering complete flexibility. of Health and former Editor- Tim is to receive double honours this year, as he is also in-Chief of JMM, on the to be made an OBE in the Queen’s Birthday Honours, for award of a CBE for services services to National Health virology service provision. to medicine and charity. To find out more contact: Tel: +44 (0) 1256 841144 Royal Society Fellows elected 2008 Fax: +44 (0) 1256 329728 Power unseen Oxoid, Wade Road, Basingstoke, Email: [email protected] The following microbiologists have been made awards: Sir Leszek Krysztof Borysiewicz In August, Bernard DEDICATED TO MICROBIOLOGY Hants RG24 8PW www.oxoid.com KBE FRS, Chief Executive, Medical Research Council; Professor Chris John Lamb FRS, Dixon’s Power Unseen Director, The John Innes Centre and John Innes Professor of Biology, University of – How Microbes Rule the East Anglia; Dr Jan Löwe FRS, Senior Scientist, Medical Research Council Laboratory World becomes available of Molecular Biology; Professor Kenneth Nigel Timmis FRS, Head of Department of as a print-on-demand Environmental Microbiology, Helmholtz Zentrüm für Infektionsforschung, Braunschweig. book. A collation of 75 vignettes about different Deaths Out-of-print books for sale micro-organisms and their The Society notes with regret the death of Dr Clifford Wray of Pyrford, Surrey, a member activities, it was originally since 1981. published by OUP, but has Professor Noel G. Carr (University of Warwick), a member since 1964, died on 30 October been out of print for several 2007. He was a distinguished microbiologist with an international reputation in the study of years. Now published by cyanobacteria who pioneered molecular studies in marine microbiology. PFD, it can be obtained through www.amazon.co.uk Staff news ASM award Congratulations to Microbiology Today Production Editor and Designer, Ian Atherton on his marriage to Alex Till on 10 May. A garden theme dominated the happy day (Ian and Bernard Roizman, Alex are keen vegetable growers), and wedding guests much enjoyed partaking of the Distinguished Service ‘cake’, which took the Professor of Virology at form of a pyramid of small the University of Chicago, Microbiology and allied disciplines, especially late 19th to mid-20th century cakes decorated with has been presented with various marzipan fruits and the Abbott–ASM Lifetime vegetables! Ian and Alex We welcome enquiries for specific titles Achievement Award at the • had a brief honeymoon recent 108th ASM General Our regular catalogues cover all biomedical sciences camping in North Wales, Meeting in Boston, USA. • before returning to the daily Sponsored by Abbott We are also interested in buying books toil of the office and garden • Laboratories, this is ASM’s centre, respectively. premier award for sustained, Bernard Dixon and Kath Adams remarkable contributions to 130 Cornwall Road the microbiological sciences. Professor Roizman is widely Ruislip Manor Tel. 01895 632390 recognized as a leading m Cinchona bark. TH Foto- Werbung / Science Photo Library HA4 6AW Email [email protected] authority in herpes simplex virus biology. b Photo Karen Rowlett
microbiology today aug 08 109 Project1:Layout 1 7/1/08 10:10 Page 1
Feedback Shipping news MRSA Tony M. Davis, author of Terrorism and the Imran Hayat, Charles River Laboratories, Maritime Transportation System, writes that writes that the February issue of he recently read with interest the article, Microbiology Today ‘was the best I have Ship ballast tanks: how microbes travel read so far’. In particular he liked the the world published in the May issue of article by Simon Foster on Staph. aureus Microbiology Today. The issue of ballast because it brought attention to community- water is one to which he has devoted acquired MRSA, which Imran feels has been an entire chapter in this new book. He overshadowed by media preoccupations considers numerous non-indigenous species with hospital-acquired infections. He that enter the ports through ballast water. believes that improved patient awareness Many folks disregard the problem and fail of the dangers of not completing a course to understand the economic damage and of antibiotics properly could do much to control costs. While the book covers a combat and prevent MRSA, however it is variety of issues generally not discussed by acquired. Televised health advertisements, the press, he hopes to educate those who similar to the ones on the dangers of may in some way be affected. smoking, could well have a big impact. b Photos.com / Jupiter Images (e [email protected]) Peter Wildy Prize for Microbiology Education Guy Newton Dr Chris Smith of the Naked Scientists will deliver his prize lecture entitled Stripping and antibiotic Down Science: The Naked Scientists, on Tuesday 9 September at the Society’s meeting at research Trinity College Dublin. The Peter Wildy Prize is awarded for an outstanding contribution to microbiology education. Guy Newton (1919–69) was an unsung hero in the Chris is a clinical lecturer in virology and fellow of Queens’ College at the University of history of antibiotics. He Cambridge. He’s also the founder of The Naked Scientists, a weekly science radio talk show, worked with Sir Edward podcast and website. Abraham at Oxford and in He joined the combined MB/PhD programme at Cambridge 1953 they co-discovered University in the mid-1990s working on the development of cephalosporin C, spawning viruses as gene therapy vectors. Mid-way through his PhD, an industry currently and during his time as a junior doctor, he found working estimated as having a global 100 hours a week was leaving him feeling under-employed, value of US$10 billion a so he set up The Naked Scientists radio show and website. year. Whilst Sir Edward achieved fame as a result, This was initially a hobby, but it has since taken over his Guy, who died at the age life, won several awards, and grown to become one of the of 50, has all but been world’s most downloaded science podcasts; since 2005 forgotten. Balliol College over 5 million copies of the show have been distributed archivist, John Jones, has internationally. Chris also appears live every week on sought to give proper national radio in Australia and South Africa to talk about recognition to Newton’s the latest scientific breakthroughs. achievements. The results When he’s not behind a microphone, Chris teaches and examines medical and science have been published in a undergraduates at Cambridge and works as a specialist registrar in a diagnostic laboratory at fascinating historical essay Addenbrooke’s Hospital, where he has a special interest in human and avian influenza and entitled The life and work emerging viral pathogens. of Guy Newton [J Pept Sci, Now busy completing his third and fourth popular science books, Chris also has a young 2008, 14, 545–555 (www. daughter who ensures that his immune system remains on high alert by infecting him with interscience.wiley.com everything circulating in Cambridge. – DOI:10.1002/psc.1014)].
microbiology today aug 08 111 KC_3717 AD:Layout 1 9/5/08 10:46 Page 1
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There’s a lot on it for you... Project1:Layout 1 9/1/08 11:11 Page 1 • Culture media database and Grants SGM has a wide range SGM journals podcast goes live product guide Upcoming deadlines of schemes to support Microbe talk: cutting-edge research • Articles and technical microbiology. See www. The deadline is sgm.ac.uk/grants for uncovered manual 26 September 2008 for details and closing dates. As part of an initiative to • Download quality receipt of applications to enhance SGM’s presence on certificates the following schemes: Enquiries should be made to the Grants Office, the HighWire site, an interview International • Request a quote SGM Marlborough House, with the author of a recent Development Fund • Place an order Basingstoke Road, paper from one of the journals will be broadcast monthly in the • Sign up for regular Watanabe Book Fund Spencers Wood, Reading form of a podcast. The first interview, Elective grants RG7 1AG (t 0118 988 Lab M online eNews 1821; f 0118 988 5656; which was launched on Friday 13 June, President’s Fund for e [email protected]). was with Professor Greg Challis of the University of THE GATEWAY TO MICROBIOLOGY TM Research Visits Warwick, a recipient of the prestigious SGM Fleming Postgraduate Student Meeting Grants Award. His paper, based on the prize lecture delivered last year at the Society meeting in Manchester, was Applications for a grant to attend the SGM’s Dublin meeting published in the June issue of Microbiology. To hear his (8–11 September) must be received by 5 September 2008. www.labm.com views on research into Mining microbial genomes for new Other schemes in brief natural products and biosynthetic pathways, download the podcast from www.sgm.ac.uk/news/podcast.cfm Scientific Meetings Travel Grants The scheme supports early career microbiologists wishing to present work at a scientific meeting, either in the UK or Microbes and Climate Change abroad. See rules on the website for eligibility criteria. This new and colourful 8-page leaflet Seminar Speakers Fund has been produced by the SGM External Relations Office, mainly for use in schools The Fund supports talks on microbiological topics in where climate change is a part of the departmental seminar programmes. Applications will be curriculum in the UK, but also for wider dealt with on a first come, first served basis during the distribution to educate the public. Most academic year. people are unaware of the fundamental Education Development Fund/PUS Awards importance of micro-organisms in climate Grants are available to members for projects intended to change and this publication seeks to lead to an improvement in the teaching of any aspect of redress the balance. It has been microbiology relevant to education in the UK. Funding researched and designed by Dariel is also available for small projects to promote the public Burdass and single copies are available understanding of microbiology, such as workshops, talks, free by emailing [email protected] demonstrations, leaflets, activities at science festivals. Applications will be considered on a first come, first served Careers Conferences 2008 basis during the calendar year. 19 November – Manchester Town Hall Retired Member Conference Grants 26 November – Royal Society, London Retired members may apply for a grant to attend one SGM Aimed at life science undergraduates, each conference meeting each year. The award contributes towards en-suite includes widely varying talks on career choices and further accommodation and the Society dinner, up to a maximum training, plus a small exhibition by a range of organizations. of £250. Applications for grants to attend the SGM meeting Under the banner, Building a career in research, these events at Trinity College Dublin are now invited. are a must for students wondering what to do on completion Technician Meeting Grants of their degree. A CV workshop will also be available. The These grants support attendance by eligible technicians conferences are being organized by several learned societies, at one SGM meeting each year. Applications for grants to including SGM, with sponsorship from the BioSciences attend the SGM meeting at Trinity College Dublin are now Federation. To register, go to www.physoc.org invited. Cost: £15, to include refreshments and lunch.
microbiology today aug 08 113 microshorts
Lucy Goodchild takes a look at some stories Probiotics that have hit the headlines recently. protect against pollen Algal Biofuel is just According to a pilot study carried out at the UK Institute bioreactors peachy of Food Research, a daily dose Scientists at the University of The extremophile Thermotoga of probiotic bacteria can modify Almeria, Spain, have embarked neapolitana flourishes in deep- Gas-reducing grass developed the immune system’s response on a research project called ocean vents in temperatures to grass pollen, reducing the The average dairy cow can produce up to 700 litres of methane a day; it is estimated that methane CENIT CO , in an attempt just below the boiling point symptoms of seasonal hay fever. 2 released by cattle in the UK could account for 3 % of the country’s total greenhouse gas emissions. In to reduce the country’s CO of water. In the laboratory, The immune system can mistake 2 a bid to curb climate change, researchers at Gramina, a joint biotech venture by Australia’s Molecular emissions. A water tank would it produces gas by-products fungal spores and pollen for Plant Breeding Cooperative Research Centre and New Zealand rural services group PGG Wrightson be placed next to gas emission that can contain up to 80 % pathogens and produce excessive Genomics is developing grass to cut the amount of methane produced by cows. According to an article points to retain pollutant hydrogen. Researchers at amounts of the antibody IgE to in Chemistry & Industry, the grass is able to grow in hotter climates, allowing farmers to maintain gases, including CO . The Clemson University, USA, have fight them. This stimulates the 2 the productivity of their herds in the face of climate change, whilst cutting methane emissions. By polluted water would then be been looking at its ability to release of histamine, resulting preventing the expression of the enzyme O-methyltransferase, the digestibility of the grass is increased passed through bioreactors use rotten peaches to produce in the swelling of airways and without compromising its structural properties, therefore ‘less burps and less methane’. However, some containing a ‘microalgae culture hydrogen, an important fuel typical hay fever symptoms. experts say overall methane production may actually increase. A diet containing more highly digestible system’. The algae would then source to combat climate The study revealed that IgE carbohydrates would lead to the microbial production of propionic acid, which in turn would create photosynthesize, using the CO , change. According to the South levels were significantly lower 2 more methane. But productivity gains would mean that less methane would be released per unit of producing organic matter and Carolina Peach Council, 20 in people who had taken a milk milk. Gramina has tested its grass in the laboratory and is now planning field trials. oxygen. The researchers say million pounds of peaches drink containing Lactobacillus the organic matter could even are discarded annually. Now, http://www.alphagalileo.org/index.cfm?fuseaction=readrelease&releaseid=529035 casei compared to those in a be used in biofuel production, scientists are hoping that who were given ordinary milk. Levels of IgG, which is thought either as a substrate or as peaches unsuitable for human m Cows (Photos.com / Jupiter) fertilizer. They hope that the consumption can be turned into Microbial partnership to be protective against allergies, system will be fully operational hydrogen biofuel. Peaches have b Biodiesel (Martin Bond / SPL); were higher in the probiotic in a year; tests can then be a high sugar content and are a peaches (Photos.com / Jupiter); becomes magnetic group. Further research is Crude oil (Paul Rapson / SPL) planned to explain these results. started on an industrial scale. good substrate for T. neapolitana. Researchers at the Helmholtz Centre for Environmental Oral delivery of Lactobacillus www.alphagalileo.org/index.cfm?fuse www.fuelcellsworks.com/ c Grass pollen grains (Photo Research (UFZ) in Leipzig and the California Institute of casei Shirota modifies allergen- action=readrelease&releaseid=529524 Supppage8307.html Insolite Realite / SPL) Technology (Caltech) in Pasadena, USA, have used a new induced immune responses technique to determine the genetic sequence of archaea in allergic rhinitis. responsible for preventing the loss of oceanic methane to the Biofuel fungus sequenced Feed microbes...... to release oil atmosphere. These archaea are syntrophic organisms, working Clinical and Experimental Allergy (2008). 1–8, doi:10.1111/ The genome of the fungus Trichoderma reesei has been sequenced Scientists at Newcastle the hydrogen with carbon in partnership with sulfur-reducing bacteria that provide j.1365-2222.2008. by researchers at the Architecture et Fonction des Macromolécules dioxide to produce methane. energy for the anaerobic oxidation of methane (AOM). Marine University and the University 03025.x Biologiques Laboratory (CNRS/Université de la Méditerranée and of Calgary, Canada, carried By providing the microbes with microbes can be difficult to isolate and culture in the laboratory, www.alphagalileo.org/ Université de Provence, France). Surprisingly, they have found that out a study showing how special nutrients, the geological so the researchers developed a new technique to study the index.cfm?fuse only a few genes are responsible for its ability to break down plants syntrophic micro-organisms. The scientists attached iron microbes use crude oil to make timescale of this process could action=read beads to the microbes and pulled them out of the sediment into simple sugars. T. reesei was discovered during World War II, methane, which was published be shortened to a few hundred release& when it destroyed American military equipment despite efforts to in Nature. Now, the researchers days in the laboratory. The on the ocean floor using a magnet. The ‘purified syntrophic releaseid= protect it using cotton cloth; thanks to its production of cellulases, have set up a company called researchers believe that similar consortia’ could then be sequenced. Genes for AOM were 529719 the fungus could break down cotton easily. Many industrial Profero Energy Inc. and have results could be obtained in an identified and, much to their surprise, the scientists found researchers are working to develop fungi capable of producing begun trials to recover oil oilfield in a timescale of a year that the archaea could fix nitrogen. There was also an different cellulases in order to manufacture second generation from an exhausted deposit in to tens of years. An estimated unexpected diversity in the microscopic partners of the biofuels. At first, the genetic sequence ofT. reesei was seen in a western Canada. According 6 trillion barrels of oil too archaea. The researchers suggest the potential for negative light because it limits the fungus to the production of to their research, microbes thick to be captured using metabolic diversity coupled with successful microbial hemicellulases and pectinases. However, researchers have realized convert oil into methane conventional methods partnerships could have led to their global that the sequence lends itself to genetic modification and are gas over tens of millions of could be unlocked as methane distribution. now investigating the addition of extra genes to make its enzymic years. Syntrophus bacteria using microbes. www.ufz.de/index.php?en=640 activity even more efficient. digest the oil and produce www.alphagalileo.org/index.cfm? http://mr.caltech.edu/media/Press_Releases/PR13141.html www.nature.com/nbt/journal/v26/n5/abs/nbt1403.html hydrogen gas and acetic acid, fuseaction=readrelease&releaseid= www.alphagalileo.org/index.cfm?fuseaction=readrelease www.alphagalileo.org/index.cfm?fuseaction=readrelease&releaseid=529445 then methanogens combine 528952 &releaseid=529276
114 microbiology today aug 08 microbiology today aug 08 115 Where does all the oxygen on Earth come from? Martha Clokie explores Microbes the roles of cyanobacteria and microalgae in oxygen production and and gives some surprising news about the input from viruses. oxygen
wo features that distinguish planet Earth from all passing it through a chain of proteins events eventually gave rise to a plethora other known planets are the presence of water on to reduce molecules such as sulfur. of lineages of primary producers that its surface and the oxygen in the atmosphere. The Cyanobacteria adapted the photosyn- constitute the higher plants and the oxygen is a waste product of photosynthesis and all thetic machinery in many ways, includ- far more diverse algae, of which the higher life on Earth is ultimately dependent on it. The ing using water as their electron source photosynthetic phytoplankton are a microbial contribution to oxygen in our biosphere and oxygen as their terminal electron subset. Tis often under-appreciated, but in this article I will discuss acceptor. After their appearance, the how microbes oxygenated and continue to oxygenate our atmosphere was gradually oxygenated The key players in oxygen planet. The microbes concerned are cyanobacteria and to the current levels of around 21 % production eukaryotic microalgae. The oceans, where oxygen-producing oxygen. Despite all the acquisition and evolu- microbes predominate, can be thought of as forgotten tion of cyanobacterial genomes, cyano- tropical rain forests where at least 50 % of carbon fixation From cyanobacteria bacteria themselves remain important and consequent oxygen production is thought to occur. This to photosynthetic oxygen producers. Indeed marine article summarizes the evolutionary and natural history of phytoplankton cyanobacteria together with photosyn- these microbes and focuses on the surprising role of viruses This oxygen-producing apparatus was thetic phytoplankton are thought in oxygen production. only invented once, but it was then to contribute equally to the global acquired by many lineages. The cyano- carbon fixation which amounts to half Cyanobacteria oxygenated Earth’s atmosphere bacteria were consumed by hetero- the total annual amount fixed, and Cyanobacteria can be considered the largest wreakers trophic eukaryotes which retained their therefore half the amount of oxygen of environmental havoc the Earth has ever experienced, genome as a plastid. Further endo- produced. However, the identity and probably causing in the past the demise of a large proportion symbiotic and horizontal gene transfer composition of the key players, parti- of the bacteria and archaea that predominated before they cularly of the photosynthetic phyto- m Composite satellite image of Earth’s came on the scene. Until around 2.6 billion years ago the western hemisphere, centred on the plankton components, are poorly under- Earth’s atmosphere was largely composed of carbon dioxide, Atlantic Ocean. NASA Earth Observatory / stood. These microbes are referred carbon monoxide, nitrogen and water. Plenty of non-oxygen- Science Photo Library to as nanoplankton or picoplankton, producing photosynthetic bacteria existed before cyano- depending on their size, and new classes b Coloured scanning electron micrograph bacteria, generating chemical energy by using energy from of the haptophyte Emiliana huxleyi. Steve are still frequently being discovered. light to remove an electron from available molecules and Gschmeissner / Science Photo Library Often this is based on molecular data
116 microbiology today aug 08 microbiology today aug 08 117 b Bacteriophage S-PM2 infecting a Synechococcus cell. Stefan Hyman & called D1 and D2. They are encoded by to be something that viruses could microalgal groups, let alone the com- Natalie Allcock, School of Biological Sciences, University of Leicester the genes psbA and psbD. In a normally do. The viral versions of the gene are position and importance of their viral . Coloured transmission electron micrograph of a section through functioning cyanobacterium or plant highly conserved at the amino acid community. Viruses that have been Prochlorococcus cells. Claire Ting / Science Photo Library there is a high turnover of these level, but vary considerably at the studied have large complex genomes and they are difficult to isolate from the oceans and to proteins, in particular D1. They are nucleotide level. Phylogenetic analyses which suggests that they play multiple culture. Important algal contributors to open ocean carbon damaged by light, so new copies are indicated that these genes originated in roles in host physiology. fixation are the green algal flagellates, the heterokonts (a constantly being generated and inserted cyanobacteria and were subsequently diverse group including the diatoms) and the haptophytes into the photosystem to maintain acquired by viruses. Final thoughts (including the calcite-precipitating Emiliana huxleyi); both active photosynthesis. Unlike higher It appears that after the viruses infect I have briefly described the who, when, these groups have red algal plastids. plants, some cyanobacteria have multi- the cyanobacteria, they shut down where and the how when it comes ple copies of the psbA gene. Different host photosynthesis machinery and to microbial oxygen production. I Cyanobacterial distribution versions are used under specific en- provide their own alternative versions will leave you with the back of the As less is known about the distribution of photosynthetic vironmental conditions with some of the proteins necessary to main- envelope calculation that leads us to phytoplankton, I will focus on the cyanobacteria which are versions being more efficient when the tain photosynthesis. This provides tentatively speculate that if half of the found in most places where water exists, playing important cyanobacteria are light-, temperature- the viruses with enough energy to oxygen produced per year occurs in environmental roles such as stabilizing desert sand for the or nutrient-stressed, and this allows replicate. the oceans, and half of this is derived colonization of other plants. They thrive in fresh water, salt them to survive where photosynthetic from cyanobacteria of whom half are lakes and hot springs, but are most numerous in the oceans phytoplankton cannot. Viruses: friends or foe? infected by viruses at any one time, where up to a million cells may be present per millilitre of It is not known how efficient the virus- then up to one-eighth of the total sea water. By virtue of extremely efficient light-harvesting Viruses and oxygen encoded photosystem is compared to oxygen we breath may have passed and nutrient-assembling machineries, surprisingly just two production that encoded by the cyanobacteria. through the photosystem encoded by genera, Synechococcus and Prochlorococcus dominate the A twist on microbial oxygen production Modes of cyanobacterial viral infec- a virus. nutrient-poor oligotrophic areas of the open ocean where comes from our recent appreciation of tion are complex and they may infect higher plants and even microalgae cannot survive. Their the role of viruses in cyanobacterial and express their genes but not Martha Clokie distribution changes according to ocean temperature, light ecology. Marine cyanobacteria are con- cause cell death in a process known Department of Infection, Immunity availability and nutrient status. Synechococcus is the hardier stantly under attack by viruses, and as pseudolysogeny. During pseudo- and Inflammation, Medical Sciences of the two and it dominates in water with a latitude of the turnover rates are thought to be lysogenic infection, cells expressing Building, University of Leicester, as high as 50 % of all cyanobacteria the viral version of psbA may be more more than 40°; Prochlorococcus is the softer cousin and is PO Box 138, Leicester LE1 9HN, numerically superior in warmer waters. lysed each day. The dynamics of efficient photosynthesizers than those UK (t 0116 2522959; e mrjc1@ Molecular studies based initially on ribosomal DNA and viral infection are not uniform; many with the cyanobacterial versions. Thus leicester.ac.uk) subsequently on whole-genome analysis have allowed us cyanobacterial viruses appear to be the viruses are acting as pseudo- to further understand the relationships, distribution and dependent on light to absorb to their symbionts. Infected cyanobacteria will physiology within Synechococcus and Prochlorococcus. Both hosts. Both cyanobacterial and algal then reproduce more efficiently than Further reading genera can be divided into multiple clades or lineages. viral infection are dependent on effi- uninfected cells, thus producing Clokie, M.R.J. & Mann, N.H. (2006). Prochlorococcus lineages are primarily correlated with light cient photosynthesis for viral replica- both more cyanobacteria and more Marine cyanophages and light. Environ availability; the distribution of Synechococcus clades is less tion to occur. viruses. A further unresolved question Microbiol 8, 2074–2082. clear, but they are correlated to some extent with nutrient Information from virus genome is. are viruses capable of ‘donating’ Falkowski, P.G. & Knoll, A.H. (2007). status and the temperature of the water column. sequencing has revealed the presence of their versions of psbA back into the Evolution of Primary Producers in the Sea. key genes involved in photosynthesis, cyanobacterial community? Finally, are Academic Press. Oxygen-producing physiology including those which encode D1 there parallels in the algal world? As I Lane, N. (2002). Oxygen: The The proteins at the heart of the photosynthetic machinery and D2. This was a huge surprise as pointed out above, we are still unclear Molecule that Changed the World. Oxford where light energy is converted into chemical energy are photosynthesis was not considered about many of the most important University Press.
118 microbiology today aug 08 microbiology today aug 08 119 ydrogen (H ) contains around three times more 2 The ability of certain potential energy by weight than petrol, making it the highest energy-content fuel available, a property exploited in space exploration. microbes to generate Life’s Perhaps unsurprisingly, a multitude of micro- organisms have developed the ability to derive hydrogen gas has many energy from H , but this is not the focus of this short H 2 article. Paradoxically, there are special and yet prevalent exciting potential applications circumstances under which micro-organisms have no better way of gaining energy than to release H into their according to Mark Redwood a gas 2 environment. The study of these phenomena began early in the last century, but biohydrogen (biologically produced and Lynne Macaskie. One H2) remained merely an academic curiosity before the fuel crises of the 1980s. The rising profile of energy issues in the new development uses public consciousness and in political agendas, combined with … and it’s scientific advances and the expansion of interdisciplinary biodegradable wastes that research, have contributed to a fresh revival and new developments in biohydrogen technologies. would normally go into Biohydrogen production by microbes The capacity for biohydrogen (bio-H ) production is 2 landfill to make biofuel. hydrogen associated with the activity of either of two very common enzymes (hydrogenase and nitrogenase), but the shortlist of candidates targeted for focused study represents relatively few classes, including the fermentative bacteria and photo- Bio-H producers synthetic micro-organisms such as cyanobacteria, micro- 2 algae and purple bacteria. The ways by which these
produce H2 are summarized in the diagram on the left.
The mechanisms of bio-H2 production within these groups are diverse, but some generalizations can be made. First, bio-
Fermentation Photosynthesis H2 production is strictly an anaerobic phenomenon because both hydrogenase and nitrogenase enzymes are destroyed by oxygen. Second, the circumstances under which it occurs always challenge the cell in some way, be it to dispose of excess reducing power, to dispatch a toxic substance or to Strictly Facultatively Oxygenic Anoxygenic cope with the absence of an important nutrient. anaerobic anaerobic For example, in anaerobic fermentation H2 is produced from oxidizable carbohydrates like sugars, and the generation of ATP is inextricably linked to the release of reducing power, which must be deposited onto a suitable acceptor for the Growth Growth Purple Heterocystous fermentation to proceed. In the cases of strictly anaerobic linked to linked to Microalgae non-sulfur cyanobacteria bacteria, hydrogenase enzymes can function to ‘dump’ the H2 formate bacteria + excess reducing power onto H , forming H2. Therefore the
fermentation is so dependent upon H2 production that feed- Clostridium Enterobacter Rhodobacter back inhibition caused by the produced H stalls growth if butyricum Anabaena 2 aerogenes sphaeroides variabilis Chlamydomonas H is not allowed to escape. Facultative bacteria carry out a Caldicellulosiruptor 2 reinhardtii saccharolyticus Escherichia Rhodospirillum similar reaction, but in this case H is produced primarily via Nostoc 2 Thermotoga elfii coli rubrum the decomposition of formic acid, a mildly toxic fermentation
product, hence the connection between growth and H2 production is indirect. m Biohydrogenic micro-organisms. Seeing the light c H2 is the only fuel with sufficiently high energy content for space exploration and its single combustion product is water, hence it is environmentally ‘clean’. In contrast to the dark world of fermentation, photosynthetic Comstock Images / Jupiter Images micro-organisms have tapped into the Earth’s most abundant
120 microbiology today aug 08 microbiology today aug 08 121 Carbon storage inclusion Heterocyst fixes nitrogen Vegetative cells (N) and produces H2 produce O2 and carbohydrate (C)
N
Photosynthetic C membrance vesicles O2
H2
m H production by heterocystous cyanobacteria occurs due to the m m 2 Purple bacteria. Sections of Rhodobacter sphaeroides cells showing Made for each other? Dark (left) and light (right) bio-H2 reactors co-operate to make bio- exchange of nutrients between specialized cell-types; heterocysts inclusions of carbon-storage polymer (poly-b-hydroxybutyrate: the H2 with high efficiency. The fan (arrowed) is powered by a fuel cell which generates electric and vegetative cells. John Walsh / Science Photo Library clear bodies) and photosynthetic membrane vesicles. Mark Redwood power from bio-H2. See movie at http://bst.portlandpress.com/bst/033/bst0330076add.htm
energy source: sunlight. When photosynthesis is in full functions to split the N2 molecule to form ‘ready nitrogen’ Light and dark: light from a large area and transmit- Mark D. Redwood
swing energy is plentiful and H2 production results from (NH3), a reaction requiring an enormous activation energy to a new way to help save ting it into the photosynthetic culture. Research Fellow the need to overcome different barriers. Access to light break the N≡N triple bond, one of the strongest bonds found the planet A second issue is connecting the energy enables photosynthetic micro-organisms to live in nature. Power comes at the expense of selectivity and here Such biochemical phenomena provide process with a reliable supply of sugary Lynne E. Macaskie Professor of Applied Microbiology by endothermic chemical reactions, which could not support H2 is formed as a wasteful byproduct. However, the purple endless fascination for scientists, but feedstock. life in darkness. For example, anoxygenic photosynthetic bacteria can be fooled into running nitrogenase even though increasing attention is becoming focus- Immense quantities of suitable sub- Unit of Functional Bionanomaterials, bacteria (APB) are able to derive carbon for growth from N2 is absent, so that only H2 and not NH3 is produced. ed on applying this knowledge to strates can be found in biodegradable relatively inaccessible substrates, including organic acids, Different branches of photosynthetic micro-organisms address some of mankind’s worsening wastes, which if dumped into landfill School of Biosciences, University such as those formed in the process of dark fermentation. (including cyanobacteria and microalgae) carry out oxygenic problems. Recent work at the University would generate landfill gases, including of Birmingham, Edgbaston, This metabolism releases reducing power from the substrates, photosynthesis, so-named because it generates oxygen. of Birmingham focuses on combining methane, a greenhouse gas 25 times Birmingham B15 2TT, UK (t 0121 414 5434; f 0121 414 which must be disposed of so that more substrate can be Since hydrogenase and nitrogenase are destroyed by oxygen, dark fermentation and photoferment- more potent than CO2. For example, a 5925; e m.d.redwood@bham. processed (hence the term photofermentation). APB solve H2 production by oxygenic micro-organisms relies on ation to generate H2 from sugary third of all household food is wasted ac.uk; [email protected]) this problem by producing highly reduced storage material separating the production of H2 and O2 either in space or feedstocks. These two bioreactions fit in the UK, totalling 7 million tonnes a (e.g. poly-β-hydroxybutyrate) and, when they are limited for in time. The simplest way of doing this is termed ‘indirect together as the organic acid products year. However, this represents only a their nitrogen supply, by fixing atmospheric nitrogen. This is photolysis’ as it involves the photosynthetic generation of of dark fermentation represent the fraction of the actual food-linked waste Further reading where nitrogenase makes a dramatic entrance. This enzyme carbohydrate by day, followed by its decomposition by night ideal substrates for purple bacteria. as the UK food industry generates at Baxter-Plant, V.S., Mabbett, A.N. & when the photosynthetic supply of oxygen ceases, allowing When assembled in the laboratory, least a further 6 million tonnes of bio- Macaskie, L.E. (2002). Bacteria, their precious metal armour and a new weapon H2 to be generated by anaerobic fermentation. Conversely, the bioprocess represents an everyday degradable waste annually. With a against waste. Microbiol Today 29, 80–81. according to ‘direct photolysis’, the reducing power generated process occurring in nature where more advanced pre-treatment, bio-H2 by photosynthesis is dissipated by hydrogenase enzymes, the two types of bacteria co-exist, but can even be produced from the cellulo- Kapdan, I.K. & Kargi, F. (2006). such that the complex pathway can be approximated to in the bioprocess the two bioreactors sic residues from food-crop cultivation Bio-hydrogen production from waste 1 materials. Enzyme Microb Technol 38, water-splitting: H2O → H2 + /2O2. Nitrogen-fixing cyano- are optimized to provide the ideal (e.g. corn stalks and husks), which 569–582. bacteria form chains of connected cells (filaments). Like the conditions for H2 production by the two represent tens of millions of tonnes purple bacteria, the cyanobacteria use nitrogenase to access different mechanisms. The maximum annually in the UK. Diverting these Macaskie, L.E. & others (2005). Applications of bacterial hydrogenases in ‘ready nitrogen’, but due to the abundance of damaging quantity of H2 that could be potentially wastes from landfill into bio-H2 pro- oxygen, it is necessary to protect nitrogenase in a specialized recovered from sugary feedstocks is duction addresses both climate change waste decontamination, manufacture of novel bionanocatalysts and in sustainable anaerobic cell called a heterocyst. Nitrogenase can function 12 mol H2 per mol hexose unit, but this and energy security. only in the heterocyst because the oxygen-producing kind of efficiency cannot be approached In a final twist, the hydrogenase in energy. Biochem Soc Trans 33, 76–79. part of the photosynthetic machinery is absent, but the by a single organism. The dual bio- the leftover bacterial cells can be used Redwood, M.D., Paterson-Beedle, M. crippled photosystem is unable to produce enough energy reactor process can approach this maxi- to scavenge precious metals from spent & Macaskie, L.E. (2008). Integrating
for carbohydrate production, so it is dependent upon its mum by producing up to 4 mol H2 in automotive catalysts to make the cata- dark and light biohydrogen production strategies: towards the hydrogen economy. vegetative neighbours to provide carbohydrate in exchange the dark reactor and up to 8 mol H2 in lytic ingredients of the fuel cell that Rev Environ Sci Technol (submitted). for ‘ready nitrogen’. the photobioreactor. A significant chal- converts H2 into electricity. Hence This situation has been recreated artificially using lenge for the development of this pro- nothing is wasted and an important Waste and Resources Action sulfur-deprived microalgae, which cannot maintain the cess to a productive scale is to design a new application can be found for Programme (April 2008). The Food We m Fermentative bacteria consume sugary substrates to produce hydrogen and smelly organic acids requiring disposal. Courtesy Geoff oxygenic part of the photosynthetic apparatus during a kind of photobioreactor that is cheap today’s waste mountain in tomorrow’s Waste. http://wrap.s3.amazonaws.com/ Gadd shortage of sulfur. to construct and capable of capturing non-fossil fuel transport and energy. the-food-we-waste.pdf
122 microbiology today aug 08 microbiology today aug 08 123 Methane: a natural gas
The methane produced by microbes is a big contributor to global warming, but as Setareh and James Chong describe, it also has great potential as a source of green energy.
ome believe that methanogens may be among years ago, before the ‘great oxygenation event’ that was of methane is even worse over a short- b Computer models of methane molecules. Prof. K. Seddon & J. Van Den Berg / Queen’s the most ancient forms of life. What is the triggered by the evolution of microbial photosynthesis. er time scale – it has a GWP of 68 University, Belfast / Science Photo Library evidence for this? These single-celled prokaryotic Methanogens have evolved a unique metabolism that allows over 20 years – but it is a relatively m Natural gas burning. Photos.com / Jupiter Images organisms belong to the domain Archaea, itself a them to survive on the energy generated by the reduction of unstable molecule once in the upper
lineage of cells that appear to be deeply rooted CO2 and other small carbon compounds by hydrogen. This is atmosphere. Contemplating the num- Biofuel potential natural gas/methane as a fuel source
between the eubacteria (‘true’ bacteria) and the not a particularly energetically favourable process and results bers is a rather frightening prospect: if Of course, not only methanotrophs are the production of CO2 and the fact Seukaryotes. Archaea were originally called archaebacteria in the biological generation of methane as a waste product all the methane produced by methano- can use methane for energy. The major that as a fossil fuel, natural gas is a until the ‘Archaea-ologists’ felt a name that more obviously (hence the name). The ‘methanogens-as-one-of-the-earliest- gens each year reached the atmosphere, flammable component of natural gas finite source of energy. Methane from demonstrated the differences between these organisms and forms-of-life’ theory suggests that methane excreted by it would be the equivalent of releasing is methane. Natural gas is currently methanogens does not have the same
eubacteria was required. While the archaea are best known for methanogens could have helped to warm primordial Earth. 23 billion tonnes of CO2. Current glo- the fossil fuel of choice due to its problems. Methanogenic methane is re-
their love of extremes – the most thermophilic, acidophilic, bal CO2 emissions are about 8 billion relatively clean burning properties and newable, and formed from recently fixed
halophilic (salt-loving) and barophilic (pressure-loving) Biological methane tonnes per year; thus, methanogens it provides more than 40 % of current atmospheric CO2, so burning methane organisms all belong to this domain – most methanogens Methanogens are the main source of biological methane on have the potential to provide three times energy needs in the UK. Methane is from a methanogenic source is effect- show distinctly mesophilic tendencies. However, methano- the planet, producing in the order of a billion tonnes per the heating effect of anthropogenic an odourless gas (if you work with ively carbon neutral. gens require an environment containing less than 10 p.p.m. annum globally. Methane is a serious greenhouse gas with carbon emissions! Fortunately, a large methanogens you always need to get
O2 (i.e. <0.001 %) to grow! For most oxygen-requiring life, 23 times the global warming potential (GWP) of CO2 over proportion of methanogen-produced this into the conversation early!) that Anaerobic digestion this could be considered to be rather extreme. This very 100 years. That is, a single molecule of methane released methane is captured by other, methano- is relatively easy to handle, and burns In the microbial world, methanogens low oxygen concentration coincides with the probable com- into the atmosphere has the same thermal retention capacity trophic, bacteria that can in turn use with oxygen to produce only water and are terminal electron acceptors, tak-
position of the atmosphere of anoxic Earth some 2.5 billion as 23 molecules of CO2 over 100 years. The warming effect methane as an energy source. CO2. Two of the main problems with ing the breakdown products from
124 microbiology today aug 08 microbiology today aug 08 125 consortia of (mainly) constitutively insignificantly low. However, by 2007 anaerobic bacteria at the end of the agricultural AD from a relatively organic degradation process. Anaerobic small number of facilities in the USA digestion (AD) has long been used as was responsible for the production a low-tech, environmentally friendly, of more than 215,000,000 kWh of way to process organic waste into electricity, emphasizing how rapidly
‘biogas’. Biogas is a mixture of CO2 and and effectively this technology can be methane that can be burned in much deployed. the same way as natural gas to provide In the UK, AD is still a very under- both heat and power. Anaerobic used technology despite Defra recently digesters tend to be more popular in making it the preferred method for great ancientness, or perhaps due to the microbes, which he observed by that their presence is good for your gut of microbiology can be smelly! However, countries with warmer environments disposing of food waste. AD is per- pervasiveness of oxygen forcing them igniting ‘combustible air’ collected flora. growing methanogens alone is nothing where the natural processes involved ceived as an unreliable and difficult tech- to hide, have been found in all of the from marshes in northern Italy in 1776. compared with trying to grow a stably- in organic matter breakdown are per- nology to use in the UK – something anaerobic ecological niches explored to As well as being hugely abundant in Growing pains interacting mixed population of an- ceived as faster. However, a number that works better at higher ambient date. There are thermophilic methano- rice paddies, swamps and landfill Despite their abundance, growing aerobes. But in order to understand the of facilities exist in the UK (mainly for temperatures. There is no scientific gens (the first archaeal genome to be sites, methanogens are endemic in methanogens in the laboratory poses a dynamics that occur in these consortia, processing wastewater) that also make basis for these notions. The Arctic sequenced was of the hyperthermo- ruminants (responsible for as much significant challenge; gases need to be these issues must be resolved. Con- use of methanogens. AD has also seen a tundra has been estimated to con- philic Methanocaldococcus jannaschii, as 15 % of global methane emissions), scrubbed of all traces of oxygen, and sortial dynamics need to be measured, recent rise in popularity in continental tain as much as 32,000 Gt (1 Gt = 109 which grows at 85 °C), halophilic termites and other insects (5 % of hydrogen must be handled in a non- understood and modelled so that the Europe, where incentives for green tonnes) of methane generated by the methanogens and psychrophilic meth- global methane emissions are due to explosive manner. Large quantities of robust but rather inefficient process of energy production have made electricity slow action of methanogenic degra- anogens (isolated from Antarctica). methanogens in termite guts). The strong reducing agents (mainly sulfur- anaerobic digestion can be improved generated from biogas a cost-effective dation of organic matter trapped under limited studies that exist concerning containing compounds) do lend a and added to the range of green energy/ method of disposing of plant and other the permafrost. So methanogens and Methanogen habitats the presence of methanogens in human certain pall to the atmosphere that biofuel options currently being exam- agricultural waste. In the USA in 2000, their associated consortia of anaerobes Alessandro Volta (the scientist who guts vary wildly, but it seems likely perhaps justifies the initial reaction ined as alternatives to mankind’s de- the amount of electricity produced can certainly tolerate the British climate. first described the Volt) was the first that more than 30% of the population many people have to the thought of pendence on fossil fuels. This is a by AD from agricultural sources was Methanogens, perhaps due to their person to describe methane from contain methanogens in their guts, and working with methanogens – this kind microbiological challenge that should no longer be neglected. m Top left. Microscale methane generation. Termites are equipped with portable anaerobic digesters that contain a huge Setareh Chong & James Chong diversity of specialized microbes for the Department of Biology (Area 5), breakdown of lignocellulose. Photos.com / Jupiter Images PO Box 373, University of York, York YO10 5YW, UK (t 01904 m Top right. A scanning electron 328628; e [email protected]) micrograph of Methanothermobacter thermautotrophicus. This organism was originally isolated from sewage sludge Further reading and grows optimally at 60 °C. Bar, 5 µm. United States Environmental Protection Meg Stark & Paul McDermott Agency (2006). Global anthropogenic
b Far left. Methanogens growing in non-CO2 greenhouse gas emissions: captivity. A 2 litre culture of Methanococcus 1990–2020. www.epa.gov/nonco2/ maripaludis growing on an 80:20 mix of H 2 econ-inv/international.html and CO2. Methane is produced as a waste product by all methanogens. James Chong Defra (2008). UK Greenhouse Gas Inventory, 1990 to 2006. ISBN b Sushi and burgers make methane. Paddy 0-95548-234-2. fields are one of the major anthropogenic methanogen niches that are expanding. www.defra.gov.uk/corporate/ministers/ In 2005, global rice cultivation was speeches/joan-ruddock/jr071016.htm responsible for the emission of ~32 million tonnes of methane (the equivalent of 672 Semiletov, I., Shakhova, N.,
million tonnes of CO2) – more than the Romanovsky, V. & Pipko, I. (2004). UK’s total greenhouse gas emissions for Methane climate forcing and methane the same year. Global enteric fermentation observations in the Siberian Arctic produced nearly three times this amount of methane (92 million tonnes) in 2005. land-shelf system. World Resour Rev 16, James Chong 503–542.
126 126 microbiology today aug 08 microbiology today aug 08 127 On the microbial That familiar pong on the beach is down genetics to dimethylsulfide (DMS) produced by microbes. Andy Johnston shows that the of seaside molecular biology behind its formation is amazingly complex and diverse. smells m Kynance Cove, Cornwall. Ian Atherton, SGM ver walk along the shore, the global sulfur cycle. (Bizarrely, the The source material, dimethylsulfoniopropionate it when stressed, perhaps liberating the resultant DMS and taking in that tangy aroma? received wisdom of that time was that The substrate for DMS production is dimethylsulfonio- acrylate as defence or signalling molecules. However, the Ever wonder how ocean the culprit was hydrogen sulfide, a gas propionate (DMSP), with around one billion tonnes of this majority of DMSP catabolism is mediated by marine bacteria, birds, such as Shearwaters with a very different aroma!) metabolite being cycled each year. As if this were not enough, some of which can grow on it as their sole carbon source. find their lunch and din- We now know that around 50 its catabolic legacy, as DMS, further adds to its importance – These include strains of the Alpha- (various Roseobacter spp.), ner over the featureless million tonnes of DMS emerge from yet how many of us are familiar with this compound? DMSP Beta- (Alcaligenes) and Gammaproteobacteria (e.g. Vibrio). Ewastes of the Atlantic? Or why seals the oceans and their margins, but this is among the most abundant intracellular molecules in the Bacteria degrade DMSP in at least two very different ways. poke their noses above water, taking in is just a ‘drop in the ocean’ (around myriads of single-celled phytoplankton, including many hap- In one, it is demethylated, the thiol products being used the air? Ever ask how clouds form over 10 %) of the total annual production. tophytes, whose forebears formed, among other places, the as sources of both carbon and sulfur. The other general the oceans? Many questions, but just The most important effect of DMS is White Cliffs of Dover. It also occurs in macroalgal seaweeds mechanism releases DMS, which acts as a chemoattractant one answer – dimethylsulfide (DMS), a that it is oxidized in the air to form and in a few known land plants. DMSP is a compatible solute, beacon for those seabirds, seals and other animals that eat gas with many influences and one, like sulfates, which in turn form cloud protecting cells against UV, oxidative and osmotic challenges, plankton, or their cohabiting fish and crustaceans – and, for the others in this issue, which is made condensation nuclei which affect local but there is still some debate about its precise role(s). What us, it contributes to that sentient seaside smell. by microbial action. weather and, perhaps, world climate. is clear, though, is that microbes catabolize DMSP in various Despite its importance, and the ease of cultivating many The great savant, James Lovelock, Thus, one of those earlier questions ways – on a massive scale, and with global consequences. bacteria that degrade DMSP, not one gene involved in the pro- realised 40 years ago that DMS is is answered, but to address the As far back as 1956, a red algal seaweed, Polysiphonia, that cess had been identified until 2006. However, recent studies the pre-dominant form of sulfur that others, we must know the provenance makes DMSP, was shown to catabolize it, via an enzyme called have begun to provide some genetic insights, although, in escapes from the seas to the air and of the starting material for DMS DMSP lyase that would also generate acrylate plus a proton. reality they set more questions on topics that range from thence back to land, thus completing production. Indeed, many plankton that make DMSP can also degrade enzymology to evolution.
128 microbiology today aug 08 microbiology today aug 08 129 The dmd and ddd genes for Gene sampling of the oceans from the of the various DMSP catabolic pathways. However, this article bacterial catabolism of DMSP comfort of one’s laptop started with rhetorical questions, and ends with real ones, The first reported gene for DMSP Thanks to the industrial-scale sequencing of the partial prompted by these tantalizing glimpses into the genetics of catabolism was dmdA, which encodes genomes of uncultured marine bacteria, done largely by DMS production. Why do bacteria use the DMS-producing DMSP demethylase, the initial step in Craig Venter’s Global Ocean Survey and other projects pathway in the first place, when demethylation would allow the demethylation pathway. Found supported by the Moore Foundation, one can survey any them to recoup all the C and S, and not see much of it drift by Mary Ann Moran’s lab in a strain given gene in the seemingly astronomical list of genes in off into the seas and the skies as DMS? This is particularly of the abundant Roseobacter clade of these metagenomes. Of the genes mentioned above, dmdA is pertinent to strains that contain both demethylation and the marine Alphaproteobacteria, close the clear ‘winner’ with hundreds of hits in these marine gene DMS-emitting pathways. How and why do they ‘choose’ homologues of DmdA occur in other databases, in keeping with the importance of demethylation which system to use under any given set of environmental marine alphaproteobacteria, including at a global level and the finding ofdmdA in P. ubique. The dddL circumstances? What are the constraints (if any) to HGT of the SAR11 bacterium Pelagibacter and dddD genes rather trail behind, with nine and six apiece, the ddd genes. And finally, there are still many environments ubique, the most populous organism but even these relatively low numbers represent trillions of such as corals and the tissues of some invertebrate animals, on the planet. total dddD and dddL genes, in bacteria strewn around the like clams, that are awash with DMSP but whose microbiology Then, the first of the ddd (DMSP- planet’s oceans. Of course, numbers are not everything, and has not been examined, certainly not at a molecular genetic dependent DMS) genes was found the levels of expression and activities of the enzymes will also level. What other surprises lie in wait in the deeps? in the gammaproteobacterium Marino- contribute to the fluxes through the different pathways. Andrew W. B. Johnston monas, isolated from roots of the grass School of Biological Sciences, University of East Anglia, Spartina, one of the few angiosperms Rampant gene transfer – Norwich NR2 7TJ, UK (t 01603 592264; e a.johnston@ known to make DMSP. A single cloned among unexpected bedfellows gene, called dddD, was enough to The ddd genes are prone to widespread horizontal gene trans- uea.ac.uk) confer to Escherichia coli the ability fer (HGT), in some cases to totally unexpected organisms. dddL Further reading to make DMS when grown on DMSP – is the least promiscuous, being found only among occasional Charlson, R., Lovelock, J., Andreae, M. & Warren, S. (1987). as detected by the evocative aroma strains of the Order Rhodobacterales, though even here, there Oceanic phytoplankton, atmospheric sulphur, cloud albedo and from the Petri dishes. However, the was one nice surprise. Going back to Cornelius van Neil’s climate. Nature 326, 655–661. m Close-up of tetraspores of the red alga seaweed Polysiphonia nigrescens from Devon. studies in the 1930s, Rhodobacter sphaeroides is something DddD polypeptide was not the expected Curson, A.R.J., Rogers, R., Todd, J.D., Brearley, C.A. & D.P. Wilson / FLPA-images.co.uk DMSP lyase, but was an acyl-CoA of a lab rat for studies on bacterial photosynthesis, motility Johnston, A.W.B. (2008). Molecular genetic analysis of a transferase that could add CoA to DMSP. . Salt grass (Spartina alterniflora), one of the few angiosperms known to make DMSP. and bioenergetics, but it had never been suspected of making John Bova / Science Photo Library dimethylsulfoniopropionate lyase that liberates the climate- The predicted DMSP-CoA product is DMS. However, of three strains of R. sphaeroides sequenced changing gas dimethylsulfide in several marinea -proteobacteria unstable, and could spontaneously in Sam Kaplan’s lab, two had a close DddL homologue and and Rhodobacter sphaeroides. Environ Microbiol 10, 757–767. release DMS, plus acryloyl CoA, with one did not. Gratifyingly, their DMS-producing phenotypes Howard, E.C., Henriksen, J.R., Buchan, A. & others (2006). the latter being further catabolized for were entirely as predicted from their genomes. Bacterial taxa that limit sulfur flux from the ocean.Science 314, growth on DMSP as carbon source. The other gene, dddD is much more adventurous. It was not 649–665. Strikingly, DddD was lacking from the totally surprising that DddD also occurs in other, known DMS- Lovelock, J.E., Maggs, R.J. & Rasmussen, R.A. (1972). deduced proteomes of several bacteria emitting marine bacteria such as Sagittula. Even here though, Atmospheric dimethyl sulphide and the natural sulphur cycle. that are known to make DMS from Sagittula is an alphaproteobacterium, so presumably it acquir- Nature 237, 452–453 DMSP and whose genomes had been ed (or donated) dddD by HGT from/to the rather distantly Simó, R. (2001). Production of atmospheric sulfur by oceanic sequenced. So, there must be different related gammaproteobacterium Marinomonas. But, wholly un- plankton: biogeochemical, ecological and evolutionary links. ways to make DMS, something that expected was the presence of DddD in some terrestrial bacteria, Trends Ecol Evol 16, 287–294. had been implied by work by Duane which interact with angiosperm roots. These included some Stefels, J., Steinke, M., Turner, S., Malin, G. & Belviso, S. Yoch some time ago. strains of root-colonizing Burkholderia (Betaproteobacteria) (2007). Environmental constraints on the production and One such ‘alternative’ system is and a highly unusual strain (NGR234) of Rhizobium, which removal of the climatically active gas dimethylsulphide (DMS) specified by thedddL gene, which was forms nitrogen-fixing root nodules on many different and implications for ecosystem modelling. Biogeochemistry 83, identified inSulfitobacter , a Roseobacter- legumes and even (uniquely) on some non-legumes. Perhaps 245–275. type marine bacterium. The DddL these root-dwelling bacteria associate with some, unknown, Todd, J.D., Rogers, R., Li, Y.G. & others (2007). Structural and polypeptide, which had no homologues angiosperms that, like Spartina, make DMSP. regulatory genes required to make the gas dimethyl sulfide in with known function, may be the long- bacteria. Science 315, 666–669. predicted DMSP-lyase, since E. coli that What next? Vallina, S.M. & Simó, R. (2007). Strong relationship between expresses dddL makes acrylate plus These are early days, but it seems likely that there will be DMS and the solar radiation dose over the global surface ocean. DMS. good progress in elucidating the biochemistry of the entirety Science 315, 506–508.
130 microbiology today aug 08 microbiology today aug 08 131 Destroying a cytotoxin, producing an Nitric oxide (NO) is one environmental toxin NO is one of the most versatile and important molecules of the most versatile and in living organisms. In higher animals and plants it is an important signalling molecule, for example it is the effector important molecules in responsible for stimulating the dilation of blood vessels. However, it is also a potent cytotoxin and specialized cells called macrophages produce NO as part of a generalized living organisms but as response to invasion by pathogenic bacteria. Such bacteria have evolved a number of enzymic systems to defend David J. Richardson, themselves against this ‘gas attack’. Soil bacteria which can denitrify also need to protect themselves from the autotoxic Andrew J. Thomson and effects of NO produced through their own metabolism. They have an enzyme, nitric oxide reductase (NOR) that has Nicholas J. Watmough evolved to keep endogenous NO levels low by converting it
to the relatively benign N2O which can be released into the describe, it is also atmosphere. From the perspective of bacterial metabolism, the job of detoxifying cytoxic NO is done when it is a potent cytotoxin. s humans we are dependent on oxygen for converted to N2O, but from an environmental perspective our respiration. We are obligate aerobes. an envirotoxin, a greenhouse gas, has been produced. When Converting it to nitrous This is not so for many species of bacteria. discussing greenhouse gas emissions, the public are acutely Faced with a shortage of oxygen in their aware of the problems posed by carbon dioxide and possibly oxide renders it relatively environment many bacterial species are able methane. However, emissions of N2O, perhaps best known to switch to using nitrate (NO–), rather than as the dental anaesthetic ‘laughing gas’ should also cause 3 harmless, but the Aoxygen to support respiration. One of these energy yielding concern. processes, known as denitrification, converts water-soluble N2O was first discovered by the British chemist Joseph nitrates to gaseous products, nitric oxide (NO), nitrous oxide Priestley in 1793 and its effects on the human senses were resultant greenhouse
(N2O) and dinitrogen (N2). This denitrification process can famously explored by a number of notable scientists and take place extensively in agricultural soils where nitrogen- poets of the time, such as Sir Humphrey Davy (President of gas causes different rich fertilizers added to stimulate plant growth can also the Royal Society 1820–1827) (Fig. 2) and Robert Southey stimulate bacterial nitrogen cycling (Fig. 1). (Poet Laureate, 1813) who both wrote about it: problems. – NO2
NO– NO NO laughing 3
NO– N O matter: the toxic 2 2
NH OH N gases of the 2 2 + NH4 c Fig. 1. The nitrogen cycle. Background: nitrogen cycle Thinkstock Images / Jupiter Images
132 microbiology today aug 08 microbiology today aug 08 133 320 b Fig. 3. Atmospheric N O accumulation Yet are my eyes with sparkling lustre fill’d atmospheric lifetime of some 150 years, the N2O produced 2 Yet is my mouth replete with murmuring sound today will potentially influence the climate experienced by since 1750. Data adapted from the 4th Assessment of the Intergovernmental Panel Yet are my limbs with inward transports fill’d our great-great grandchildren. This is most definitely not a on Climate Change. Background: Molecular
And clad with new-born mightiness around. laughing matter and so it is important to predict the impact 310 model of nitrous oxide reductase (N2OR) Sir Humphrey Davy of N O emissions on environmental change and devise from Paracoccus denitrificans drawn using 2 the co-ordinates 1FWX.
strategies to mitigate these releases now. (p.p.b.) I am sure the air in heaven must be this wonder working gas of delight Understanding the denitrification enzymes 300 concn Robert Southey
that make and break N O O 2 2 N When Joseph Priestley discovered N2O, its atmospheric The pathways by which denitrifying bacteria produce NO levels had been steady for millennia. However, throughout from nitrate are now well understood from a molecular 290 the 20th century (Fig. 3), and continuing into the 21st level, with the structures of enzymes that convert nitrate to century, N2O in the environment has increased by 50 parts nitrite (nitrate reductases) and nitrite to nitric oxide (nitrite
per billion. The levels of this atmospheric loading are rising reductases) being known. These enzymes are metalloproteins Atmospheric 280 by 0.25 % each year, with most commentators linking the that depend on transition metals such as molybdenum, iron increase to intensive use of fertilizer to improve farmland and copper for activity. productivity in the 20th century (Fig. 3). Although its The molecular structure of the membrane-associated 270 atmospheric levels are only a fraction of that of CO2, N2O enzyme complex (NOR) that synthesizes N2O in bacteria is has a 300-fold greater global warming potential. Thus when not yet known. It is, however, a close relative of the enzyme 1750 1800 1850 1900 1950 2000 expressed in terms of CO2 equivalents, it represents around in the mitochondria of human cells that allows us to respire Year 9 % of total global emissions of greenhouse gases. With an oxygen. The chemical reaction takes place at a special di-
nuclear metal centre in the heart of to the active site which is known as improve the prediction and manage-
the enzyme that binds two iron ions. CuZ, that breaks the N–O bond to ment of agricultural N2O emissions
In order to produce one molecule of make N2 which is not a greenhouse will benefit from a better under-
N2O, bacterial NOR requires not only gas. The correct assembly of CuZ, a standing of the factors that influence
two molecules of NO, but also two tetranuclear copper sulfide centre, uni- the net production of N2O by electrons and two protons (hydrogen que in biology, utilizes a dedicated bacteria. It is imperative that the ions) whose arrival at the enzyme’s biosynthetic pathway that is limited outcomes of this research are trans- active site (which consists of two iron by the bioavailability of copper in the lated into policy and practices through atoms) must be carefully co-ordinated. environment. the development of appropriate
The enzyme that breaks down N2O is management techniques for a range of a copper-containing enzyme (nitrous How can we mitigate soil systems that both mitigate emis-
oxide reductase; N2OR). It is the major N2O release? sions and improve existing agricultural enzyme on the planet responsible for The largest source of anthropogenic and waste-treatment practices.
catalysing the two-electron reduction of N2O emissions is agricultural soils N O to N . Without it, the atmospheric because of the application of nitro- 2 2 David J. Richardson, levels of N O would be much greater genous fertilizers to soils that began 2 Andrew J. Thomson & than they currently are. in the early 1900s and continues to Nicholas J. Watmough The molecular structure of N OR increase today. This intensive use of 2 The authors are all members of is known. It exists as a functional fertilizers provides an interesting para- homodimer (one monomer is shown dox for policy makers in that some a new Nitrous Oxide Focus Group as the background to Fig. 3), that strategies based on biofuel production (www.nitrousoxide.org) that brings contains 12 atoms of copper with each designed to mitigate the effects of together scientists from a range of disciplines with various stakeholders subunit having two different types of CO2 release from fossil fuel actually copper clusters. The dinuclear cluster, lead to increases in global warming with the aim of sharing knowledge known as CuA, serves to pass electrons potential because of the increased on nitrous oxide and exploring requirement for artificial fertilizers. strategies for mitigating release. Since the UK signed up to the Kyoto University of East Anglia, Norwich b Fig. 2. Sir Humphrey Davey and colleagues Protocol, many non-biological sources NR4 7TJ, UK (e d.richardson@uea. at the Royal Institution inhaling gases such of N O emissions have been reduced, ac.uk; [email protected]; as nitrous oxide as part of the science of 2 pneumatics. Coloured etching by J. Gillray, but emissions from biological sources [email protected]) 1802. Wellcome Library, London are less easy to manage. Efforts to
134 microbiology today aug 08 microbiology today aug 08 135 meetings
registering on the website should arrangements. Conference Partners Autumn08 Trinity College Dublin contact the Meetings Office. offer an online booking service: www. OtherEvents Meetings on the web conferencepartners.ie/sgm2008/ rd Registration fees per day (incl. For up-to-date information on 8–11 September 2008 163 Meeting t +353 (0)1 296 8688 refreshments, conference literature, Biochemical Society/SGM future Society meetings and to e [email protected] welcome reception) Molecular biology of Archaea book online see www.sgm.ac.uk Plenary Special Events Earlybird (up to 8 August 2008) Postgraduate Conference St Andrews – 19–21 August 2008 Behaviour of biofilm Monday 8 September Ordinary Members* £40 Grants www.biochemistry.org/meetings/ Meetings organization Welcome Reception Student/Associate Members* £20 programme.cfm?Meeting_No=SA079 bacteria: from cooperation For full details, see www.sgm.ac.uk/ The organization of SGM meetings Non-members £110 and communication to Get to know your fellow delegates grants/pg.cfm programmes is co-ordinated by Retired/Honorary Members* Free control over a glass of wine on the first evening Federation of Infection the Scientific Meetings Officer, of the conference. Venue: Trinity Full (after 8 August 2008) Offered Poster Presentations Societies Conference Professor Hilary Lappin-Scott, 8–9 September 2008 College Dublin. Ordinary Members* £50 Delegates whose offered posters have Cardiff City Hall and Deputy Scientific Meetings Organizers: G.M. Gadd, Tuesday 9 September Student/Associate Members* £30 been accepted should note that an 2–4 December 2008 Officer, Professor Chris J. Hewitt. P.S. Handley, P.R. Langford, Society Dinner Non-members £120 area of 90x90 cm only is available on www.fis2008.co.uk Suggestions for topics for future the poster boards for their display. symposia are always welcome. H.M. Lappin-Scott, M.M. Tunney, A four-course meal with inclusive wine Retired/Honorary Members* £10 M. Upton & J. Verran and pre-dinner drink will take place at *Please note: to qualify for earlybird Microscene Noticeboard Recent Independent Administration of meetings is the Guinness Storehouse, St James’s rates, 2008 membership fees must be Virology Researchers’ carried out by Mrs Josiane Dunn at At the meeting, a board will be set Gate, Dublin. paid by the deadline of 8 August. (RIVR) Meeting SGM Headquarters, Marlborough Programme Booklet up with notices of jobs, postdoctoral Breadsall Priory Hotel, near Derby House, Basingstoke Road, Spencers A booklet giving full details of positions, studentships, courses, Wood, Reading RG7 1AG (t 0118 the programme is enclosed with this Registration Accommodation conferences, etc. Contributions are 5–6 January 2009 988 1805; f 0118 988 5656; issue of Microbiology Today. Registration is through the SGM For this event, o/n accommodation welcome and may be either brought For further details, contact Alain e [email protected]). Any changes will be posted on the website (www.sgm.ac.uk/meetings). is not available through the Society to the meeting or sent beforehand to Kohl ([email protected]) or Chris SGM website. Anyone experiencing problems and delegates must make their own Janet Hurst (e [email protected]). McCormick ([email protected]) Abstracts Titles and abstracts for all presentations are required in a standard format and should be Programme Other sessions: Spring09 Harrogate submitted through the SGM The Legacy of Fleming Molecular virology website. Deadlines for submissions Environmental microbiology are published in Microbiology Spring09 International Centre This is the main theme of the Today and on the web. For further meeting. 80 years after Alexander Metagenomics information contact the Events 30 March–2 April 2009 Fleming discovered penicillin, our Food preservation Administrator. scientific sessions will consider the PLUS 6 virology workshops on a range Legacy of Fleming – 80 years since the discovery of penicillin latest developments in the diagnosis, of subjects. prevention, control and treatment of infectious diseases. Topics include: Prize Lectures From 2009, Society meetings will Career development and microbiology The new SGM Prize Medal IrishDivision have a new look. The scientific education will also be covered. The Impact of medical intervention on ever-popular Gala Dinner will retain its evolution of microbes / Multi-drug Colworth Prize sessions over three and a half days 23–24 April 2009 will cover the latest topics in modern Tuesday evening slot. resistant TB / Production, formulation Fleming Award and delivery of antimicrobials / Innovative models and systems for microbiology, within a framework of The first conference under the new New antibiotics / Infection control / Careers and education events studying microbial pathogenesis fewer parallel sessions in the mornings, system will take place at Harrogate Novel therapeutics / Susceptibility to stand-alone keynote lectures and International Centre. This is an University Challenge: the transition University of Cork, Ireland infection and disease / Mechanisms afternoons packed with workshops, excellent venue, with a range of high- from school to university For further details, contact John of resistance / Antibiotic resistance in debates, demonstrations and mini- specification lecture theatres, a large Careers in clinical microbiology Morrissey (e [email protected]). symposia catering for all areas of staphylococci / Bedside diagnostics / exhibition hall and plenty of space Careers planning for postgrads microbiological science. for poster boards and networking. Molecular evolution of virus pathogens. Careers drop-in for postdocs For details of other Irish Division Poster-viewing will take place over a Accommodation to suit all tastes and Related events activities, contact Evelyn Doyle drink in the evenings. pockets is available in the town. (e [email protected]) Lessons in history: the microbiology SGM plant virologists will also be of war wounds holding a joint one-day meeting with The human microbiota the Association for Applied Biology.
136 microbiology today aug 08 microbiology today aug 08 137 schoolzone
Schools Membership costs only £10 a year. Benefits include d A susceptible host (human), The peak danger period for Fact versus fiction large overcrowded settlements often e.g. someone with underlying poor transmission is between 10 days and used to house conflict- or disaster- Microbiology Today, advance copies of new teaching resources In 2004, there were no serious nutritional levels, as malnutrition a month after a natural disaster as this epidemics and no cases of cholera associated people. and discounted fees on SGM INSET courses. To join see increases the risk of death from is usually when water, hygiene and reported to the WHO or other health d adequate drinking and washing communicable diseases. sewage facilities are at their poorest and www.sgm.ac.uk/membership. Enquiries: [email protected] surveillance bodies in the 4 months water were supplied to the camps. A person killed in a natural disaster levels of overcrowding are particularly after the tsunami, even though more or go to www.microbiologyonline.org.uk for full details of through trauma, etc., is no more likely high due to population displacement. than 175,000 people died. Several The real risk of an epidemic than any other person from the local For example, if a survivor carrying factors may have been responsible: in Myanmar resources and activities. V. cholerae is housed in an overcrowded population to have a communicable According to WHO medical facility with poor or no toilet facilities d cholera occurs in Indonesia disease. So unless they were carrying epidemiologist, Dr John Watson, and the sewage is leaking into the between March and September and an infectious agent when they died, Myanmar is at higher than usual risk drinking wells, then the microbe could the tsunami hit in December their bodies do not pose a risk to of a communicable disease because spread rapidly through the population d the displaced population was housed Epidemics following human health. Micro-organisms at least a quarter of a million people via the faecal–oral route. in small camps compared with the associated with the decay of the have been displaced, coupled with human body (the decomposers) are ‘Access to clean water and sanitation remains a major serious overcrowding. Also the not usually human pathogens. underlying nutritional levels in the natural disasters health challenge in Myanmar.’ WHO, 4 June 2008 country are poor and there is very Persistence limited access to health services. With Misconceptions reported in the media may distort the When the host dies, pathogens respect to gastrointestinal infections usually have limited viability, as they such as cholera, approximately 75 % science behind a story – so students should look to primary cannot sustain their growth alone. of people in Myanmar have no toilets Consequently, they are unable to and defecate outside. As the water sources for the real facts. Dariel Burdass asks if people are survive for long in the surrounding levels are so high, this excrement more at risk from the living or the dead? environment and present little is contaminating water supplies, infectious risk. The ability of a micro- putting those displaced at greater organism to survive outside the human risk. Appropriate disposal of human Following a natural disaster, such or floating in the floods is unlikely body is called its persistence. For all faecal matter can reduce diarrhoea by as the tsunami on 26 December to cause an epidemic. Survivors with pathogens, survival is dependent on a 40 %. It is also the cholera season in 2004, which overwhelmed much of diseases (Table 1) are a far greater range of factors, including temperature; Myanmar and cholera is endemic in Indonesia, and the cyclone, which hazard to health than the dead. microbes will persist for longer at the Irrawaddy delta. So in this area the devastated Myanmar (Burma) on Deaths following natural disasters lower temperatures. However, because dangers of a cholera epidemic are real. 3 May 2008, reports in the media are usually due to blunt trauma, pathogens do not die immediately after often overstate the risk of epidemics The online version of this article has crush-related injuries or drowning, their host does, transmission from a of highly infectious diseases such as links to a number of useful websites: not communicable diseases. For an dead body to a living person is still cholera, hepatitis and typhoid. This www.sgm.ac.uk/pubs/micro_today infection to be successfully transmitted possible, but those most likely to be is mainly due to the fear associated b Cyclone-affected families living in from person to person, three factors at risk are not the general population with the presence of numerous dead temporary accommodation near Yangon, are necessary: but relief workers who can minimize Myanmar, on 25 May 2008. Khin Maung bodies in an affected area. However, their exposure to potential pathogens Win / AFP / Getty Images evidence has shown that disease d The presence of an infectious by following basic hygiene rules such outbreaks following a natural disaster agent e.g. in the case of cholera, the as hand washing and using appropriate are a rare occurrence and that a dead bacterium Vibrio cholerae protective equipment such as gloves. body decomposing either on the land d Exposure to that agent Bioscience Outreach in Schools Colloquium Transmission Tuesday, 28 October 2008 – National Science Learning Centre, York Table 1. Micro-organisms most commonly linked by the media and some health officials with transmission from dead bodies The factors which influence the The Biosciences Federation Education Committee In addition to showcasing the outreach opportunities transmission of infectious diseases (chaired by Sue Assinder, SGM Education Officer) is available, the Colloquium will explore strategic questions Mode of transmission Micro-organism Disease from person to person after a natural organizing this Colloquium in partnership with the about outreach provision and result in publication of a Gastrointestinal tract Salmonella typhi Typhoid disaster are National Science Learning Centre. It will aim to bring formal stakeholder report. The Colloquium will be preceded Shigella sonnei Dysentery d the size of the displaced population together school biology teachers with deliverers of outreach on the previous afternoon by a professional development Vibrio cholerae Cholera d access to clean water (e.g. learned societies, academics and industry) to discuss event for A level biology teachers. The SGM is providing Blood-borne Hepatitis B and C Hepatitis effective practice and make recommendations on how financial sponsorship to the Colloquium and Janet Hurst d sewage facilities HIV AIDS activities within the biosciences might be co-ordinated. and Dariel Burdass are playing a major role in organizing the Air-borne Mycobacterium tuberculosis TB d health status of the population Professor John Holman (National STEM Director) has event. Registration details are available on the Biosciences Vector-borne Plasmodium spp. Malaria d whether a disease is endemic locally agreed to give a keynote talk. Federation website (www.bsf.ac.uk).
138 microbiology today aug 08 microbiology today aug 08 139 obituary
Germ Proof Your Kids: Antibiotic The Complete Guide to Protecting Professor Norbert Pfennig (without Overprotecting) Your resistance Family from Infections By H.A. Rotbart (08.07.1925–11.02.2008) challenge – Published by the American Society for Microbiology (2008) Norbert Pfennig, former professor of limnology and microbial poster ISBN 978-1-55581-427-4 ecology at the University of Konstanz, Germany, has died, aged 82. As the healthy daughter of parents Born in 1925, he studied biology in Göttingen and soon concentrated who firmly believe in the hygiene competition hypothesis and think sawdust and on microbiology under the guidance of August Rippel-Baldes. In soil are perfect additions to a toddler’s 1952, he obtained his doctoral degree in organic chemistry under Key Stage 3 Science students are diet, I was initially sceptical about this Hans Brockmann. He became an adjunct professor of microbiology invited to enter an exciting poster book. In fact, I was looking forward in Göttingen in 1964 and later the head of a research group for competition. Their eye-catching to writing a scathing review. But I poster should aim to encourage should have paid more attention to the nutritional physiology of micro-organisms. friends and family not to go to the without overprotecting caveat: this book GP for antibiotics for coughs and is excellent and deserves a place on When Hans Schlegel joined the Göttingen Institute for Micro- and quality, and metabolic exchange with partner organisms. colds as these do not work on such every parent’s bookshelf and would be biology in 1959 and brought along water samples from a pond Inspired by this philosophy and his new position, he entered virus infections. It is important that a useful addition to any school library. much depresses the immune system) with obvious development of purple phototrophic sulfur a new phase in his career, extending his research on the getting cold and catching one (the bacteria, Norbert decided to try to cultivate them. Within 2 interaction of microbes with their natural environment. Lake people understand when they should The first chapter, ‘Worthy Enemies’, is jury is still out) and exercise (regular years, he had explored the growth demands and invented a Konstanz and small lakes and ditches in the area became the use antibiotics and when it is not an introduction to pathogens and their exercise good, extreme exercise bad). specific technique employing defined media to further enrich objects of research and teaching, with a focus on the activities appropriate. transmission. Rotbart also provides and finally isolate these barely cultivable, fastidious bacteria. of anaerobic bacteria, especially the phototrophs, the sulfate In the UK, the Department of Health’s a glossary of infections that includes The final chapter ‘The Wisdom of Ages’ A research visit with Cornelis van Niel at Pacific Grove, reducers and syntrophic methanogenic co-cultures. Advisory Committee for Antimicrobial the most common childhood ailments offers guidance in dealing with California, deepened his interest in phototrophs, and he Unlike many traditional professors, he gave an enormous Resistance and Healthcare Associated plus those that children are unlikely what is described as the continuous remained an admirer of van Niel as a researcher and teacher. amount of freedom to his scientists and acted more like a Infection is holding a national to contract but are parents’ greatest onslaught of newspaper fear factors. After the discovery of the importance of vitamin B12 for colleague, always curious to exchange news. His lectures and conference to mark European fear. The profiles of diseases, such His advice is to respond with prudence, the cultivation of phototrophs, a broad range of these bacteria courses were characterized by a similar attitude; he did not Antibiotic Awareness Day which will as measles and polio, which are ‘so not paranoia and the ‘good sense to was isolated in pure culture and characterized in depth. From regard himself as someone who simply had to transfer knowl- take place on 18 November at the last generation’ remind readers of the recognize the nonsense’. So, when his days in van Niel’s lab, co-operations arose with Germaine edge, but to convey the attitude of asking questions, always Science Museum, South Kensington, importance of vaccination and the running late on a Monday morning, I Cohen-Bazire and Roger Stanier, leading to detailed electron willing to learn from the microbes. He enjoyed discoveries London. The target audience will be consequences of complacency. will continue to leave the house with wet hair; but I will be washing (and microscopic studies of the intracellular membrane arrange- like any graduate student, even the small breakthroughs, and health/science journalists and health In ‘Weapons in War’, the author drying) my hands as frequently as ment and the discovery of the Chlorobium vesicles. The follow- used to express this by his unconstrained laughter. professionals. The winning poster will explains the basics of immunology, Lady Macbeth and discarding my dish ing years were filled with numerous studies of phototrophs He was awarded the Research Prize of the Deutsche Gesell- be printed to coincide with the day the science of vaccination and the cloths daily. I will ensure my children and their taxonomic organization, to which his first postdoc, schaft für Hygiene und Mikrobiologie in 1980, he was a and displayed at the conference. treatment of infections. He provides are up-to-date with their vaccinations Hans Trüper, contributed, and he served Bergey’s Manual as a corresponding member of the Academy of Sciences in Göttin- Prizes include an iPod Nano for the clear explanations, with easy-to- and I won’t be asking the doctor for Trustee for many years. gen, and an honorary member of the SGM and the Vereinigung winner and £1,000 worth of science understand analogies, of concepts that antibiotics to treat a cold. New research fields opened up during a study of green für Allgemeine und Angewandte Mikrobiologie in Germany. equipment for the school, which will can be difficult to grasp. The section phototrophs. From an enrichment culture of Chlorobium-like He was awarded the Bergey Medal in 1992 and received an The book is scientifically accurate and be presented at the conference. The on vaccination provides detailed phototrophs on ethanol, the first pure cultures of ethanol- and Honory Doctoral Degree from the University of Bonn. up-to-date. As a reference book it is a winning school will also be invited information about specific vaccines acetate-oxidizing sulfur reducers were obtained (with Hanno The microbiological community in Germany and abroad reliable resource that is easy to navigate. to visit a microbiology laboratory. and a balanced discussion of parental Biebl), along with the discovery of a syntrophic co-operation has lost one of its most prominent members and founding As bedtime reading, its mixture of Three runners up will receive £25 concerns and recent controversies. through a sulfur/sulfide cycle. These and numerous sulfate fathers, one of the last representatives of a general microbiology humour and common sense make it entertainment vouchers and £100 The section about the use and misuse reducers (with Friedrich Widdel) were also the basis for a based on a specific feeling for the microbes’ capabilities an enjoyable read. Rotbart manages to worth of science equipment for the of antibiotics is informative. long-lasting friendship with Rudolf Thauer who studied the and demands from the ecological perspective. Several of his correct misconceptions and debunk school. ‘Wear Your Boots in the Rain’ is a biochemistry of these novel bacteria. discoveries changed and extended our understanding of the myths while sensitively dealing with Information on how to enter is guide to personal, domestic and In 1979, Norbert accepted a professorship at the University action of microbes in nature. Those closer to him lost a contentious issues and parental anxiety. available at www.nhs.uk/arc and community hygiene, nutrition and of Konstanz until his retirement in 1990. As a scientist always personal friend of unusual modesty, an honourable person- It is an antidote to all the rubbish includes teachers’ notes, lesson plans, the reality behind ‘miscellaneous searching for holistic explanations, he saw the micro-organism ality with an open mind. Our sympathy is with his wife science that we are too often bombarded key facts, the competition rules and momisms’. These include: chicken not only as a cell or strain with metabolic capabilities, but Helga, five children and nine grandchildren. with. I would highly recommend it. entry form. Closing date for entries is soup (it tastes nice, nothing more), also as part of the ecosystem with its specific challenges, 10 October 2008. sleep (yes, you need it), stress (too Gemma Sims, SGM including limiting substrate supply, light of varying intensity Friedrich Widdel, Bremen; Bernhard Schink, Konstanz
140 microbiology today aug 08 microbiology today aug 08 141 gradline
Gradline aims to inform and entertain members in the early The direct approach high strategic importance to the research council. These personal circumstances. Applicants have usually completed fellowships are targeted to different institutes and different one or two postdoctoral contracts, although it is possible to There are a number of schemes to areas of science each year. Both schemes award a salary for apply to the scheme after completion of a PhD project. stages of their career in microbiology. If you have any news support early-career scientists who wish 5 years and a significant grant towards research costs. or stories, or would like to see any topics featured, contact to strike out on their own. Funding Some of the other fellowships outlined earlier can also be bodies do want to support talented The Natural Environment Research Council (NERC) awarded to scientists wanting to work on a part-time basis Jane Westwell (e [email protected]). early-career researchers and can offer makes about 30 3-year Postdoctoral Research Fellowships (usually for a minimum of 50% full-time hours). It is worth financial support at this crucial stage. each year, aiming to support outstanding environmental checking the fellowship handbooks (published on the Eligibility criteria (such as EU or UK scientists as they become independent. Although applicants funding bodies’ websites) for full details. citizenship) for these awards can be a are usually expected to have at least 1 year of postdoctoral Microbiologists planning a career year to consider the proposals. Grants experience, some grants are made to candidates before International perspective in research very often follow their are usually for 2–3 years and include factor, so it is worth checking carefully before starting the application process. they are awarded their PhD. Postdocs with at least 2 years Some fellowship opportunities are funded by the EU Marie PhD studentship with a spell as a staff salary costs and associated of experience who can prove their ability as independent postdoc, employed on one or more research expenses. This approach Microbiologists whose research is Curie Actions scheme. Grants allow early-stage researchers researchers can apply for an Advanced Fellowship. NERC to spend a period of 1–2 years in a host laboratory. This short-term contracts. The funding is can offer postdocs the opportunity rooted in the biomedical sciences fellowships are open to any nationality. sought by the principal investigator to develop skills in writing a good can apply to the Wellcome Trust and funding is viewed as a training grant, so must form part of Mid-career postdocs (with 1–3 contracts behind them) who usually maintains an overview proposal, but because the application Medical Research Council (MRC) for a long-term plan for professional development. Marie Curie can apply to the Royal Society’s University Research of the project’s direction. Postdocs must be made by the established support. Newly qualified postdocs Intra-European Fellowships support travel to labs within Fellowships scheme. The fellowships last for 5 years with on this type of contract can build up researcher (the PI) it isn’t a fast route can apply for a Sir Henry Wellcome the European Union. International Outgoing Fellowships the possibility of a further 3 years of funding. At the end of a good portfolio of laboratory skills to recognition as an independent Postdoctoral Fellowship. Applicants for Career Development support travel by European the fellowships, it is expected that candidates would be in a but, for those aiming at a long-term scientist. However, some funding are expected to identify an important researchers to a laboratory outside of Europe. Conversely, strong position to obtain permanent university posts. research career, it is necessary to bodies do accept applications made biomedical research question and International Incoming Fellowships support researchers develop as an independent researcher. jointly by experienced postdoctoral develop a research programme. The The Leverhulme Trust offers Early Career Fellowships to from outside Europe to work on research projects in an One of the stages on that journey researchers with a principal applicant fellowship is 4 years full-time, but scientists with a proven record in research. Applications are EU member state with a view to developing collaborations to independence is getting funds to who has been in a permanent post may be taken up on a part-time basis accepted in any discipline, and in 2008 they expect to award between that country and the researcher’s home country. support your own research ideas. for at least 5 years. It is worth bearing with the tenure of award lengthened 55 fellowships which can be held at any UK university or Grants include a monthly living allowance, travel and research institution. The fellowships are for 2 years and limited research costs. include 50% of total annual salary costs and up to £5,000 The Newton International Fellowships scheme was Getting funding to a year to support research costs. The host institution is launched this spring. The scheme is run by a group of become a successful expected to make up the salary shortfall and it is anticipated organizations, including Research Councils UK and the that the fellowship will lead to a permanent position. Royal Society. It funds promising early-career scientists from independent researcher any country outside the UK who want to carry out work Funding your Returning to research is tricky, but it can be at a UK research institution for up to 2 years. The awards The Daphne Jackson Trust provides university and provide a substantial contribution towards subsistence and done, as Jane Westwell industrial fellowships to help scientists who have had a research expenses, plus a one-off relocation allowance. career break of more than 2 years. Applicants must have describes. The long-term aim is to encourage new international research completed their PhD before the career break started. The collaborations and a feature of the grant is a 10-year follow- fellowships are usually of 2 years duration, are carried out up package, for those who remain in research, to support Stepping stones in mind that the success rate for accordingly. Biomedical researchers flexibly and involve an element of retraining and updating activities that maintain links with the UK. £$€£$€The problem for most postdocs response mode grant applications to with 3–6 years postdoc experience £$€£$€of skills. Projects can be hosted by university departments seeking to establish themselves is a the Research Councils can be lower can apply to the Wellcome Trust for a or by research divisions of industrial establishments. Getting an award than 30%, so even the most carefully Postdoctoral Fellowship or to the MRC lack of track-record, but there are The Wellcome Trust runs a similar scheme for researchers in Competition for these funding schemes is strong and the targeted grant application may not for a Career Development Award. Both ways around this. Some researchers the biomedical sciences. Their Career Re-entry Fellowships majority look for researchers with potential to be leaders always meet with success. schemes cover the applicant’s salary, take the opportunity to develop their are tenable for 2–4 years and may be taken up on a full or in their chosen field. If you are thinking of applying for research expenses and sometimes the own ideas whilst still fulfilling the Industrially funded researchers part-time basis. any of these grants, give yourself plenty of time, target cost of employing support staff. obligations of their contract. They may spot a good opportunity for the application very carefully, and it is a good idea to then work up an idea for a new project further funding and develop a project The BBSRC offers up to 10 David Flexible approach find a mentor who will support you during and after the with their principal investigator (PI) proposal, with their PI, which they Phillips Fellowships each year to For those who require an element of flexibility in balancing application process. who submits a grant application to pitch to the sponsor. This would scientists with 2–6 years postdoctoral their work and home commitments, the Royal Society a funding body. This type of grant is probably involve developing a good experience who want to establish administers the Dorothy Hodgkin Fellowships. Women Further information awarded under the response mode – written proposal followed by meetings themselves as independent are particularly encouraged to apply to the scheme which cordis.europa.eu www.bbsrc.ac.uk funding bodies outline their research to discuss the work to ensure it researchers. They also offer Institute is designed to help successful candidates progress to priorities and scientists submit matches the sponsor’s requirements (as Career Path Fellowships to early- permanent academic positions in the UK. A useful feature www.daphnejackson.org.uk www.mrc.ac.uk applications within the relevant remit. well as offering the postdoc the chance career researchers wishing to work is that successful fellows can work on a full- or part-time www.nerc.ac.uk www.newtonfellowships.org Committees meet a few times each to do some publishable research). in a BBSRC institute in areas of basis or even convert from one to the other, depending on royalsociety.org www.wellcome.ac.uk
142 microbiology today aug 08 microbiology today aug 08 143 addresses
Working towards a career in council07–08 Officers Members President – Prof. Robin Weiss Prof. Mike R. Barer university research & teaching Division of Infection and Immunity, University College London, 46 Cleveland Street, Infection, Immunity and Inflammation, University of Leicester, London W1T 4JF Medical Sciences Building, PO Box 138, University Road, Leicester LE2 4FF t–0207 679 9554;–f–0207 679 9555;–e–[email protected] t–0116 252 2933;–f–0116 252 5030;–e–[email protected] Gail Ferguson is a senior lecturer being in a lab with plenty of Treasurer – Prof. Colin R. Harwood Dr David J. Blackbourn money to an empty lab with very School of Cell and Molecular Biosciences, University of Newcastle Medical School, University of Birmingham, Cancer Research UK Institute for Cancer Studies, Framlington Place, Newcastle upon Tyne NE2 4HH Edgbaston, Birmingham B15 2TT at University of Aberdeen. She shared little money. I had to go back to t–0191 222 7708;–f–0191 222 7736;–e–[email protected] t–0121 415 8804;–f–0121 414 4486;–e–[email protected] basics – filling tip boxes and pouring General Secretary – Dr Ulrich Desselberger Prof. Neil A. R. Gow Dept of Medicine, University of Cambridge, Level 5, Addenbrooke’s Hospital, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Cambridge CB2 2QQ my own gels! However, there are many Aberdeen AB25 2ZD her experience with early-career t–01223 763403;–e–[email protected] or [email protected] funding opportunities in the UK for t–01224 555879;–f–01224 555844;–e–[email protected] Scientific Meetings Officer – Prof. Hilary M. Lappin-Scott Dr Richard M. Hall new investigators and I was lucky Dept of Biosciences, University of Exeter, Geoffrey Pope Building, Biological Reagents and Assay Development (BR&AD), GlaxoSmithKline R&D, microbiologists at the Spring Meeting Exeter EX4 4QD to be awarded several grants. It has New Frontiers Science Park – North Site SC1, H31/1-047 (Mail Code H31111), f–01392 263434;–e–[email protected] taken a while to get re-involved with Third Avenue, Harlow, Essex CM19 5AW International Secretary – Prof. George P. C. Salmond t–0127 962 7172;–f–0127 962 7014;–e–[email protected] this year. Dept of Biochemistry, University of Cambridge, Tennis Court Road, Building O, the UK and European microbiology Dr Kim R. Hardie Downing Site, Cambridge CB2 1QW University of Nottingham, Centre for Biomolecular Sciences, University Park, Profile since my research experience had community, but I very much enjoy the t–01223 333650;–f–01223 766108;–e–[email protected] Nottingham NG7 2RD Education Officer – Dr Susan J. Assinder mostly focussed on E. coli, I wanted UK system and am happy to be back. t–0115 846 7958;–f–0115 586 7950;–e–[email protected] Name Gail Ferguson Age 38 to gain further experience in more Director of Education, Liverpool School of Tropical Medicine, Pembroke Place, How do you see your Liverpool L3 5QA Dr Paul A. Hoskisson Present occupation Senior Lecturer, Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, diverse bacterial species before taking Editor, Microbiology Today – Dr Matt Hutchings School of Medicine, University of Q future? 204 Geroge Street, Glasgow G1 1XW School of Biological Sciences, University of East Anglia, Norwich Research Park, up a permanent position. I went to t–0141 548 2819;–e–[email protected] Aberdeen I would like to continue in academia Norwich NR4 7TJ work in the USA at MIT, due to its t–01603 592257;–e–[email protected] Dr Catherine O’Reilly Previous employment Lecturer and build my research group. I enjoy Dept of Chemical and Life Sciences, Waterford Institute of Technology, Cork Road, Editor-in-Chief, Microbiology – Prof. Charles J. Dorman reputation and that of the ‘Boston Waterford, Ireland in Biological Sciences, University the university environment and the Dept of Microbiology, Moyne Institute, Trinity College, Dublin 2, Ireland Bacterial’ community. I chose to t–+353 51 302858;–f–+353 51 378292;–e–[email protected] of Edinburgh (Sept 2004–May t–+353 1 608 2013;–f–+353 1 679 9294;–e–[email protected] balance between research and Prof. Petra C. F. Oyston go to Graham Walker’s lab as I was Editor-in-Chief, JGV – Prof. Richard M. Elliott 2007); Postdoctoral Associate, TL Molecular Bacteriology, Dstl, B07A Microbiology, Porton Down, Salisbury SP4 0JQ teaching. Centre for Biomolecular Sciences, School of Biology, University of St Andrews, Massachusetts Institute of really interested in his work on t–01980 613641;–f–01980 614307;–e–[email protected] What advice can you offer people North Haugh, St Andrews, Fife KY16 9ST Technology (Oct 1999–Sept 2004); Sinorhizobium and Brucella. t–01334 463396;–e–[email protected] Prof. Bert K. Rima planning a career as an academic? School of Biology and Biochemistry, Medical Biology Centre, Wellcome Trust Postdoctoral Q Editor-in-Chief, JMM – Prof. Charles W. Penn How did this compare with your School of Biosciences, University of Birmingham, Edgbaston, Birmingham The Queen’s University of Belfast, 97 Lisburn Road, Belfast BT9 7BL During your postdoc, aim to develop t–028 9097 5858;–f–028 9097 5877;–e–[email protected] Toxicology Fellowship, University of Q previous postdoctoral experience? B15 2TT Aberdeen (Oct 1996–Sept 1999); the skills for running your own lab: t–0121 414 6562;–f–0121 414 5925;–e–[email protected] When I arrived in the USA I was given Postdoctoral Associate, University of a bench and just had to get on with it. Gain experience in writing and Aberdeen (Jan 1994–Oct 1996). Graham was fantastic in terms of the reviewing papers and grants Education University of Aberdeen, ‘big picture’, which was exactly what Develop projects that you can take PhD Microbiology; University of groupconveners Stirling, BSc Biochemistry Hons (2i). I needed in terms of my career at that with you to your own lab stage. However, I would recommend Cells & Cell Surfaces – Dr Ian R. Henderson Fermentation & Bioprocessing – Prof. Chris J. Hewitt Apply for fellowships (and check Division of Immunity and Infection, University of Birmingham Medical School, Dept of Chemical Engineering, Loughborough University, Loughborough LE11 3TU What attracted you to that people do at least one postdoc deadlines!) Edgbaston, Birmingham B15 2TT t–01509 222503;–e–[email protected] Q microbiology research? before going to the USA where more t–0121 414 4368;–f–0121 414 3599;–e–[email protected] Food & Beverages – Dr Cath E. D. Rees Make sure that you get a wide range Clinical Microbiology – Prof. Dlawer Ala’Aldeen University of Nottingham, School of Biological Sciences, Sutton Bonington Campus, is expected of postdocs since the PhD I became fascinated with microbiology of experiences during your postdocs Molecular Bacteriology and Immunology Group, Division of Microbiology, Loughborough LE12 5RD during my undergraduate degree, there is longer (5–7 years).The work School of Molecular Medical Sciences, University Hospital, Nottingham NG7 2UH t–0115 951 6167;–f–0115 951 6162;–e–[email protected] (courses, work on different microbial t–0115 823 0748/0771 (secretary);–f–0115 823 0759;–e–[email protected] Irish Branch – Dr Evelyn Doyle ethic is a bit different in the USA. Most during which I conducted two systems and in different labs) Clinical Virology – Prof. Judy Breuer School of Biology and Environmental Science, Ardmore House, summer projects and an honours people arrived in the lab around 10 ICMS Centre for Infectious Disease, Barts and the London Medical School, University College Dublin, Belfield, Dublin 4, Ireland Publish your research regularly and 4 Newark Street, London E1 2AT t–+353 1716 1300;–f–+353 1716 1183;–e–[email protected] project on trichomonads. From this am and worked until 8–10 pm, yet t–0207 882 2308;–f–0207 882 2181;–e–[email protected] Microbial Infection – Dr Nick Dorrell try to aim for high-quality journals experience, I knew that I wanted to Graham did not micromanage and Education & Training – Prof. Joanna Verran Pathogen Molecular Biology Unit, Dept of Infectious and Tropical Diseases, Dept of Biology, Chemistry and Health Science, Manchester Metropolitan University, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT pursue a research career. I would was more interested in progress. He Help in the supervision of student Chester Street, Manchester M1 5GD t–0207 927 2838;–f–0207 637 4314;–e–[email protected] thoroughly encourage undergraduates was also very happy to allow people to projects t–0161 247 1206;–f–0161 247 6325;–e–[email protected] Physiology, Biochemistry & Molecular Genetics – Prof. Maggie C. M. Smith take holidays and wasn’t strict about Environmental Microbiology – Prof. Geoffrey M. Gadd Molecular & Genetics, University of Aberdeen, Institute of Medical Sciences, to gain research experience as this can Do some teaching but do not take Division of Environmental and Applied Biology, Biological Sciences Institute, Foresterhill, Aberdeen AB25 2ZD ensure that you choose a PhD in an this as long as people worked hard. School of Life Sciences, University of Dundee, Dundee DD1 4HN t–01224 555739;–f–01224 555844;–e–[email protected] on too much – at the end of the day, Systematics & Evolution – Prof. Niall A. Logan area that interests you. He was a very positive role model, t–01382 344765;–f–01382 348216;–e–[email protected] its your research record that will get Eukaryotic Microbiology – Dr Alastair Goldman Dept of Biological and Biomedical Sciences, Glasgow Caledonian University, Cowcaddens Road, Glasgow G4 0BA managing to balance work and life and Molecular Biology & Biotechnology, University of Sheffield, Firth Court, What influenced your decision to you the position t–0141 331 3207/8510 (admin assistant);–f–0141 331 3208;–e–[email protected] still be extremely successful. Sheffield S10 2TN Q work as a postdoc in the USA? Have a mock interview for t–0114 222 2779;–e–[email protected] Virus – Prof. Rick E. Randall School of Biology, Biomolecular Sciences Building, University of St Andrews, After my Wellcome postdoc fellowship How did you find the transition fellowships or academic positions North Haugh, St Andrews, Fife KY16 9ST I had to make a decision whether or Q to an academic post in the UK? as it’s important to know the types t–01334 463397;–f–01334 462595;–e–[email protected] not to apply for lectureships. However, It was a bit of a shock. I went from of questions you may be asked.
144 microbiology today aug 08 microbiology today aug 08 145 hotoffthepress
Science writer Meriel Jones takes a look at some recent animals, recounted by Slovenian transmitting signals within cells. This Researchers from around the world that some epidemic strains lack toxin researchers, suggested a further can kill the cells and researchers from shared information about the prevalence A. The prevalence of these strains has papers in SGM journals which highlight new and exciting undesirable possibility of spread Hannover Medical School in Germany of C. difficile in hospitals within their been between 0.2 and 56 % in reports through the food chain. In contrast, talked about their detailed study of own countries. For example, scientists from around the world. Unfortunately, developments in microbiological research. researchers from the Alimentary these events. Despite several gaps in from the Netherlands explained how some tests rely on detecting this Pharmabiotic Centre in Ireland supplied our knowledge, the importance of the the realization that NAP1/027 strains toxin so that the infection is mis- the novel idea for a therapy using toxins to illness is very clear and has led had caused epidemics in eight Dutch diagnosed, emphasizing the importance designer probiotics to neutralize both to suggestions that a new therapeutic hospitals in 2005 led rapidly to new of developing appropriate routine C. difficile cells and toxins in the gut. approach would be to develop hygiene guidelines and a review of the identification methods. In addition, There is an essential link between the compounds that block recognition use of antibiotics prior to each outbreak. work from the research group at the amount of toxins (toxin A and toxin between the toxins and human cells. Staff from the Austrian Agency for London School of Hygiene and Tropical Health and Food Safety had checked B) produced by C. difficile and the The immune system is essential in Medicine, UK, indicated that the toxin 149 samples from Austrian hospital severity of the illness. The biosynthesis resistance to bacterial infections and situation was becoming even more laboratories in 2006 to discover what of the toxins is controlled by a series researchers from the University of complex since some virulent strains ribotypes were present and whether of positive and negative controls Edinburgh, UK, showed very clearly have novel versions of toxin B. they differed in lethality. They identified within the cell, in response to the cell’s that patients with illness caused by At the end of the symposium, the 41 different ribotypes and pointed out environment. The human gut is stressful C. difficile did not differ from apparently delegates agreed what the future that finding several infections with for bacteria, and researchers from the healthy people harbouring the research priorities should be. Advances the same ribotype in a hospital should UK presented their initial analysis of bacterium in terms of their immune have be made on several since June prompt an in-depth investigation in how all the genes within C. difficile react response. This is good news for 2007, and they include the areas of case the source was in the hospital itself. to this situation. Partial loss of control proposals to develop treatments, epidemiology, establishment of better Twelve of the patients had died, infected over toxin biosynthesis, as well as including vaccines, that rely on the nomenclature and typing systems for with six different ribotypes, illustrating resistance to antibiotics, is characteristic immune system, recounted by scientists isolates, and research to gain greater that there is serious danger from more of the epidemic strains. French and from Italy, Ireland and the UK. understanding of both pathogenesis German researchers told the symposium than the NAP1/027 strain. b of the bacterium and the reasons for about studies hinting that antibiotics Coloured SEM of C. difficile on a surface. Annie Cavanagh and Dave McCarthy/ The experience of Korean researchers susceptibility of its unwilling human Clostridium difficile –a special issue may actually influence the ability of Wellcome Images between 2000 and 2005 made the point hosts. Clostridium difficile is a bacterial species has emerged in Europe and North C. difficile to colonize the gut as well as affecting toxin production. In that lives in oxygen-free conditions. It is America and is responsible for a large Pig gut bug one of the very many types of bacteria increase in both illness and death. At addition C. difficile can synthesize, in the healthy human gut, and although least 27 further very virulent strains and tolerate, the toxic disinfectant Baele, M., Decostere, A., Vandamme, P., Ceelen, L., of ulcers and gastritis in pigs, the only piece of molecular relatively uncommon in adults, can have also been identified. p-cresol and researchers from the Hellemans, A., Mast, J., Chiers, K., Ducatelle, R. & genetic information matched some helicobacters from people be detected in at least two out of London School of Hygiene and Tropical Haesebrouck, F. (2008). Isolation and characterization of suspiciously well. There was also epidemiological evidence The Second International C. difficile three infants. However, one side-effect Medicine, UK, presented their work Helicobacter suis sp. nov. from pig stomachs. Int J Syst Evol that people who had contact with pigs had a higher risk of Symposium, with delegates from 24 of life-saving antibiotic therapies, looking at whether this provided any Microbiol 58, 1350–1358. H. heilmannii infection, suggesting that the bacteria might countries in five continents, was held first recognized in 1977, can be that competitive advantage. Their study transfer from pigs to humans. in June 2007 in Maribor in Slovenia. The bacterial species Helicobacter pylori lives in the C. difficile multiplies rapidly and causes showed that two of the virulent strains It brought together researchers stomachs of about half the human population and is involved To resolve the identity of these pig bacteria, the Belgian diarrhoea, which can be extremely tolerated significantly higher levels of studying the fundamental biology of in causing stomach ulcers. Its spiral-shaped cells inhabit researchers went to great lengths to devise a way to grow them serious and life-threatening. p-cresol than some others. In addition, this bacterium, clinicians and those researchers in Scotland described the mucus lining of the highly acidic stomach. Researchers in the laboratory. Finally, starting from the mucus scraped The biology of the bacterium provides focusing on new treatment strategies. their experiments indicating that toxin have also detected other helicobacters in some people, from pig’s stomachs that had been soaked in dilute acid, they resistance to some antibiotics and also The June 2008 issue of J Med Microbiol potency might be affected by additional distinguished by their more tightly coiled spiral-shaped cells were able to obtain cultures. The special growth medium allows it to form structures that are (vol 57, part 6) is devoted to the ideas proteins on the C. difficile surface. and differences in gene sequences. These bacteria also have they devised contained a complex mixture of components, highly resistant to disinfectants and and information that came from the an association with stomach ulcers and lymphoma. They have including activated charcoal, vitamins and several antibiotics The toxins are large, complex, sugar- other hygiene measures, making it easily symposium. been provisionally named Helicobacter heilmannii, although maintained in an atmosphere that was very low in oxygen coated proteins that recognize the spread in places like hospitals. Indeed, there seems to be more than one type. Unfortunately, it has and high in carbon dioxide. Obtaining a quantity of pure For clinical practice, the way that surface of human cells, get inside it is now the most frequently identified proved impossible to grow H. heilmannii type 1 as a pure ‘Candidatus Helicobacter suis’ allowed them, for the first time, C. difficile is unaffected by the widely and then wreak havoc in the gut. cause of hospital-acquired diarrhoea. culture in the laboratory, hindering further investigation. to perform a battery of cultural and molecular tests on the used fluoroquinolone antibiotics, used Researchers at both the Institut Pasteur bacteria. A system called ribotyping to identify to treat a very wide range of bacterial in Paris, France, and the University of Helicobacter species also live in animal stomachs. For strains of C. difficile has been devised at infections, is very important. The Freiburg, Germany, provided overviews example, DNA from ‘Candidatus Helicobacter suis’ can The results made it very clear that the bacteria from the Cardiff Anaerobe Reference Unit, European Study Group on C. difficile of the current ideas on exactly how be detected in at least 60 % of all pigs. Although these pigs belong to the same species as type 1 strains of UK, and is now used worldwide. In the (ESGCD) reported on the alarming these processes happen. The damage bacteria were first observed around 1990, they also have H. heilmannii from people, and are different from any other last few years, C. difficile has become pattern across Europe of increasingly is caused because the toxins attach a never been isolated or studied in detail. Researchers at well-characterized species of Helicobacter. To resolve the even more notorious because a new, widespread antibiotic resistance. The glucose molecule to a specific point in Ghent University in Belgium became interested because, in question of what to call it, the researchers have proposed very virulent epidemic strain (NAP1/027) presence of C. difficile disease in farm human proteins that are essential for addition to a potential role in animal welfare as the cause that Helicobacter suis is used from now on.
146 microbiology today aug 08 microbiology today aug 08 147 Pro-Lab Advert A4:Layout 1 10/1/08 14:46 Page 1
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Isoniazid is the Researchers have conflicting evidence current mainstay in treatments. It interferes with the synthesis of mycolic acids that for the role of this pathway in BSE. In 280 Plate capacity form an essential, fat-rich permeability barrier around the Mycobacterium tuberculosis • principle, NF-κB signalling could be Low gas consumption cell. Researchers would like to find more drugs that affect this process to provide beneficial or deleterious, depending on • treatments for the new drug-resistant cases of TB. • Low running costs the consequences of the signals. These Large rapid interlock for plate, Mycolic acid biosynthesis involves two enzyme complexes and the second one, could enhance the survival of neurons • FAS-II, only occurs in bacteria, plants and some parasites. 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A key step is dehydration and the gene progress of prion disease in mice that Energy saving fluorescent illumination Rv0636 is a strong candidate for control of the process. Finding chemical compounds • lack components of the NF-κB pathway. Foot operated high intensity halogen that inhibit this step could solve the identity of the gene and suggest new therapies. • One set of mice lacked a component inspection lamp Researchers at the University of Birmingham, UK, are looking for new anti-TB for pro-inflammatory signalling in most Excellent temperature stability drugs. They have tested the effects of two series of chemicals that should inhibit brain cells while others lacked part of • the dehydration enzyme activity. In each case, they started with a chemical that an alternative NF-κB signalling pathway • Automatic humidity control was already known to inhibit the enzyme, made a small modification to this throughout their bodies. 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Tel – 44 (0)151 353 1613 Fax – 44 (0)151 353 1614 email – [email protected] www.pro-lab.com 148 microbiology today aug 08 microbiology today aug 08 149 goingpublic
Science communication takes many forms. In this issue we cover some It is a short video with some basic is empowering them to become the Our own blog (www.micropodonline. information about creepy crawlies that broadcasters of tomorrow (YouTube. com/blog) covers diverse topics, of the latest ways by which microbiologists can keep in touch with each live on us humans, including microbes. com, May 2008). including the effect of TV adverts on Other popular videos include Bacterial the public opinion of microbes and other and their subject. We also pay a visit to the Welsh Assembly to conjugation (http://tinyurl.com/ Blogs the increase in STIs at Christmas. For yvehqs) with 28,296 views and Great New media has brought along with blog authors, a major advantage is promote microbiology. microbiologists, as told by Lego men it a cascade of new words, which can the facility that enables readers to (http://tinyurl.com/6akanj). make it seem even more difficult to comment and provide feedback. decode. One of these is blog. Blog Podcasts These three podcasts cover a spectrum Many of the microbiology videos on comes from the term web log, which Social networks of understanding, aimed at everyone YouTube are aimed at students. It is refers to a web page or website Social networks are beginning to The term ‘new media’ can be rather from the interested school student and possible to learn all sorts of things, content that is written and maintained grow out of the blogging world. vague. It is often applied to anything the concerned parent to the postdoc from the history of microbiology regularly, often consisting of opinions Twitter.com is a fledgling network internet-based that isn’t a static researcher and the seasoned scientist. to plate-streaking methods. Videos and descriptions of events – that is based on ‘real-time micro- web page. One such application is a Just like a magazine, information come from a multitude of different a sort of online diary. The word can blogging’: people interact via short podcast: an audio file that is connected can be presented in different ways, sources, including universities, labs also be used as a verb, meaning to (140 character) blogs. Twitterers to an RSS feed, which enables including news items, discussions and and people’s living rooms. The benefit? write or maintain a blog. Blogs can can reply to each other’s ‘tweets’, subscribers to be alerted when a new interviews. The content is convenient According to YouTube.com: ‘Everyone be (and are) written on just about creating a dialogue in a network. (usually regular and frequent) episode to the user who, perhaps, does not can watch videos on YouTube. People everything imaginable, including Yesterday, I asked for opinions. is available. Perhaps unsurprisingly, the have time to sit and read a monthly can see first-hand accounts of current microbiology. According to Google, Googler martynj said ‘I think Twitter’s majority of the most popular podcasts magazine, but can easily listen to a events, find videos about their hobbies MicrobiologyBytes is the most popular great for serendipitous discovery of are based on music and comedy 10-minute podcast while walking to and interests, and discover the quirky microbiology blog: with over 250,000 complimentary ideas/techs.’ AJcann (15 of today’s top 25 podcasts on work, driving, etc. But perhaps most and unusual. As more people capture page views in the last year. ASM also said ‘Benefits to microbiology = iTunes have comedy content; 2 are importantly, by making audio available, special moments on video, YouTube has a blog, Small Things Considered. community of practice, especially for professionally isolated folks.’ Social networks are often in the spotlight. An estimated 200 million people are registered on MySpace Microbiology and new media and at least 170 million people are on Facebook. In the UK, Bebo ranks factual) but there is certainly a place the producers are better connected second in the social network ranks for science. The Naked Scientists’ to the users, making them feel more and was purchased in March 2008 by podcast and The Guardian’s Science involved with the subject matter and AOL for $850 million (http://tinyurl. Weekly are both popular in the therefore likely to return for more. com/3ac2c8). Bebo, YouTube, Facebook ‘Science and Medicine’ category, And hearing a scientist speak about and MySpace are in the top 10 most If I wanted to, in the next 5 minutes and microbiology is not neglected. their research makes it real, accessible, searched for items in 2007 (http:// I could download a podcast about A handful of podcasts is available understandable and relevant. tinyurl.com/5vf6vc) and 1 in 50 UK astrobiology, comment on a blog by (free) subscription, including the network visits are to Facebook (http:// discussing the pros and cons of ASM’s Microbeworld, University Video tinyurl.com/yt6ax5). mandatory vaccination, watch an of Leicester’s (Dr Alan Cann) Around 9% of BBC Online content Social networks provide facilities for instructional video teaching me how MicrobiologyBytes, and Micropod is video. People are watching less like-minded people to gather virtually to streak an agar plate and join a group online, the product of a recent television, preferring to find relevant and share links, videos, podcasts, of sexy microbiologists just by clicking collaboration between SGM and the video content to view online. Videos pictures and ideas. People group my computer mouse a few times. Society for Applied Microbiology access yet another audience, which themselves in all sorts of ways, by Such are the benefits of new media (SfAM) (www.micropod online.com/ may otherwise remain out of reach. profession (e.g. microbiologists), by and web 2.0 technology. The podcast.html). For example, YouTube attracts around hobby (e.g. brewing), by interest (e.g. advantages to me as a consumer are For the ASM, University of Leicester, 20 million views each month and is microbiology) and even by campaign clear: I have a wealth of information, in SGM and SfAM, podcasts are a popular with a younger audience. The (e.g. ‘I support the HPV vaccine!’). The a variety of formats, at my fingertips. I new way to make information available number one viewed microbiology group Micropodonline is made up of all can even interact with the information, to the public. (MicrobiologyBytes has video on YouTube is called We are not sorts of people, each with an interest offering feedback and opinions. But attracted 100,000 downloads in the alone (http://tinyurl.com/5xyqu6). in topical microbiology. Some social what’s in it for microbiology? last year and there are approximately It has had 257,451 views and been networks are tailored to science and m Photos.com / Jupiter Images 1,500 regular weekly subscribers.) awarded a 5-star rating by the viewers. scientists. Nature Network enables
150 microbiology today aug 08 microbiology today aug 08 151 A few useful URLs It is projected that by 2012, 80% of online interaction will be via virtual MicrobiologyBytes videos What? Who for? Where? worlds. Does this mean we should Nature Network Professional scientists http://network.nature.com/ throw away our pens and paper? I The widespread availability of broadband internet makes Society, I am currently producing at least one video podcast Biomed Experts Professional scientists www.biomedexperts.com don’t think so. Whatever happens, it highly feasible to distribute short video clips online. As per month (http://tinyurl.com/5zbmgw). The production Facebook Everyone www.facebook.com there will still be a place for traditional Lucy Goodchild describes on p. 150, the most obvious of video is more time-demanding than the production of MySpace Everyone www.myspace.com media. People enjoy flicking through manifestation of this potential is the rapid growth in an audio podcast, but the new audience and publication (micropod online group http://tinyurl.com/5lqhgf) a magazine, reading a newspaper, popularity of YouTube and similar video-sharing services. A channels the video format makes possible means that this is Twitter Bloggers www.twitter.com watching TV and listening to the recent report indicates that YouTube looks set to overtake worthwhile. The videos are ‘branded’ with the SGM identity Plurk Bloggers www.plurk.com radio. As the horizon changes, plain BBC.co.uk in its share of UK website visits (http://tinyurl. and a link to the Society website. com/34gndf). Although the penetration of this technology Second Life People with some spare time www.secondlife.com information will still be needed to The aims of MicrobiologyBytes are to: YouTube Video lovers www.youtube.com form the basis of new content, be it into the student population is very high, teachers and UStream Video lovers www.ustream.tv a podcast, blog or discussion forum. academic staff are lagging seriously behind in the take-up d Promote understanding and awareness of current issues Microbiology can certainly benefit from of this new form of communication. Online video has a in microbiology in the general public, potential students of scientists to create a professional UN CCC meeting in Indonesia, to new media by making itself accessible high acceptability to young learners. In addition to ongoing microbiology and the media profile, including their areas of see whether we could add value to to users, therefore more readily investment by educational institutions, online video provides d Promote awareness of SGM, benefits of membership, and expertise, interests and publications. that event, open a window for extra consumed. Microbiologists themselves enormous flexibility to learners via computers, game resources available on the Society’s website Members can discuss scientific issues participation for people over that will benefit from being part of online consoles and mobile devices such as phones and video d Promote awareness of career possibilities in microbiology and methodology, or just discuss fortnight.’ The virtual event was a huge networks, but this does not spell the players. last night’s episode of a TV soap. success, becoming a model for similar and microbiology-related fields. end for traditional conferences. To In a past issue of Microbiology Today, I have described the BiomedExperts, ‘your scientific match events in the future. make the most of new media, we first great and still increasing success of my blog and podcasts Based on the success of the last year, I believe these aims point’ is similar to Nature Network; have to be willing to dip our toes into on microbiologybytes.wordpress.com This site has achieved have been realized, but extension of the project into the and is created around professional What next? web 2.0. its aim of engaging with the public about topical aspects of highly attractive online video field will further increase the collaborations; members are connected So what does the future hold? Gone audience. SGM has done just this. www. microbiology. I have also conducted pilot experiments with by publication, becoming part of a are the days when it was sufficient to micropodonline.com is proving to be video formats in the podcast and blog, and these have been Alan Cann huge group of associated researchers. put something interesting on a website a success, followed by the recent very popular. With the support of an award from the University of Leicester (e [email protected]) and let people find it. Alan Cann thinks launch of the SGM journals podcast Virtual worlds there will be a ‘growth in participatory (see p. 113). We have a Facebook Taking this one step further, you media and user-generated content. group, a MySpace page, Wikipedia reach virtual worlds, where your Much of this will be driven by social entries and RSS feeds in development online profile is given a 3-dimensional networks such as Facebook and Twitter. Science and the Welsh Assembly – watch this (virtual) space! To find out presence, or avatar. As Mellifera Slade There will also be a lot more user- more or how to contact me via web On Tuesday 20th May, the Royal the 2005 outbreak of Escherichia that had been hung against the glass in Second Life, I can talk to my virtual generated video chat through sites such 2.0, email [email protected] Society of Chemistry held its annual coli O157, the largest ever outbreak windows at the front of the building. friends using my real voice. I can as Ustream.tv and Seesmic.’ To hear Science and the Assembly event in in Wales, it seemed appropriate to Visible from both inside and out, this attend lectures (a recent event on the Alan’s response in true web 2.0 style, Lucy Goodchild, SGM External Cardiff, split between the fabulous present information on the food- temporary artwork, which was due to Nature Island was a talk on bluetongue see http://seesmic.com/v/x12PBvDIco Relations Administrator Wales Millennium Centre and the poisoning agent verocytotoxin- be unveiled the next day, was one of virus), peruse the literature at the stylish Senedd. producing E. coli (VTEC). This included a pair. The other portrait was of NHS Second Life Centers for Disease Control a short movie showing the interaction founder and Welsh hero, Aneurin and Prevention building or sit under a This event aims to bring together of E. coli O157 with the epithelia of Bevan. parasol and listen to the latest episode scientists and the Welsh Assembly the gastrointestinal tract. of the Nature podcast. Virtual worlds to discuss topical science issues, Faye Stokes give institutions the opportunity to and began with a keynote speech The Senedd is a space open to the Public Affairs Administrator create virtual areas that are accessible from Jane Davidson AM, Minister public and throughout the day there to anybody with a computer. More for Environment, Sustainability and was significant interest in the SGM Further reading www.rsc.org/ScienceAndTechnology/ than 100 universities have campuses in Housing. High profile researchers from display. The hand soaps (there to Parliament/Events/Scienceandthe Second Life, on which courses are run around Wales then delivered scientific promote good hand hygiene, which Assembly2008.asp and lectures given. According to Peter presentations. Afterwards, a buffet and is key in helping to prevent food Armstrong, founder of OneWorld.net, exhibition in the Senedd, specifically poisoning) were especially popular with http://new.wales.gov.uk/ecoliinquiry/ ?lang=en it won’t be possible for people to fly to timed to follow the Assembly’s plenary visiting school children. conferences in the future, due to the session that afternoon, allowed the However, the undisputed talking www.sgm.ac.uk/news/hot_topics.cfm pressures of climate change. Second delegates to mingle and chat, as well as point of the day at the Senedd, which www.vet.ed.ac.uk/zap/research/ Life is an opportunity for people to explore the displays. divided opinions of visitors and highlights_movie.htm meet without having to travel. ‘We The SGM participated in the exhibition. politicians alike, was the huge tinplate http://news.bbc.co.uk/1/hi/wales/ tested it last December against the With the ongoing public inquiry into portrait of Baroness Margaret Thatcher 7411199.stm
152 microbiology today aug 08 microbiology today aug 08 153 reviews
If you would like your name to be added to our database of additional chapters that could be Leishmania’ and ‘the implications in real burden of infection in humans Our main criticism is that although bundled loosely as systems biology. In terms of discovering novel diagnostics, in unknown, where the introduction the book is entitled Staphylococcus book reviewers, please complete the book reviewer interests the latter I particularly enjoyed a review chemotherapeutic agents and vaccines’, of new drugs is threatened by misuse, Molecular Genetics, seven chapters on signal transduction in archaea, which 48 authors in 13 chapters unzip the where the differing sensitivities of are devoted entirely to S. aureus form at www.sgm.ac.uk. A classified compendium of reviews captures the frontiersman spirit of some molecular biology of the pathogen that diagnostics between countries cannot with only one chapter describing be explained, complex problems must research into Archaea. causes the complex parasitic disease S. epidermidis and other coagulase- from 1996 to the present is also available on the website. leishmaniasis. The Leishmania parasite be considered at all levels from the The book begins with some hardcore negative staphylococci. This is a flagellated protozoan, existing genome to access. Let us enjoy a volume biochemistry, which is mercifully well undoubtedly reflects the current as an extracellular promastigote in that provides a valuable overview of the organized and interesting, reviewing the staphylococcal research situation the female sandfly vector and as molecular biology and biochemistry experiment on the front of the book metabolic diversity that allows Archaea of these fascinating parasites, their where the focus is placed the clinical means that anyone with an interest in to occupy bizarre habitats. The front an intracellular amastigote in the metabolic pathways, differentiation importance of S. aureus. microbial alternative energy production cover of the book also expresses this mammalian host, where it survives and process, and their surface molecules should consider obtaining a copy. well, showing a relaxed bison affront multiplies in the inhospitable location We hope that this book will be regularly without burdening important scientific steaming solfataras. I was drawn to of the phagolysomal compartment of reviewed and updated in line with this James Chong, University of York advances with unreal expectations. the chapter reviewing Archaea–metal the macrophage, and subsequently rapidly expanding field. interactions; an unusual topic that subverts the host immune response to Simon L. Croft, London School of Hygiene Archaea – New Models was easy to read. Chapters on DNA cause leishmaniasis. The understanding and Tropical Medicine Madeline Stone & Kathy Bamford, for Prokaryotic Biology and RNA processing are covered with of the mechanisms that enable this Imperial College London varying degrees of thoroughness and process, the variation between the 17 Edited by P. Blum Staphylococcus Molecular there is some overlap. In chapter 7, different species of Leishmania that Reviews on the web Published by Caister Academic Press on DNA repair, the subsection covering infect humans, and their different Genetics (2008) tissue tropisms and virulence patterns Reviews of the following books are recombination is sketchy and badly Edited by J.A. Lindsay £150.00 / US$300.00 pp. 247 pose a major challenge. The genome available on the website at www.sgm. referenced, but chapter 6, on Published by Caister Academic Press ISBN 1-90445-527-1 (and ancillary ‘-omes’) are helping us ac.uk/pubs/micro_today/reviews.cfm recombination, is excellent in covering (2008) to resolve some of these questions. After avoiding the limelight for about this in detail. The chapter on DNA £150.00 / US$300.00 pp. 278 Sulphate-reducing Bacteria – The recent publication by Peacock three billion years, Archaea were outed replication holds it own against several ISBN 1-90445-529-5 Environmental and Engineered in the 1970s and 80s by molecular recent review articles in journals. et al. (2007) has demonstrated how Systems This is an incredibly useful book for phylogenetics (Carl Woese) and some of the challenges around species The book is timely and the publishers anyone with in interest in staphylococci. Microbes for Human Life Bioenergy biochemical studies on RNA polymerase differences can be unravelled. More will promise a ‘state-of-the-art overview of It provides a broad and in-depth Edited by J.D. Wall, C.S. Harwood & (Wolfram Zillig & others). This led to come when studies are more focused on Sampling for Biological Agents in the Archaea’. In this it mostly works, and its synopsis of up-to-date staphylococcal A. Demain the new prokaryotic domain Archaea the disease relevant amastigote and we Environment slimness (246 pages) reflects a concise research. This book is very well suited Published by American Society for arising from ‘Archaeabacteria’, the label are clearer about the predictive value of and mostly well-referenced style. It to its target audiences, researchers who Pneumococcal Vaccines Microbiology (2008) previously held by these organisms mouse models for human disease. would be a pity if the hefty price (£150) are relatively new to the field and also Emerging Protozoan Pathogens US$139.95 pp. 454 within domain Bacteria. This new discourages buying it outright, because The volume is up-to-date; the genome as a suitable reference for those with ISBN 9-78155-581-4 book on Archaea settles on two main New Antibiotic Targets it conveys plenty of the novelty and was published in 2005 and the most greater experience. themes: nucleic acid processing Surely any book with a picture of an oddity in Archaea that captures the recent references in the book were The Study of Plant Disease Epidemics and bioenergetics/metabolism, with The first five chapters are particularly explosion on the cover has to be worth imagination of students, researchers published in 2007. There is a richness Antimicrobial Drugs – Chronicle of a informative, providing an excellent browsing? In this respect Bioenergy and PIs. I hope it does not become a of information – chapters on gene Twentieth Century Medical Triumph overview of the staphylococcal does not disappoint. The editors have reference work that struggles to make regulation and the metabolome are sequencing projects, population Vaccination: A Tool for the Control of sought to identify and summarize the it beyond the doors of the university particularly engaging. It is therefore a structure and evolution of S. aureus, Avian Influenza areas in which microbiology could library. shame that some errors, for example as well as analysis of the methods play a part in producing renewable over chemotherapy (details and facts), Bacterial Pathogenesis: Methods and Edward Bolt, University of Nottingham used. A lot of focus is placed on energy. The text is made up of 31 in other chapters create concern. A Protocols published data from the UK, perhaps reviews written by researchers active in further problem lies in the aims of not fully recognizing the interesting RNA and the Regulation of Gene these areas and provides an excellent Leishmania After the the volume itself and the concept and often challenging problems of Expression: A Hidden Layer of condensed summary of each area and Genome of ‘implications’. The premature day-to-day hospital- and community- Complexity the current state-of-the-art for each expectation of great revelations from the Edited by P.J. Myler & N. Fasel acquired infections of S. aureus on subject. Due to the style of presentation, genome is a minor concern compared Bacterial Physiology and Metabolism Published by Caister Academic Press a more international level. there is inevitably some overlap in the with the expectation that the genome How to Write and Illustrate a Scientific (2008) content of different chapters, and some is the basis of discovery of new tools The chapter on ‘Global regulators of £150.00 / US$300.00 pp. 308 Paper, 2nd edn conflicting opinions or interpretations for disease control – it is only a small Staphylococcus aureus virulence genes’ ISBN 1-90445-528-8 Corynebacteria: Genomics and of recent results. Bioenergy provides (and early part) of the process. As is excellent. There is a multitude of an excellent primer for students or With the laudable aim of showing ‘how pointed out in the vaccine chapter, publications concerning the regulation Molecular Biology researchers new to this exciting area. the genome has informed and changed the ‘roadblock is to identify a mode of virulence and this chapter provides a Plasmids: Current Research and Future The picture of the recreation of the Volta our understanding of the biology of of delivery’. With a disease where the thorough review of the literature. Trends
154 microbiology today aug 08 microbiology today aug 08 155 Microbiology is almost always in the news. But how reliable is its reporting? While a high profile for our discipline is welcome, John Heritage wonders if this comes at the expense of misrepresentation and public misunderstanding comment of the issues? titleBad reporting in the media is hard to swallow
A popular television news programme undergraduates, at least at Level 1, may synoptic module in which students recently ran a campaign based around struggle to identify which is correct, let develop their critical analysis. The most matters microbiological. My heart alone tell you what the ‘O’ in ‘O157’ popular examination question this year, sank as I watched the daily reports, means, but it is simply sloppy reporting and the one that attracted the highest based in a kitchen in ‘Middle England’, to use both without questioning which mean score, was a critical analysis of a showed how easily ‘bacteria’ can be is correct, and why. microbiology-themed newspaper article. spread by cleaning materials: assuming Later in the week, viewers were We must also learn to communicate all bacteria to be bad. I am not for one treated to a demonstration, again from better with journalists. Theirs is not an moment suggesting that we should a kitchen, of the difference between easy life; they need to become instant ignore the dangers posed by pathogenic ‘best before’, ‘sell by’ and ‘use by’ dates. experts on topics dictated by their bacteria that use food as a vector for To illustrate the point, among other editors. When journalists seek our infection or intoxication; nor do I items, the reporter pulled a yoghurt advice, we should not try to dodge our believe that unhygienic practices are to carton from the fridge that was beyond responsibilities to explain as clearly as be encouraged. What concerns me is its ‘sell by’ date and questioned the possible the science behind the story. the demonization and trivialization of family about whether they would Given the deadlines to which they microbes to grab viewers. eat it. Part of the question contained work, we should not be surprised that Further disappointment ensued on the, to my ears somewhat sneering, offers to check articles for veracity visiting the programme’s website, where suggestion that ‘experts say that eating are often not taken up. By improving I found that ‘The number of cases [of E. this is probably safe’. The irony here communication we will have a better- coli O157] in the UK has tripled in the is that yoghurt evolved as a method educated media, which, in turn, will last decade, jumping from 361 in 1991 of safe food preservation; a means of inform the public more accurately. to over 1,000 in 1997.’ Those figures are prolonging the shelf life of an otherwise over 11 years old! In 1997 human cases highly perishable foodstuff. John Heritage of E. coli O157 peaked, with over 1,087 Perhaps I am sensitive to the reporting Senior Lecturer, Faculty of Biological isolates referred to the Health Protection of science by the media. After all, I was Sciences, University of Leeds, Leeds Agency. There followed a sharp decline the ‘scientist(s) [who] warn of GM crops LS2 9JT (t 0113 343 5592; in referrals until 2002 when there were link to meningitis’, according to one e [email protected]) 595 human isolates, with a steep rise national newspaper – I believe this to be to 1,003 cases in 2003. It seems lazy a gross misrepresentation of my views. Further reading to report old data, particularly when This caused me significant problems Verocytotoxin-producing E. coli O157 the new data are even more interesting. for a few hours. I was, however, greatly strains examined by LEP reported to What is more, within two sentences the comforted by a piece of advice from the Health Protection Agency Centre for programme’s subsequent website refers a senior civil servant with whom I Infections. Isolations from Humans England both to ‘O157’ and ‘0157’. I am sure a spoke as the storm raged: ‘… today’s & Wales, 1982–2006. HPA [www.hpa.org. significant proportion of microbiology newspapers are tomorrow’s fish and uk/webw/HPAweb&HPAwebStandard/ chip wrappings’. HPAweb_C/1195733780833?p=120403 What is the answer? I believe we 1521097 (accessed 16.06.08)]. m ‘Today’s newspapers are tomorrow’s fish and chip wrappings.’ GustoImages / Science Photo need better education and better Please note that views expressed in Comment do not Library communication. At Leeds, we have a necessarily reflect official policy of the SGM Council.
156 microbiology today aug 08