Caister Academic Press New Books for 2009 www.caister.com Acanthamoeba Lactobacillus Real-Time PCR microbiologytoday Biology and Pathogenesis Current Technology and Author: Naveed Khan Molecular Biology Applications ... available now! c. 220 pp., February 2009 From Genomics to Probiotics Edited by: J. Logan, K. Edwards and N. Saunders ISBN: 978-1-904455-43-1 $310 / £150 Edited by: Åsa Ljungh and Torkel Wadström x + 284 pp., January 2009 The first comprehensive review of c. 220 pp., January 2009 ISBN 978-1-904455-39-4 $310 / £150 Acanthamoeba research to be published. ISBN 978-1-904455-41-7 $310 / £150 A comprehensive guide to the latest PCR The current state of research on every aspect An essential reference for all dairy of this organism, detailing major advances platforms, fluorescent chemistries, validation technologists, microbiologists and in areas such as genomics, molecular and software, data analysis, internal and external cellular biology, life cycles, geographical biotechnologists. Includes phylogenetics, controls and a wide range of applications: distribution, role in ecosystem, morphology, taxonomy, comparative genomics, functional clinical diagnostics, biodefense, RNA vol35|nov08 genomics, the intestinal microflora, surface motility, phylogenetics, genotyping, metabolism, expression studies, validation of array data, quarterly regulation of morphogenesis, host-parasite proteins, stress responses, interaction with mutation detection, food authenticity and interactions, the molecular and immunological the immune system, probiotics, anti-cancer legislation, NASBA, and molecular halotyping. basis of pathogenesis, methods of transmission, potential, and much more. Essential reading for magazine of epidemiology, clinical manifestation, diagnosis, all scientists involved with lactic acid treatment, new target development and drug or probiotic research and a recommended book the society resistance. 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The focus binary bacterial toxins, molecular epidemiology, c. 550 pp., April 2009 is on the topical and most relevant aspects metabolic networks, genetic knock-out systems, ISBN: 978-1-904455-42-4 $310 / £150 and the authors aim to give readers an insight surface structures, anti tumor potential, and Extensive publication on bacterial secreted into the current understanding of the subject antibiotic resistance determinants. proteins, secretory systems and their vital role and the future direction of research. Topics in bacterial pathogenesis. Immense value covered include strain variation and evolution, to all microbiologists, molecular biologists, hypervirulent strains, electron transport and public health scientists and other researchers Plant Pathogenic respiration, lipid biosynthesis, DNA repair, and professionals engaged in the study ... available now! of pathogenesis, drug design and vaccine oxygen signaling, sulphur metabolism, protein Bacteria development. A skillful selection of topics and secretion, the protein kinase family, and Genomics and Molecular Biology a panel of acknowledged experts as authors much more. A valuable reference text for all Edited by: Robert W. Jackson have ensured that this volume will become an microbiology laboratories and essential reading xii + 330 pp., January 2009 important reference source for many years to for all scientists and researchers involved with ISBN 978-1-904455-37-0 $310 / £150 come. mycobacteria. An invaluable, up-to-date summary of the molecular biology and genomics of plant pathogenic bacteria. Includes: bacterial Other Books of Interest evolution, diversity and taxonomy, adaptation, Agrobacterium, Leifsonia, Pectobacterium, • Plasmids: Current Research and Future Trends Pseudomonas, Ralstonia, Xanthomonas, and • Pasteurellaceae: Biology, Genomics and Molecular Aspects Xylella, MAMPs and innate immunity, virulence • Vibrio cholerae: Genomics and Molecular Biology factors, regulation, plasmids and bioinformatics. • Pathogenic Fungi: Insights in Molecular Biology • Helicobacter pylori: Molecular Genetics and Cellular Biology ... available now! • Corynebacteria: Genomics and Molecular Biology FULL DETAILS AT Microbial • Staphylococcus: Molecular Genetics • Leishmania: After The Production of • Archaea: New Models for Prokaryotic Biology WWW.CAISTER.COM • Legionella: Molecular Microbiology Biopolymers and • RNA and the Regulation of Expression: A Hidden Layer of Complexity • Molecular Oral Microbiology Polymer Precursors • Epigenetics Applications and Perspectives • Animal : Molecular Biology Edited by: Bernd H. 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Includes metabolic engineering. shedding light on photorhabdus ORDER FROM (UK/Europe): Caister Academic Press, c/o Book Systems Plus, BSP House, Station Road, Linton, Cambs CB21 4NW, UK an inside job – bdellovibrio Tel: 01223 894870 Fax: 01223 894871 http://uk.caister.com ORDER FROM (USA): Caister Academic Press, c/o ISBS, Inc., 920 NE 58th Avenue, Suite 300, Portland OR 97213-3786, USA nature’s experiment – bacteriophages Tel: 503 287-3093 Fax: 503 280-8832 http://usa.caister.com contents

vol35(4) regular features 159 News 202 Schoolzone 212 Hot off the Press 166 Microshorts 206 Gradline 215 Going Public 199 Conferences 209 Addresses 218 Reviews other items 196 National Subject Profiles 210 Obituary – Professor Chris Thurston articles 168 Microbial diseases of bees 184 An inside job: Bdellovibrio Travis Glare & Maureen O’Callaghan bacteriovorus Bees play an essential role in the world’s ecosystems, but Liz Sockett microbial diseases are posing a big threat to these vital These predatory bacteria hunt down and eat their insects. organisms.

172 Ancient fungal farmers 188 Bacteriophages: nature’s most of the insect world successful experiment Garret Suen & Cameron Graham Hatfull Currie Phages could well be the world’s biggest reservoir of Leaf-cutter ants not only grow fungi to eat. They unidentified genetic material. weed their ‘gardens’ and apply pesticides too. 192 1983: a vintage year for 176 Bacterial sequences in an discovery invertebrate genome Robin Weiss Julie Dunning Hotopp & Jason Rasgon Important findings about three major infectious diseases were made 25 years ago. Some arthropods and nematodes need their bacterial inhabitants to survive. 220 Comment: 180 Photorhabdus: shedding light Scotoma in contemporary on symbioses microbiology Susan Joyce and David Clarke Howard Gest Which amazing microbe can make nematodes glow in the Are some bacteria really ‘unculturable’? Probably not dark and yet kill certain insects? according to this writer.

Cover image Macrophotograph of the head of a worker honey bee (Apis mellifera). Dr Jeremy Burgess / Science Photo Library 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. 159 SGM; 203, 219 Comstock / Jupiter Images; 207, 213 Stockbyte; 209 Digital Vision / Getty claims of advertisers © 2008 The Society for General Microbiology––ISSN 1464-0570––Printed by Latimer Trend & Company Ltd, Plymouth, UK be guaranteed. Set your PhD on the right track with a New Student NEB Starter Pack news

FREE New SGM Prize Medal Surveys on Open Access Journals to all new research Stanley B. Prusiner accepts award for 2009 I represent SGM on the Biosciences Federation (BSF) Journals SGM is pleased to announce that Dr Stanley B. Prusiner, Committee. We have recently carried out surveys of BSF students* Director of the Institute for Neurodegenerative Diseases learned societies with journal publishing interests, and of at University of California, San Francisco, has accepted society members as authors and readers, to find out some of the invitation to be the first recipient of the Society’s new the wider implications of the open access (OA) movement, and Prize Medal. Amongst many awards, Dr Prusiner won the the state of awareness about the issues. This stems from the Nobel Prize in Physiology or Medicine in 1997 for his work desire of some research funders, such as the proposing an explanation for the cause of BSE (‘mad cow and Research Councils UK, that papers from work they have disease’) and its human equivalent, CJD. He coined the funded should be made freely available online at or shortly term prion, which comes from ‘proteinaceous infectious after the time of publication. The concern of publishers is that particle that lacks nucleic acid’ to refer to a previously an increase in the proportion of articles with OA could lead to undescribed form of infection due to protein misfolding. a loss of subscription income. Research funders have varied in their willingness to provide money for author-side payments for Dr Prusiner will deliver his Prize Lecture entitled Prion OA, to replace this possible loss of subscription income. There Biology and Disease on 1 April 2009 at the SGM Spring appears also to be confusion about what mechanisms different Conference at Harrogate (www.sgmharrogate2009.org.uk). funders have set up to provide OA funds. A special symposium on prion research will also take place on the same day. The first survey indicated that publishing societies earn surpluses on their journal sales, which they recycle to support student grants, educational activities, advocacy and public Back content awareness, and subsidized conferences. Publishing scientific journals is of course a global business: on average, around 90% of IJSEM goes of our institutional sales are ‘exports’. However, to take a UK online perspective, the 14 publishing societies in the survey received a total of £1,790k p.a. in subscription and other journal income The whole back content of from UK universities, but returned a total of £3,864k in direct the journal, which started support (grants, bursaries, conferences) and a further £2,299k out as the International in indirect support (educational and other charitable activities). Bulletin of Bacteriological If grossed up for all UK publishing learned societies, this clearly Nomenclature and Taxonomy would amount to a very substantial amount of support for our in January 1951, becoming education system and the students involved. It would be an International Journal of unfortunate example of the Law of Unintended Consequences Systematic Bacteriology in if this support was threatened by funders’ OA mandates which 1966 before being retitled were not matched by appropriate funding. REGISTER FOR YOUR STARTER PACK AT WWW.NEB.UK.COM International Journal of Systematic and Evolutionary Microbiology in 2000, is now In the second survey, it was clear that authors and readers Starter Pack Includes: *Starter Packs are available to all new research students who are not available on the HighWire site. This is a significant event in were much more in favour of OA through journals’ own online currently on the NEB UK mailing list. Quick-Load™ 100bp & 1kb DNA Ladders the history of microbial classification. It will greatly benefit sites or established bodies such as PubMed, than they were Please provide supervisor’s name and your name and departmental the scientific community to have this archive freely available of ‘self-archiving’ on personal or departmental web pages, or Prestained Protein Marker address when you place your request. worldwide without a journal subscription (current access institutional repositories. However, it was also clear that many ™ Crimson Taq DNA Polymerase A Cell Signaling Technology New Student Starter Pack is also available controls will remain for content that is less than 2 years authors and readers were confused about what the different Phire™ Hot Start DNA Polymerase from NEB UK. Please visit www.neb.uk.com for details. old). Papers will be available in fully searchable PDF format. types of OA and self-archiving were, and about the difference The archive will include hundreds of species descriptions between OA and online (subscription-controlled) journals. Offer closes 12th December 2008. Contents may vary from those shown above. This pack is only available in the UK for customers serviced by NEB (UK) Ltd (while stocks last). and many seminal articles in prokaryotic systematics and The BSF press release about the Committee’s report is available An NEB New Student Starter Pack is available to customers in Germany - please contact taxonomy that have never been available online before in at www.bsf.ac.uk/journals/BSF_OA_press_release_Final.pdf [email protected] (pack contents may vary in Germany). full text. IJSEM is the official journal of record for novel and the text of the full report is at www.bsf.ac.uk/journals/ Phire™ Hot Start DNA Polymerase is manufactured by Finnzymes, Oy. prokaryotic taxa and is published by the SGM on behalf of BSF_survey_report_July_2008_FINAL.pdf. The Committee the International Committee on Systematics of Prokaryotes. has also prepared a guide for authors about background issues NEW ENGLAND The back content of Journal of General is already and UK funders’ policies, which is at www.bsf.ac.uk/journals/ online and that of Microbiology and Journal of Medical journals_authors’guide.htm ® Microbiology will be available soon. Ron Fraser, SGM Chief Executive New England Biolabs (UK) Ltd, Knowl Piece, Wilbury Way, Hitchin, Herts SG4 0TY BioLabs Call Free: 0800 318486 Call Free (Technical): 0800 6522890 Fax Free: 0800 435682 email: [email protected] the leader in technology microbiology today nov 08 159

NEBStarterPackAdMBT08.indd 1 30/9/08 11:01:36 am Nobel Prize Council – new structure New elected members of Council in Physiology A Special Resolution to amend the Society’s Articles of Association was passed at the The following will serve on Council for 4 years from 9 September 2008: or Medicine AGM on 9 September 2008. This will enable implementation of the changes to the SGM’s Professor Mark Harris governing Council that were described on p. 106 of the August issue of Microbiology I graduated with a first class honours degree in Biological Sciences from Plymouth Polytechnic in 2008 Today. With effect from the AGM to be held in 2009, Council will consist of six Officers 1983 and then undertook my PhD at the Institute of Virology in Glasgow, working with Ron Hay on This year’s Nobel Prize and the number of Ordinary Members will be reduced to six over the period from then adenovirus DNA replication. After a postdoc at the NERC Institute of Virology in Oxford working on rewards the discoveries to September 2011. Much of the business will be transacted by subcommittees. The new baculoviruses with Bob Possee, I moved back to Glasgow to the Department of Veterinary Pathology, of two viruses causing Articles are available on the website at www.sgm.ac.uk/about/articles.pdf severe human diseases. switched from DNA to RNA viruses, and began working on the Nef protein of HIV-1 in the lab One half will go to Harald of Jim Neil. After 5 years as a postdoc I obtained an MRC Senior AIDS Research Fellowship and Council – July meeting highlights subsequently moved to Leeds in 1997, taking up a Lectureship post in what was then the Department zur Hausen (German of Microbiology. Whilst retaining an interest in HIV, my lab has moved over almost entirely to the Cancer Research Centre, The SGM Prize Medal in The Gambia where Sir Howard and his study of hepatitis C . My research is focussed both on basic mechanisms of virus replication as Heidelberg, Germany) Council devoted a significant amount of wife Kira carried out charitable work. well as virus–host protein interactions. Our funding comes from a variety of sources including research for his discovery of time to careful consideration of nominations SGM finances councils, the Wellcome Trust and industry. I have always been a strong supporter of the Society – I am human papilloma viruses for the new SGM Prize Medal to be Council approved the membership fees currently an Editor of Journal of General Virology and serve on the Virus Division committee. I welcome causing cervical cancer. awarded in 2009. It was agreed that the and SGM journal subscription prices for the opportunity to make a further contribution to SGM activities as a member of Council. The other half will be President should approach Dr Stanley 2009. These will increase by on average shared between Françoise Prusiner and he has been pleased to accept 4%. Dr Gary Rowley Barré-Sinoussi (Institut (see p. 159). A more detailed appreciation Gary Rowley is a lecturer of bacterial pathogenesis within the School of Biological Sciences, University Laboratory-based microbiology Pasteur, Paris, France) and of Dr Prusiner’s work will be published in of East Anglia. He did his PhD with Professor Mark Roberts, University of Glasgow, and then moved Luc Montagnier (World projects for medically qualified a future issue of Microbiology Today. graduates to the Institute of Food Research, as a postdoc in Professor Jay Hinton’s Laboratory. He moved to UEA Foundation for AIDS Honorary Membership The Treasurer announced that there will be in 2007 to take up a Faculty position. His research interests focus on the environmental regulation of Research and Prevention, a new grant scheme to support medically bacterial virulence using the intracellular pathogen Salmonella Typhimurium as a model organism. Paris, France) for their Council has bestowed Honorary qualified graduates taking up a career in Recent work has focused on investigating the role of the envelope stress response in pathogenesis and discovery of human Membership of the Society on Dr Volker medical microbiology. The grants will fund the mechanisms that Salmonella uses to detoxify nitric oxide. immunodeficiency virus. ter Meulen, Professor Emeritus for Virology the consumables part of short-term research See the article by Robin and Immunology, Universität Würzburg, and projects in a ‘home’ hospital or another host Weiss on p. 192. President of the ‘Leopoldina’, Gesellschaft für Naturforscher und Ärzte, Sachsen- laboratory. Applications to the scheme are Congratulations to … Deaths Anhalt, in recognition of his outstanding invited for 2009; see www.sgm.ac.uk/ 2008 contributions to the molecular biology of grants SGM Education Officer Dr Sue Assinder on University’s Faculty of Science. Professor The Society notes her appointment as Director of Education, Hunter has been Professor of Molecular with regret the deaths of: Address Book paramyxo- and coronaviruses and chronic Retiring members of Council virus–host relationships, as well as for his Liverpool School of Tropical Medicine. Microbiology for the past 13 years. A copy of the latest edition The President thanked the retiring Professor Peter Gilbert engagement in SGM activities, science Professor David Baulcombe (University of Professor Richard James (Head of the of the Society’s Address member of Council, Professor Bert (University of Manchester), management and international microbiology Cambridge) on winning the 2008 Albert School of Molecular Medical Sciences, Book, giving contact details Rima, Queen’s University, Belfast, for his a distinguished expert on promotion. Lasker Basic Medical Research Award. Along ) on being of members, should have highly appreciated input to the activities biofilms and a member with Victor Ambros and Gary Ruvkun, the awarded the SfAM Communications Award been enclosed with your Professor Sir Howard Dalton of Council. He also noted the significant since 1974. Professor contributions of Professors Iain Hagan award honours the scientists who revealed 2008 for raising the profile of his applied mailing of this magazine. Council was pleased to hear that SGM had Gilbert was due to speak at and Rick Randall, who had resigned from an unanticipated world of tiny RNAs that microbiology work to the public. If you did not receive one, been remembered in the will of former the recent SGM meeting in Council earlier in the year, before the end regulate gene activity in plants and animals. please get in touch with President, the late Professor Sir Howard Douglas Kell, Professor of Bioanalytical Dublin and the programme of their terms of office. Baulcombe made his discovery whilst the Membership Office Dalton FRS. The bequest of £2,000 will be Science, University of Manchester, who was changed so that probing how plants defend themselves ([email protected]). used to promote microbiological projects Ulrich Desselberger, General Secretary is to be the new Chief Executive of the Professor Michael Brown against viruses. Biotechnology and Biological Sciences could deliver a tribute. A Professor Nigel L. Brown, former Director Research Council. He is a leading figure in reception was also held to SGM Staff of Science and Technology at the BBSRC the world of systems biology. honour Peter’s memory. who has moved to the University of Congratulations to Stefan Sidorowicz and his wife Helen on the birth of a baby daughter Laura in July, and to Nicolas Professor Hilary Lappin-Scott (University of Professor Christopher Edinburgh as Vice-Principal and Head of the Fanget and his wife Amina on the birth of a baby son Bilal in October. Exeter and SGM Scientific Meetings Officer) Thurston, a member since College of Science and Engineering. Farewell to Gemma Sims who worked here for a year to develop a microbiology teaching resource to meet the who will be taking up a new post at Bangor 1972, died in August after a requirements of the new A levels. This should be ready for distribution to UK schools early in 2009. We wish Gemma well Professor Iain Hunter (University of University in January 2009 as Pro Vice long illness. A full obituary in her new post as teacher of biology at Leighton Park School in Reading. Strathclyde) on his new post as Dean of the Chancellor for Research. appears on p. 210.

160 microbiology today nov 08 microbiology today nov 08 161 Project1:Layout 1 7/1/08 10:10 Page 1

Grants NEW! – Medical Trainee Support Grants Scientific Meetings Travel Grants Funding for medical microbiology trainees (during This scheme is open to a range of early-career foundation or specialist training) to carry out short lab- microbiologists resident within the EU, ranging from based projects on a microbiological topic. The grant covers postgraduate students through to first postdocs and newly a contribution towards consumables costs only. Closing appointed lecturers. Funding is tiered according to the dates: 20 March and 25 September 2009. location of the meeting. The maximum grants are: UK (or country of residence) – £200; within Europe – £350; Rest Student Schemes of World – £500. These grants may also be used to support GRADSchool Grants attendance on short courses. Postgraduate Student Associate Members registered for a President’s Fund for Research Visits PhD in a UK university can apply for funding to support the Grants are available to support short research visits full cost of course fees for a GRADschool. Students funded (1–3 months) by early-career microbiologists resident by Wellcome Trust, BBSRC, NERC, MRC or EPSRC are within the EU, ranging from postgraduate students through entitled to a free place on a GRADSchool course and should to first postdocs and newly appointed lecturers. Funding is not apply to this scheme. Applications, on the appropriate limited to a maximum of £3,000. Retrospective applications form, are considered throughout the year but must be will not be accepted. Closing dates: 20 March and made before booking a place on a course. 25 September 2009. Student Meetings Grants Public Understanding of Science Awards Grants contribute towards travel, registration and Are you planning any projects to promote the public accommodation expenses for attendance at one SGM understanding of microbiology? Have you got a National meeting each year. Applicants must be Postgraduate Science Week event in mind? SGM can help. Grants of Student Associate Members resident and registered for a up to £1,000 are available to fund appropriate activities. PhD in an EU country or Undergraduate Members based at Applications are considered on a first come, first served a university in the UK or Ireland accepted to present work basis throughout the calendar year. the meeting. Closing date for Edinburgh: 27 March 2009. Elective Grants SGM has a wide range of grant schemes to support Funding for medical/dental/veterinary students to work microbiology. See www.sgm.ac.uk/grants for details on microbiological projects in their elective periods. Closing and closing dates. dates: 20 March and 25 September 2009. Enquiries should be made to the Grants Office, SGM, Marlborough House, Basingstoke Road, Spencers Wood, Vacation Studentships Reading RG7 1AG (t 0118 988 1821; f 0118 988 5656; The 2009 scheme is now open for applications. As e [email protected]). described on p. 208, the scheme offers a great opportunity for undergraduates to work on microbiological research projects during the summer vacation before their final year. Lister Institute Research The awards, which are made by competition, aim to give Prizes 2009 students experience of research and to encourage them Applications are now invited applicant’s research proposal to consider a career in this area. The studentships provide from young clinicians and and track record. Applications support at a rate of £185 per week for a period of up to biomedical scientists for the may be in any area of 8 weeks. An additional sum of up to £400 for specific 2009 Lister Research Prizes. biomedical science or related research costs may also awarded. Applications must be The Prizes offer £200,000 to areas. Further information from SGM members on behalf of named students. be spent on the recipient’s and forms are available from research in whatever way The closing date for applications is 13 February 2009. the Lister’s website (www. they choose, other than for lister-institute.org.uk) or Student Society Sponsored Lectures personal salary, and therefore directly from the Institute’s These cover the travel and other expenses of up to two provide unfettered research Administrator (secretary@ speakers on microbiological topics per Society each year funding. Prizes will be lister-institute.org.uk). Closing at student society meetings. allocated on the basis of the date: 5 December 2008.

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There’s a lot on Project1:Layout 1 2/10/08 11:09 Page 1 it for you... • Culture media database and Centre for Bioscience – The Higher Education Academy product guide National Teaching • Articles and technical Individual awards for 2008 have been made to two SGM members, Dr Annette Cashmore (University of Leicester) and manual Dr Julian Park (University of Reading). The awards recognize and celebrate individuals who make a significant impact on the • Download quality student learning experience. certificates Report on first-year undergraduate practicals • Request a quote This report is the outcome of a workshop held in April 2008 by the Centre to discuss first-year undergraduate work in the • Place an order biosciences. Participants shared experiences of delivering practical classes where problem-solving, research investigation, • Sign up for regular creativity and innovation are key features. Amongst several disciplines, the report describes five microbiology investigations which can be downloaded from the Centre website (www.bioscience.heacademy.ac.uk/events/themes/1styrpracticals.aspx).

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Membership category Annual Additional subscriptions for publications (print only) www.labm.com subscription Microbiology JGV IJSEM JMM £ US$ £ US$ £ US$ £ US$ £ US$ Ordinary 54 108 106 212 106 212 106 212 60 120 Associate Postgraduate Student Retired 25 50 48 96 48 96 48 96 48 96 Microbiologist with annual salary <£26.5k Undergraduate 10 na na na na na na na na na School 10 na na na na na na na na na Corporate Tier 1 350 na na na na na na na na na Tier 2 500 na na na na na na na na na For airmail despatch of Microbiology Today, add £19/US$36 to subscription. Members are reminded that their 2009 subscriptions are due for payment by 1 December 2008. As in previous years, no journal or meetings information will be despatched to members who are in arrears, and there will be no guarantee of provision of back numbers of journals for members who pay their subscription late. Payment against invoice subscription notice and returned it to the membership Invoices were despatched recently to all members who pay office by 10 November 2008. However if you have missed by this method. If you did not receive one, please inform this deadline, your amended notice will be accepted if the Membership Office. it is submitted immediately. New secure online credit card renewal payment Please note If you pay against invoice, you can renew your subscription Continuous credit card payments are no longer available. online via the SGM website (www.sgm.ac.uk/members) Alternative methods are by direct debit (for UK bank with either a credit or debit card. Please see your invoice account holders) or one-off credit/debit payment online. for details. Income tax relief on membership subscriptions Payment by direct debit Members who are liable for UK income tax are reminded Subscription notices were despatched recently to all that their annual subscriptions to the Society have been members paying by direct debit. To continue your present approved by the Inland Revenue as qualifying for income status and journal requirements, no further action is tax relief. Any member who would like further information necessary. To change your membership status or journal or has difficulty in obtaining this relief should contact the requirements for 2008, you should have amended your Chief Executive ([email protected]).

microbiology today nov 08 165 microshorts

Lucy Goodchild takes a look at some stories Historical research that have hit the headlines recently. highlights The entire back-catalogue of IJSEM is now GM cotton Scientists discover online – here’s a snippet from the content. reduces pest ‘virophage’ 2005: Scientists identify olive fly symbiont after 96-year search Scientists have discovered a virus that can be infected by another damage virus, according to research published in Nature. The giant virus, In 1909, Petri described an example of A 10-year study by scientists called mamavirus, infects amoebae. When researchers from the hereditary symbiosis in the olive fly after at the Chinese Academy of Université de la Méditerranée in Marseille, France, studied the observing unidentified bacteria under a Agricultural Sciences in Beijing virus using an electron microscope, they discovered an associated microscope. He suggested that the has revealed that the benefits virus, which they called Sputnik. This smaller virus is incapable symbiont might be Bacterium (Pseudomonas) of genetically modified cotton of infecting cells on its own. As it has only 21 genes, Sputnik savastanoi, which causes olive knot disease, extend further than had hijacks mamavirus machinery in order to infect cells, so it has as it could be isolated from the larvae. previously been anticipated. been dubbed a ‘virophage’. By hijacking it, Sputnik reduces Petri postulated that the bacterium might Cotton modified with a gene the infectivity of mamavirus. Giant viruses are able to infect be unculturable, a speculation that has from Bacillus thuringiensis climatically important plankton, which produce dimethylsulfide. remained the case for almost a century. In to make its own insecticide Therefore, by reducing the infectivity of mamavirus, Sputnik virus 1965, Buchner analysed the bacterium, was able to resist attack could potentially affect climate change. m Two variants of the Harlequin ladybird. Sheila Terry / Science Photo Library followed closely by Hagen in 1966, but from its biggest pest, the www.nature.com/news/2008/080806/full/454677a.html neither disputed Petri’s designation. cotton bollworm. The study, In 2005 Capuzzo et al. from Università di published in Science, showed Ecologists find invasive ladybird’s Padova and Università di Udine in Italy that the GM crop resulted in proposed the novel species ‘Candidatus a ‘dramatic long-term decline’ Bar-coding midges to stop Achilles’ heel Erwinia dacicola’. By sequencing the entire in damage. The pest-resistant The Harlequin ladybird was introduced to the UK 4 years ago as a form of biological spread of bluetongue 16S rRNA gene, they were able to show crop even reduced the control of aphids and it has since become an invasive species, posing a major threat to Scientists have developed a method of genetically ‘bar-coding’ marked similarity with enterobacterial cotton bollworm population native ladybirds. The Harlequin is larger and more aggressive than native ladybirds and is biting midges that could help prevent the spread of bluetongue lineages, with close matches to Erwinia in neighbouring fields, a also resistant to a deadly , Beauveria bassiana, that threatens native species. Although disease. Researchers from the University of Aberdeen collected 1 persicina and Erwinia rhapontici. m Cotton bollworm caterpillar. Nigel Cattlin / surprising result Harlequin ladybirds do not succumb to infection with the fungus, the number of eggs they million midges in 37 light traps SPL for the researchers. lay after exposure to the pathogen is dramatically reduced. However, because the fungus is Adults of the olive flyBactrocera oleae, the in Scotland between late 2007 so deadly to the already endangered native ladybirds, it is not a viable means of controlling most important pest of olive trees, carry the c Biting midge (Culicoides sp.) feeding on www.timesonline.co.uk/tol/news/uk/ and early 2008. They used a human blood. Sinclair Stammers / SPL science/article4783078.ece the invaders. Speaking at the British Ecological Society’s conference at Imperial College bacteria in an organ called the oesophageal pioneering DNA test to identify London, scientists say they are now looking at semiochemicals, which the insects use for bulb. The bacteria replicate rapidly and the midges Culicoides obsoletus, communication, to control Harlequin ladybirds. form masses that reach the midgut. The C. chiopterus, C. dewulfi and C. Vaccines for bacteria www.alphagalileo.org/index.cfm?fuseaction=readrelease&releaseid=531792 mother transmits the bacteria to her eggs scoticus, and create a map of during oviposition, then the bacteria Bacteria used in industrial processes could be protected from their geographical distribution multiply inside the larvae. By rearing virus infections using a kind of vaccine, according to research in Scotland. In southern Mosquitoes lured by odourless the flies on artificial media, the scientists published in Science. German researchers at Wageningen University Europe, Culicoides imicola carries observed that the progressive loss of the uncovered the mechanism some bacteria use to defend themselves various strains of bluetongue chemical symbiotic bacteria resulted in lower vitality in the long term against potentially lethal viruses: this has potential virus and is responsible for its Catching mosquitoes is a key part of the low doses and extensive field research in and fertility of the flies. Furthermore, flies to protect good bacteria and target pathogenic species. Bacteria spread across the continent. surveillance of vector-borne diseases like Brazil showed it is as effective as the lure lacking the symbionts were more prone to insert pieces of viral DNA into their own genome. The ‘adopted’ However, the virus has been West Nile virus, encephalitis and lymphatic currently used. Gravid female traps target infection by other microbial species. segment is used like a snapshot to help the bacterium remember found in different midge species filariasis. People who monitor the mosquito mosquitoes that have fed on blood and the virus and kill it during a subsequent infection. The researchers in the UK and scientists are traps, and even those who live near them, are ready to lay eggs. Because mosquitoes Although the evidence suggests a symbiotic identified six bacterial proteins involved in the defence system; one tracking them to gauge the have to suffer the highly offensive smell lay hundreds of eggs at a time, catching relationship between the bacteria and cuts the ‘adopted’ segment out of the bacterial genome and helps speed at which the virus might of the attractants currently in use. Now, females ready to lay can reduce the number the olive fly, the bacteria still could not the other five proteins to compare it to the DNA of the invading spread if it reaches Scotland. scientists at the University of California, of mosquitoes capable of spreading be cultured. However, the availability of virus. This mechanism could be utilized to protect industrially The study revealed that midge Davis in the USA have developed a diseases dramatically. The research could modern DNA-based methodologies allowed important bacteria from being attacked by bacteriophages. It numbers were dependent low-cost attractant that lures mosquitoes play a key role in surveillance and control the researchers to succeed where Petri had could also be targeted to combat antibiotic-resistant bacteria; by on climatic and geographic without making humans hold their programmes for Culex mosquitoes. not: to clarify the systematic placement of the microbes and to trace their connections deactivating the system, bacteria would be left defenceless and conditions. noses; it is odourless to us, but enticing www.newspostonline.com/sci-tech/killing- susceptible to bacteriophage attack. www.alphagalileo.org/index.cfm?fuseact to mosquitoes. The synthetic mixture mosquitoes-without-raising-a-stink-just-became-a- to related species. www.alphagalileo.org/index.cfm?fuseaction=readrelease&releaseid=531517 ion=readrelease&releaseid=531840 contains trimethylamine and nonanal in reality-200808313789 IJSEM 55, 1641–1647 (doi: 10.1099/ijs.0.63653-0)

166 microbiology today nov 08 microbiology today nov 08 167 Microbial he humble bee has a special collapse of bee colonies. The name place in our lives. Essential describes the symptoms of diseased 1 for pollination of many plants, brood; infected cells become dis- diseases including food crops, the coloured, sunken and there is a char- provider of honey and royal acteristic smell. Adult bees are not jelly and many other products, affected. This disease has traditionally Tbees are important to the economies been treated with the antibiotic oxy- of countries and, as ecosystem tetracycline, but some bacterial strains of bees service providers, have few equals have developed resistance to this and among insects. There is a quote, often the disease is now increasing in preva- attributed to Einstein, suggesting that lence around the world. Although the if all the bees disappeared then disease was first described over 200 humans would follow within 4 years. years ago, much is still unknown about While this is perhaps an overstate- this infection. A German research team ment, a recent estimate of the has only recently discovered how the contribution of insect pollination, bacteria kill larvae, by building up to 2 mainly by bees, to agriculture was very high numbers in the gut before €153 bn. bursting into the haemocoel, causing There are many threats to bee death. survival, including the risk of disease European foulbrood (EFB) is caused caused by micro-organisms. The vast by the non-spore-forming bacterium majority of our knowledge of bee Melissococcus (=Streptococcus) plutonius. diseases focuses on the honey bee, Apis Unlike AFB, EFB usually affects mellifera, although there are actually unsealed brood, and the recently dead over 20,000 species, both stingless larvae present as watery and yellowish and stinging, from those with solitary brown cadavers twisted inside the cell. lifestyles to complex societies such as Despite the importance of EFB, the honey bee hives. disease is poorly understood, but like Viruses, fungi, protozoa and bacteria AFB, has increased in prevalence in are all known to cause infections in recent years. 3 bees, sometimes leading to collapse of Of the fungi known to infect bees, colonies, and causing serious threats species of the fungus Ascosphaera are to the bee-keeping industry. Bees have the most common. Ascosphaera apis is two distinct life forms, brood (egg, larva the causative agent of the well known and pupal stages which develop within chalkbrood disease in honey bees, so the hive) and adult. Most diseases are called because of the chalky appear- specific to just one of these life stages. ance of infected brood. Chalkbrood is While the list of diseases is quite long, usually considered a minor disease of only a few are of serious concern to bees, as is stonebrood, caused by the apiculturists. fungus Aspergillus. Bees come under attack Viruses can also cause devastation Major disease of bees in bee colonies. At least 18 types of Various evocative names, based on the viruses have been found infecting from a wide range of microbes. visual symptoms of diseased bees, are honey bees alone. Going by some m 1. Sunken brood capping with holes suggests used to describe the most problematic delightfully descriptive names (e.g. American foulbrood (AFB). Zachary Huang, Michigan Travis R. Glare and Maureen diseases, for example foulbrood, sac- deformed wing virus, chronic paralysis State University, USA brood and chalkbrood. virus, acute bee paralysis, sacbrood 2. A dead larva killed by AFB usually forms a ‘false American foulbrood (AFB) is caused virus and black queen cell virus), tougue’ pointing upward. M.V. Smith, University of O’Callaghan consider the role of bee by the spore-forming bacterium Paeni- these viruses range from non-lethal to Guelph, Canada bacillus larvae. The disease was first causing significant mortality in nests. 3. Larvae showing typical European foulbrood (EFB) symptoms. These larvae show yellow streaks. M.V. Smith, diseases in the worldwide decline of described in 1769. AFB is probably One of the more interesting aspects University of Guelph, Canada the most virulent disease of honey bee of viral disease is that many infections b A honey bee (Apis mellifera) feeding. Dr John brood and is capable of causing the cause no obvious symptoms much of Brackenbury / Science Photo Library these key ecosystem providers.

168 microbiology today nov 08 microbiology today nov 08 169 1 2 3 4

m 1. Chalkbrood, whereby the larvae become mouldy with white (adult) honey bees on several continents, especially North detected in the semen of honey bee others. Some strains of bees are capable understanding of the cause of CCD, hyphae, then hardened to be similar to pieces of white chalk. This America. The sometimes startlingly high mortality rates have drones, suggesting that mating may of recognizing diseased brood well no cure will be possible, but when disease is mostly considered a stress disease, only occuring in weak, or in otherwise stressed colonies. M.V. Smith, University of Guelph, not been attributed to a particular cause. Several recent spread some disease both horizontally before it is a threat to the hive, and the factors are known, many large and Canada studies suggest that some colony collapse is caused by a and vertically. can be remove diseased individuals. In some small mitigations can be used. m 2. Close-up of the head of a larva killed by Sacbrood. M.V. Smith, combination of disease and the parasitic attentions of Varroa transmitted in bees and sometimes cases, the task of disposing of diseased The risk is that with increasing University of Guelph, Canada mites. Various studies have found that prevalence of viral in bee products, prompting many insects falls to specialist ‘undertaker pressure from civilization, bees could c 3. A honey bee (Apis mellifera) with two Varroa jacobsoni mites on and protozoan diseases is higher in Varroa-infected­ hives countries to closely regulate the bees’ that appear to be old workers. suffer increasingly from threats and its thorax. Maryann Frazier / Science Photo Library and Varroa is thought to be capable of acting as a vector importation of bees and honey. Bees are also assisted in resisting dis- stress, including increasing prevalence c 4. Coloured SEM of a Varroa sp. honey bee mite. Steve Gschmeissner for pathogenic microbes. In some cases, viral diseases that ease by propolis, present in the of disease. A better understanding of / Science Photo Library do not usually cause high mortality are rampant in hives How do bees defend plant resins collected by honey bees bee dynamics and the development with Varroa or have been associated with CCD. Israeli Acute themselves from disease? and used as a sealant in the hives. of mitigations is urgently required. the time. Kashmir bee virus can persist in bee populations Paralysis Virus (IAPV) was recently found to be the most The high density populations and Propolis is known for its antimicrobial causing no obvious symptoms, only to explode into lethal consistent indicator of CCD, as well as Kashmir bee virus conditions within the bee colony properties. Travis R. Glare & Maureen infections, possibly triggered by bee stress factors such as and Nosema spp. However, no causal link has been made (enclosed, moist, dark, poorly venti- O’Callaghan attack by the Varroa mite. Varroa mites are parasites on honey between IAPV and CCD. As with all living things, stress lated) are ideal for the outbreak What hope is there for AgResearch, Lincoln, Private Bag bees and have spread around most of the world, causing increases the susceptibility of the host to a pathogen, and and spread of disease. Fortunately, the future? 4749, Christchurch, New Zealand significant losses in hives as well acting as vectors for some if bees are under stress, disease can be more debilitating. because bees are constantly exposed With increasing prevalence of disease, (t +64 3 321 8825; e travis.glare@ viruses. Virus infections can be hard to detect and diagnose, Whether CCD is only caused by the interaction between to pathogenic micro-organisms, they unexplained disappearance of bees on agresearch.co.nz) as symptoms, if any, resemble other mortality causes. a specific stress such asVarroa and some diseases, or have evolved strategies to resist infec- some continents and the emergence widespread interaction between a number of stresses is tion. The cuticle of bees acts as a barrier of new diseases, bee populations are Emerging diseases unclear. Combinations of stresses could include multiple to penetration, and immune system- under threat. Fortunately, increasing Further reading Microbes are constantly evolving, leading to the emergence diseases. Using molecular techniques, several studies have based defence can prevent infection sophistication of research methods is Bailey, L. (1968). Honey bee pathology. of new strains with novel pathogenic abilities. For example, shown multiple diseases infecting single bees. So diseases, of many minor pathogens. However, allowing unprecedented understand- Annu Rev Entomol 13, 191–212. some honey bee diseases appear to have widened their host some of which may not normally cause death, could act the recent completion of the honey ing and insights into bee pathology Chen, Y.P. & Siede, R. (2007). Honey range in recent years. Protozoa of the genus Nosema infect together to kill. Additionally, nutritional stress can exacerbate bee genome sequence has shown that by allowing detection of cryptic bee viruses. Adv Virus Res 70, 33–80. many invertebrates, and individual species are typically the incidence of pathogens. they have only about a third of the infections, generation of epidemiolo- Cox-Foster, D.L. & others (2007). A quite limited in their host range. Nosema apis has long been number of known immunologically gical data and detailed understanding metagenomic survey of microbes in recognized as causing one of the most important diseases How do diseases spread? related genes when compared to flies of bee–pathogen interaction. With honey bee colony collapse disorder. in adult honey bees, infecting the guts of adult bees. How- How diseases spread between individuals is still largely or mosquitoes, suggesting that bees increasing understanding comes a Science 318, 283–287. ever, Nosema ceranae, thought to infect only the Asiatic or unknown. Both horizontal transmission (where viruses are rely less on individual immunity than better appreciation of the role of dis- Evans, J.D. & others (2006). Immune Eastern honey bee, Apis cerana, has recently been shown transmitted among individuals of the same generation), and most insects. ease and methods for reducing impact. pathways and defence mechanisms in to infect the European honey bee, A. mellifera. Evidence vertical transmission (where the disease is passed from Bees, in common with a number of For example, the presence of Kashmir honey bees Apis mellifera. Insect Mol Biol is emerging of recent spread of N. ceranae in honey bee queens to their offspring) are known. Modern molecular- other social insects, have well devel- bee virus has been detected in the 15, 645–656. populations around the world since around 1998. There based techniques have contributed significantly to our oped behavioural responses to combat UK, despite never being identified as Paxton, R.J. & others (2007). Nosema is ongoing risk that other highly virulent diseases of honey understanding, allowing investigation of whether pathogens disease. These behavioural responses a cause of infection in UK bees based ceranae has infected Apis mellifera in bees will emerge. are present inside eggs, and by establishing the relatedness are collectively known as hygienic on visual symptoms. This suggests a Europe since at least 1998 and may of occurrences of disease in different hives. It is obvious behaviour and include recognition and potential non-lethal role for this virus. be more virulent than Nosema apis. Bees under stress how some diseases spread; the presence of large numbers removal of diseased brood by worker Detection of virus associated with Apidologie 38, 558–565. There is still so much we don’t know about how combinations of spores, whether fungal, bacterial or protozoan, inside a bees. Bee species, and even different CCD may also lead to a cure. Wilkins, S. & others (2007). The of microbial diseases, parasites, pollution and urbanization hive will contaminate brood and/or workers that come in hives of the same species, differ in their Separating the various factors affecting incidence of honey bee pests and are affecting bees. Colony Collapse Disorder (CCD) is the contact. However, some more unusual routes have also ability to perform hygienic behaviours, bee colonies will allow the causal diseases in England and Wales. Pest name given to the recent widespread mortality of worker been demonstrated. DNA from viral pathogens has been with some colonies far superior to agents to be directly treated. Without Manage Sci 63, 1062–1068.

170 microbiology today nov 08 microbiology today nov 08 171 Ancient fungal farmers Not only humans practise agriculture. of the As Garret Suen and Cameron R. Currie describe, ants have amazing systems of insect growing fungal crops in their ‘gardens’ too.

b A worker of the leaf-cutting ant Acromyrmex octospinosus tends to her fungus garden. These ants grow bacteria on their body and use the antibiotics the bacteria produce to protect their world gardens against infection from invading pathogens. Heidi Horn ake a stroll through a rain forest in South America not cut leaves, but instead collect fruit, the colony produces male and female and you might find yourself walking in a river, not leaf litter and decomposing organic winged reproductives called aletes, of water, but of leaves. Leaf-cutter ants swarm in the material, such as caterpillar dung, to which mate in a spectacular display underbrush, carrying their precious cargo back to grow their fungus. of flying ants. The newly-mated queens their nest with an apparent single-minded deter- Fungus-growers also have diverse then go on to found new colonies. mination. This conspicuous behaviour has made colony sizes, with some species con- Young queens transport a small piece Tthese ants one of the most dominant herbivores in the Neo- taining only a few hundred workers, of the fungus garden in a special organ tropics, and one of the most successful social insects in nature. while many leaf-cutting ant species known as an infrabuccal pocket when A closer look at the ants reveals that they are ancient farmers, can contain upwards of 5 million. All they leave the nest for their mating having developed the secret of agriculture over 50 million species, however, follow the same life flights, and thus ensure that they can years ago. Using their freshly-cut leaves, they incorporate cycle. Organic material is brought into successfully start a fungus garden in them into gardens where they grow a specialized fungus the colony by foragers and is then the new colony. that they consume for food. This relationship between ant processed to form a garden matrix and fungus has been described as a breakthrough in animal where the fungus grows. New material Garden microbiology behaviour, and parallels the practice of sustainable agriculture is continuously incorporated into the Until about a decade and a half in humans, arguably the most important development in gardens in order to propagate the ago, research on fungus-growing ants human civilization that, in our opinion, resulted in the fungus, and old material is removed focused primarily on the ants and their dominance of humans on planet Earth. by the ants and placed in special refuse foraging behaviour. It wasn’t until the Leaf-cutting ants are the most highly-derived group of ants dumps away from the colony. In many early 1990s that this focus shifted to that practice fungus growing. A total of four other fungus- groups of fungus-growing ants, the the fungus gardens and their associated growing ant agricultural systems have been described, fungus produces specialized packets microbial communities. Since the spanning over 200 different species of ants, each based on of nutrients called gongylidia that the ant gardens are maintained in soil the type of fungus grown and the material incorporated into ants eat and feed to their developing chambers, they are routinely exposed their gardens. The vast majority of fungus-growing ants do brood. At the start of the rainy season, to a number of potential pathogens

172 microbiology today nov 08 microbiology today nov 08 173 Farming ants The fungus feeds on a supply of freshly cut leaves brought by the farming ants.

Acromyrmex

Lepiotaceae

Fungus crop The fungus crop provides the ants with nutrient-rich food.

b Fig. 1. The fungus-growing ant system. The ants grow a fungus crop for food in gardens, which often get attacked by invading crop pests. The ants deal with these attacks by growing bacteria on the surface of their bodies that produce antibiotics capable of stopping the pest. Cara Gibson & Angie Fox

Bacteria Crop pest . Fig. 2. A fungus garden from a 1-year-old Like human farmers, the ants can’t Bacteria that grow on the surface of ants’ bodies colony of Acromyrmex echinatior. Note that produce an antibiotic that attacks the crop pest. keep their crops free of disease They stop the pest from destroying the crop. organisms. An invading pest called many of the garden workers are covered Escovopsis infects the fungus crop. with the antibiotic-producing bacteria. David R. Nash Escovopsis c Fig. 3. Rivers of leaves. Foragers of the leaf- cutter ant Atta cephalotes bring freshly-cut leaves back to their nest. Alexander Wild

that could infect and overtake a garden. Mutualism happens In fact, many of the ant colonies The interaction between the ants and their fungus crop, infects the gardens of the ants they are associated with. do become overgrown by fungal and the ants and the bacteria is known as a mutualistic Interestingly, the tight association between ant, bacteria and pathogens, often resulting in the death relationship. In general a mutualism is established when pathogen will sometimes result in the pathogen winning. of the colony. Intensive sampling of both members of the interaction derive a benefit from the This interplay has been described as a chemical ‘arms race’ the fungal communities within the gar- association. In the ant–fungus mutualism, the ants obtain between the bacteria and fungus, with one side beating the dens revealed that a specialized micro- nutrients from the fungus, and use this to feed the entire other as new compounds are evolved. At the moment, we are fungal pathogen selectively attacks colony. This mutualism is so tight, that the loss of fungus beginning to understand the chemical warfare at the genetic the gardens of the fungus-growing by the ants results in the death of the entire colony. In level, and it is likely that these types of interactions are more ants. These fungi, which belong to the return, the fungus receives a continuous supply of growing prevalent in nature than previously thought. genus Escovopsis, directly attack and material, protection from the environment, and the removal So how exactly does an ant go about forming partnerships kill the crop fungus, and can overrun of disease-causing agents and competitors through the with a fungus and a bacterium? No one really knows. With the garden in a similar fashion to the ants’ weeding behaviour and pesticide application. new advances in molecular and genetic technologies, such way weeds and pests can ruin human So what do the bacteria get out of producing pesticides as whole-genome sequencing, we will hopefully begin to gardens. for the ants? For starters, they get food. Many species of understand how these associations were established, and A curious observation that researchers fungus-growing ants have evolved special crypts on their gain further insight into how these interactions resulted in noted was that some workers had a bodies where the bacteria live and grow. It is thought that the remarkable fungus-growing ability of the ants. white wax-like substance across the ants provide nutrients to the bacteria through glands their bodies. It was thought that this connected to these crypts. Furthermore, the bacteria gain Garret Suen & Cameron R. Currie substance was a wax produced by the a protected environment in which to grow, away from the Department of Bacteriology, University of Wisconsin- ants themselves, with an unknown intense competition they would face if they lived in other Madison, Madison, Wisconsin 53706, USA function. However, when viewed un- environments such as the soil. Since the ants are invested in (e [email protected]; [email protected]) der a microscope it was discovered that these bacteria as a producer of pesticides, they are carried this covering was not a wax, but a by young queens that found new nests, and thus gain access bacterium! Isolation of these bacteria to new resources that ensure their continued existence and Further reading Currie, C.R. (2001). A community of ants, fungi, and bacteria: revealed that they belong to the genus worker ant bodies is correlated to the onerous task! When Escovopsis is survival. a multilateral approach to studying symbiosis. Annu Rev Microbiol Pseudonocardia, which are part of the incidence of infection. At the onset detected by garden workers, there is 55, 357–380. actinobacteria, a group of prokaryotes of invasion by Escovopsis, the actino- an immediate flurry of activity as ants A chemical arms race that produces over 80% of the anti- bacteria will cover the workers’ bodies, begin to comb through the garden Research in our laboratory has revealed a number of interest- Currie, C.R., Scott, J.A., Summerbell, R.C. & Malloch, D. biotics used by humans. Further work presumably to increase the production matrix. Upon finding the pathogenic ing properties between the bacteria and the pathogenic (1999). Fungus-growing ants use antibiotic producing bacteria on this ant-associated actinobacteria of the pesticide. This discovery was fungus, they weed them out and fungus. The bacteria appear to be specially suited to to control garden parasites. Nature 398, 701–704. has shown that it produces antifungal the first demonstrated example of discard them into their refuse dumps inhibiting the pathogenic fungi that infect the ants’ fungus Currie, C.R., Poulsen, M., Mendenhall, J., Boomsma, J.J. & compounds that inhibit the specialized an animal, other than humans, that away from the garden. By weeding garden. Even though these parasitic fungi belong to a single Billen, J. (2006). Coevolved crypts and exocrine glands support microfungal pathogen that attacks the employ bacteria to produce antibiotics and applying pesticides, the ants genus, they are differentiated into various species and strains mutualistic bacteria in fungus-growing ants. Science 311, 81–83. garden. As a result, it is now known in order to deal with pathogens. have developed a system to keep their that are each associated with particular groups of ants. We Poulsen, M. & Boomsma, J.J. (2005). Mutualistic fungi control that these ants employ these bacteria as As a second line of defence, the gardens pest-free, an impressive feat have found that the actinobacteria associated with any crop diversity in fungus-growing ants. Science 307, 741–744. a source of pesticides to control the in- ants have also adopted the practice of given that they grow their fungal crop given species of fungus-growing ant is effective at inhibiting Schultz, T.R. & Brady, S.G. (2008). Major evolutionary vading pathogenic fungi. Interestingly, weeding. Anyone who has ever weeded in monoculture, an ability which has some strains of pathogenic fungi, but not all; they tend to be transitions in ant agriculture. Proc Natl Acad Sci U S A 14, the spread of the actinobacteria on a garden can readily identify with this evaded human agriculturalists. most effective against the pathogenic fungus that specifically 5435–5440.

174 microbiology today nov 08 microbiology today nov 08 175 The of many nematodes and arthropods contain bacterial Bacterial sequences. How did they get there? Julie sequences in C. Dunning Hotopp and Jason Rasgon an invertebrate explain.

m Wolbachia infect the most abundant animal phyla including nematodes and arthropods. This includes some bees and butterflies like genome those shown here. J.C. Dunning Hotopp

olbachia pipientis is the most prolific into reproductively capable females, and (4) cytoplasmic Unlike infections in arthropods, that Wolbachia provide the host with the obligate symbioses between these intracellular endosymbiont on earth. incompatibility, the most common phenotype, whereby the treatment of nematodes with anti- necessary nucleotides, cofactors and bacteria and their hosts. These bacteria infect not only 70% of offspring of uninfected females and infected males fail to biotics that are targeted at elimin- vitamins. insects, but also the most abundant develop. Wolbachia are maternally inherited, being transferred ating the Wolbachia infection also Despite maternal inheritance in Interdomain lateral gene animal phyla, including nematodes and through the egg cytoplasm. Therefore, these reproductive kills the host. This suggests that Wol- arthropods, arthropod-borne Wolbachia transfer arthropods. phenotypes favouring Wolbachia-infected females increase bachia form an obligate mutualistic do not evolve with the host. Instead, the In 2001, Natsuko Kondo and W The arthropod-infecting Wolbachia exert unusual effects on the proliferation of Wolbachia-infected arthropods. Wolbachia symbiosis with filarial nematodes, bacteria are transmitted horizontally colleagues described a variant of a host reproduction, including: (1) parthenogenesis, whereby are parasitic endosymbionts, since the interaction benefits since neither organism can survive and infections are lost, although the bean beetle, Callosobruchus chinensis, infected virgin females produce infected female offspring, Wolbachia while exerting a negative effect on the host by without the other. The exact nature mechanisms are not understood. In where Wolbachia genes had moved (2) male killing, whereby infected male embryos fail to limiting genetic exchange. However, a mutualistic role of the mutualistic interaction is not contrast, filarial nematodes and into the insect chromosome. This develop, (3) feminization, whereby genetic males develop benefiting both organisms cannot be excluded. known, but it has been proposed Wolbachia evolve together, reflecting movement of DNA from an organism

176 microbiology today nov 08 microbiology today nov 08 177 to an unrelated one is called lateral gene transfer (LGT). and development, the genomes of both organisms were obligate mutualistic symbiosis with their Wolbachia strains. In filarial nematodes, an LGT event is responsible for the sequenced simultaneously, complicating assemblies and The origin of the symbiosis is thought to have arisen about presence of two degenerate Wolbachia gene fragments in leading to the removal of many Wolbachia reads during 50 million years ago and occurred in the ancestor of the the nematodes Onchocerca volvulus and O. ochengi. It has genome assembly (>98% identity over 90% of the read Onchocercinae and the Dirofilariinae, theWolbachia -infected also been proposed that mosquitoes acquired a Wolbachia length on the basis of the independent BAC-based genome clades. However, since that time there appears to have gene involved in the resistance of Anopheles mosquitoes to sequence of wBm, the Wolbachia endosymbiont of B. malayi). been at least six independent losses of Wolbachia infection. Wolbachia infection. However, this claim is supported only Despite this, the genome of B. malayi contains 249 contigs Although Wolbachia infections can successfully be trans- by homology searches, which are inadequate to assign the with Wolbachia sequences; PCR and end-sequencing ferred to Wolbachia-free lineages, the infection is lost on directionality of LGT events. In fact, these proteins have confirmed nine of these inserts. The transfer of at least one culturing in animals, suggesting that the association is no only been found in Wolbachia and mosquitoes, making it region containing a degenerate fragment of the Wolbachia longer stable. The nature of the instability has not been impossible to assign directionality. aspartate aminotransferase gene (Wbm0002), predates the established. But it is plausible that an LGT event from the These are examples of interdomain LGT events, where divergence of three species, B. malayi, B. timori and B. pahangi. endosymbiont to the filarial nematode may have conferred DNA moves between two of the three domains of life While the D. ananassae nuclear insert appears to be in one the nematode with the ability to live without its once-obligate (eukaryotes, eubacteria, archaea). Most described LGT events large piece, the B. malayi genome seems to have multiple symbiont. occur within a single domain of life. LGT is most common inserts scattered through the genome with some large inserts in eubacteria where it is responsible for movement of genes of numerous Wolbachia genes, and other smaller inserts of a Julie C. Dunning Hotopp for antibiotic resistance, pathogenicity and bioremediation. single gene fragment. Institute for Genome Sciences, Department of A very striking example of interdomain LGT is in the We have found numerous Wolbachia LGT inserts in the Microbiology & Immunology, University of Maryland hyperthermophilic eubacterial lineage Thermotoga maritima, genomes of diverse invertebrate animals, including fruit Baltimore, 20 Penn Street, Room S203B, Baltimore, which has 81 archaeal genes clustered in fifteen 4–20 kbp flies, wasps and nematodes. Of 26 arthropod and nematode MD 21201, USA (t +1 410 706 5673; f +1 410 706 1482; islands. genomes in the trace repositories, 11 contain Wolbachia e [email protected]) Interdomain transfers in higher multicellular eukaryotes sequences. Of the Wolbachia-containing genomes, eight are thought to be uncommon and unimportant, but several show evidence of having LGT between the endosymbiont Jason L. Rasgon important cases have been documented. Most notably, the genome and the host chromosomes. We have characterized The W. Harry Feinstone Department of Molecular plant pathogen Agrobacterium tumefaciens transfers 10– host–endosymbiont LGT in five of these hosts. These results Microbiology and Immunology, The Johns Hopkins 30 kbp of T-DNA from the Ti plasmid (200–800 kb) to suggest that such inserts are common. Given that Wolbachia Malaria Research Institute, Bloomberg School of Public plants. Upon transfer, the T-DNA is targeted to the nucleus, are among the most abundant endosymbionts, and their Health, Johns Hopkins University, 615 N Wolfe Street, incorporated into the plant chromosome by illegitimate hosts represent the most abundant animal phyla, the view Room E4626, Baltimore, MD 21205, USA (t +1 410 502 recombination, and the genes are transcribed from eukary- that interdomain transfers are uncommon and unimportant otic promoters encoded in the T-DNA. Although normally in multicellular organisms needs to be re-evaluated. 2584; f +1 410 955 0105; e [email protected]) associated with crown gall disease and subsequently the plant’s death, this has also been used to introduce novel Endosymbiont lateral gene transfer ratchet Further reading Doolittle, W.F. (1998). You are what you eat: a gene transfer genes in plants (e.g. genetically modified crops). A lateral gene transfer ratchet has been proposed by W. Ford ratchet could account for bacterial genes in eukaryotic nuclear Doolittle to explain the accumulation of nuclear genes of genomes. Trends Genet 14, 307–311. Lateral gene transfers between Wolbachia and organelle origin. The idea is that at some low frequency host chromosomes organelle genes will be inserted into the nuclear genome, and Dunning Hotopp, J.C. & others (2007). Widespread lateral In every genome sequencing project, sequences remain that with some even lower frequency this will occur in positions gene transfer from intracellular bacteria to multicellular do not end up in the final assembly and are often considered that allow expression of the protein with an appropriate eukaryotes. Science 317, 1753–1756. chaff or garbage. When combing through the chaff of the fruit leader sequence for organelle targeting. Once this occurs, Keeling, P.J. & Palmer, J.D. (2008). Horizontal gene transfer in fly Drosophila ananassae genome, we discovered numerous either the nuclear copy or the organelle copy will be lost. If eukaryotic evolution. Nat Rev Genet 9, 605–618. segments of DNA that belong to both Drosophila and the organelle copy is lost, the gene will become fixed in the Kondo, N., Nikoh, N., Ijichi, N., Shimada, M. & Fukatsu, Wolbachia genes. We verified the structure of some of these nuclear genome, and as such becomes a successful transfer. T. (2002). Genome fragment of Wolbachia endosymbiont regions by PCR and demonstrated by in situ hybridization Otherwise, the process can repeat itself, until all the genes transferred to X chromosome of host insect. Proc Natl Acad Sci of polytene chromosomes that a large part of the Wolbachia that can insert in the nuclear genome have done so. U S A 99, 14280–14285. genome has been integrated into the D. ananassae Hawaii 2L It seems reasonable to extend this theory to endosym- Stouthamer, R., Breeuwer, J.A. & Hurst. G.D. (1999). Wolbachia chromosome. Variably sized Wolbachia inserts were detected bionts and their hosts. In the case of endosymbionts, a pipientis: microbial manipulator of arthropod reproduction. Annu in four lines of D. ananassae from Asia and the Pacific, second option is available upon transfer of the gene to its Rev Microbiol 53, 71–102. indicating that the insert may be widely distributed and host. If the genes transferred now fulfil the host’s needs, m To p. These cultured Anopheles gambiae Sua5B mosquito cells are degenerating. Lastly, we have found transcription of at least the endosymbiont might become obsolete and can be lost. infected with the Wolbachia strain wRi. The Wolbachia are red while 28 D. ananassae genes of Wolbachia origin. In the case of an obligate endosymbiont, this would result the mosquito cell nuclei are stained blue. Jason Rasgon In the filarial nematode Brugia malayi, we characterized in the presence of endosymbiont-free lineages in clades of m Bottom. These Drosophila simulans ovaries are infected with the inserts in the whole-genome shotgun-sequencing project. organisms with co-evolving obligate symbionts. Wolbachia strain wRi. The Wolbachia are red while the Drosophila As Wolbachia infection is required for the worm’s fertility Such a situation exists in filarial nematodes that form an cell nuclei are stained blue. Jason Rasgon

178 microbiology today nov 08 microbiology today nov 08 179 When living in a complex association with a nematode, the bioluminescent bacterium Photorhabdus can be deadly to insects, according to Susan A. Joyce and David J. Clarke. Photorhabdus: shedding light on symbioses

ext time that you are on the beach, walk m Insect larvae infected with Photorhabdus luminescens photographed P. asymbiotica has just been completed carrier flavin mononucleotide (FMN). attraction of a mate. Unfortunately the into the dunes and take a sample of the in a dark room using the light produced by the bacteria. The at the Sanger Centre (www.sanger.ac. The aldehyde is then bound to the role of bioluminescence in Photorhabdus insect hosts are final instar larvae of the greater waxmoth (Galleria sandy soil within the area where the dune mellonella). Susan Joyce (Sand dunes, Photos.com/Jupiter) uk/Projects/P_asymbiotica/). luciferase enzyme (encoded by luxA is not yet understood, although, as all grass is growing. Place your soil sample and luxB) which, together with O2, isolated Photorhabdus strains produce in a flask, add a few insect larvae (readily of cases, to be associated with infections in humans. These Bioluminescence forms an unstable ternary complex light, it is likely that there is a strong available from your local bait or pet shop) infections, although not fatal, do result in rather serious One of the most striking features that rapidly decomposes, releasing selection for this activity. and the chances are good that the insects will be dead wounds that are difficult to treat. Fortunately, these cases of Photorhabdus bacteria is that they H O, fatty acid and energy in the N 2 within 2–3 days. Take these dead insects into the darkest appear to be restricted to the southern states of the USA (in are bioluminescent and, indeed, it form of photons. The requirement for The life cycle room in your house and within 5–10 minutes you should particular Texas) and the Gold Coast of Australia. However, is this feature that gave the bacteria electrons suggests that one function of Photorhabdus are normally found colon- see that some, if not all, of the insect cadavers will glow it is rather intriguing that, under certain conditions Photo- their name, i.e. photo (referring to the light production may be to act as an izing the guts of the infective juvenile in the dark. This bioluminescence is due to the presence rhabdus does appear capable of ‘jumping’ from insect to ability to produce light) and rhabdus electron shunt that allows the recycling (IJ) stage of the nematode Heterorhab- of the bacterium Photorhabdus, a highly virulent insect human. Interestingly, in the laboratory, most strains of P. (rod). Photorhabdus have a lux operon of essential electron carriers without ditis. The IJ is a soil-dwelling, motile, pathogen (entomopathogen) that you have isolated in a luminescens and P. temperata do not grow at temperatures that contains all of the genes required the production of ATP and/or biomass. non-feeding stage of the nematode nematode vector from the soil. Together, Photorhabdus and >32°C, whilst P. asymbiotica can grow at 37°C. Therefore, for the production of light from fatty Although bacterial bioluminescence is whose role is to actively seek out and

the nematode vector (Heterorhabditis) form a deadly complex perhaps the high ambient temperature of Texas and the Gold acids and molecular O2, i.e. luxCDABE. quite common in the marine environ- infect susceptible insect larvae and that is naturally lethal to insect larvae. Coast has allowed P. asymbiotica to adapt to growth at the The of light production ment, Photorhabdus is the only terrestrial release the Photorhabdus into the insect Photorhabdus are members of the family Enterobacteriaceae relatively high temperature of humans. in bacteria is well described and it bacterium that is known to produce bloodstream. Here the bacteria begin and are, therefore, quite closely related to familiar pathogens Comparing the genomes of insect and human isolates of involves the conversion of a fatty acid light. In the sea, many light-producing to divide whilst producing a wide such as , Salmonella, Yersinia and Erwinia spp. Photorhabdus may uncover some interesting insights into the into an aldehyde through the action bacteria are involved in symbioses range of toxins and hydrolytic To date three species of Photorhabdus have been described; evolution of mammalian pathogenicity in environmental of a fatty acid reductase (encoded by with marine animals and the role of that serve to kill the insect within 2–3 P. luminescens, P. temperata and P. asymbiotica. Although P. micro-organisms. To this end, the genome sequence of P. luxC and luxD). This reaction requires bacterial bioluminescence can vary days and facilitate the conversion of luminescens and P. temperata only appear to infect insects luminescens TT01 has been available since 2003 (http://genolist. a supply of electrons that are delivered from protection (counter-illumination the internal organs and tissues of the P. asymbiotica has been found, in a relatively small number pasteur.fr/PhotoList) and the genome sequence of a strain of to the enzyme by the reduced electron in the Vibrio–squid symbiosis) to the insect into an environment where

180 microbiology today nov 08 microbiology today nov 08 181 b GFP-tagged Photorhabdus in the gut of a Heterorhabditis IJ. Bars, 50 µm (left) and 20 µm (right). Catherine Easom

. The Tc toxins are orally toxic to larvae of Manduca sexta (the tobacco hornworm moth). In a typical bioassay, 2nd instar insect larvae are allowed to feed on a wheatgerm-based diet that can be treated with preparations of the Tc toxin complex. The larvae do not feed on the food with the Tc complex added (right) and fail to develop compared with controls (left). Nick Waterfield

From a more fundamental perspective, we expect that the tripartite interaction m The molecular structure of 3’-5’-dihydroxy-4-isopropylstilbene (ST). David Clarke between Photorhabdus, Heterohabditis and insect will also help us to answer b A hand infected with P. asymbiotica. John Gerrard / Nick Waterfield a very important question: what is the the nematode can reproduce. During development, the and Photorhabdus produce toxins that target the cellular real role of such bioactive molecules nematodes feed on the Photorhabdus biomass within the branch of innate immunity. Analysis of genome sequence data in nature? insect cadaver and after 2–3 generations of reproduction, has revealed that Photorhabdus encodes an impressive array environmental conditions stimulate the development of IJs of toxins. Indeed studies in Photorhabdus have resulted in the Susan A. Joyce & David J. Clarke that are colonized by Photorhabdus before the IJ emerges identification of a new family of toxins that have since been Department of Microbiology, from the insect cadaver into the soil. A single IJ infecting shown to be found in other bacteria, including mammalian University College Cork, Ireland the insect will result in >100,000 IJs emerging from the pathogens. The Tc toxins from this family are large protein (t +353 21 490 3624, insect cadaver 2–3 weeks later. The interaction between complexes that can be poisonous when fed to insect larvae. e [email protected]) Photorhabdus and Heterorhabditis is, in effect, a highly effective When cloned into the model plant Arabidopsis, the Tc toxins symbiosis of pathogens and it is so effective that it is produced provide protection against insect pests, suggesting a potential the role of ST was to protect the insect mutualist in one host and as a pathogen and marketed by several companies as a biocontrol agent alternative to Bt toxin. cadaver from saprophytic organisms in in another, including the occasional Further reading for a variety of insect pests, in particular the weevil. There- the soil. However, recent studies have human. Its complex life cycle, related- Ciche, T.A., Kim, K.S., Kaufmann- fore, this bacterium has the ability to act as a pathogen in one Mutualism and signal production shown that ST is also an inter-kingdom ness to important mammalian patho- Daszczuk, B., Nguyen, K.C. & host (insect) and a mutualist in another host (nematode). The Photorhabdus–Heterorhabditis association is highly signal that is involved in controlling gens and amenability to genetic Hall, D.H. (2008). Cell invasion specific, and nutritional interactions do make a contribution the development of Heterorhabditis into manipulation have contributed to the and matricide during Photorhabdus Pathogenicity and toxin production to this specificity. Therefore, a particular isolate of the IJ stage. The IJ is developmentally development of this genus as an exci- luminescens transmission by Photorhabdus is extremely virulent and, in some insect hosts, Heterorhabditis cannot feed on all Photorhabdus bacteria. analogous to the dauer stage in the ting model for studying bacteria–host Heterorhabditis bacteriophora nematodes. injection of a single cell is sufficient to kill the host within Nutritional interactions are common in many mutualistic model nematode Caenorhabditis elegans. interactions. However, Photorhabdus Appl Environ Microbiol 74, 2275–2287. 2–3 days. Photorhabdus are capable of killing a wide range associations, e.g. exchange between plant cells In C. elegans, dauer formation is a res- is also quickly emerging as a source of Clarke, D.J. (2008). Photorhabdus: a of insects from the Orders Coleoptera (beetles), Lepidoptera and Rhizobium bacteroides, but the details of these interactions ponse to the low availability of food and/ novel bioactive compounds. In total model for the analysis of pathogenicity (moths, butterflies) and Diptera (flies). However, in the are not yet known in the Photorhabdus–Heterorhabditis system. or high nematode numbers. Therefore, there are 22 genetic loci in the genome and mutualism. Cell Microbiol doi environment the host range appears to be limited by the In addition, successful colonization of the IJ is essential for it is possible that ST is perceived by of P. luminescens TT01 that contain 10.1111/j.1462-5822.2008.01209.x ability of the IJ to penetrate the potential host. Photorhabdus both partners in the association, and it has been shown that Heterorhabditis as an indication that genes predicted to be involved in Schmidt, E.W. (2008). Trading grow exponentially in the insect, achieving high cell densities IJs will only be colonized by the nematodes’ cognate bacterial food (i.e. bacteria) is plentiful. The the production of small bioactives, molecules and tracking targets in within the host [approx. 109 c.f.u. per Galleria mellonella partner (or in some cases a very close relative). Photorhabdus ST molecule is multipotent and has including polyketide synthases (PKS), symbiotic interactions. Nat Chem Biol (greater waxmoth) larva] and converting all of the internal is transmitted to the IJ via the mother in a very complex also been shown to dampen the insect non-ribosmal peptide synthases (NRPS) 4, 466–473. organs and tissues of the insect into a biomass that is required process that results in her infection and death. immune system so that the nematode or PKS-NRPS. These loci occupy 7% of Waterfield, N.R., Wren, B.W. & for the growth and development of the nematode partner. During the stationary phase of growth, Photorhabdus and bacteria are invisible to the insect the TT01 genome compared to 4% in Ffrench-Constant, R.H. (2004). There is a close correlation between the growth rate of produces several small bioactive molecules, including immune system post-infection. Streptomyces, the organism responsible Invertebrates as a source of emerging Photorhabdus and the time taken to kill the insect, suggesting a redox-active, anthraquinone pigment and a stilbene for the production of many important human pathogens. Nat Rev Microbiol that pathogenicity is dependent on bacterial growth. molecule, 3′-5′-dihydroxy-4-isopropylstilbene (ST). The ST The future is bright (or should antibiotics. Therefore, it is expected that 2, 833–841. Insects have a very sophisticated innate immune system molecule is produced in large quantities when Photorhabdus that be light-producing!) screening libraries of Photorhabdus DNA Wilson, T. & Hastings, J.W. (1998). that has striking parallels with the innate immune system in are grown in either LB broth or insect larvae, and it was Photorhabdus is a Gram-negative bac- will identify new bioactive compounds, Bioluminescence. Annu Rev Cell Dev vertebrates. This system is highly effective at killing bacteria, originally identified as an antibiotic. It was suggested that terium that is equipped for life as a including toxins and antibiotics. Biol 14, 197–230.

182 microbiology today nov 08 microbiology today nov 08 183 An inside job: Bdellovibrio bacteriovorus Some predatory ‘bugs’ eat other ‘bugs’ from inside, as Liz Sockett and her research group have found.

dellovibrio are small (0.25× Bdellovibrio where the acquisition of a large number of genes periplasmic growth phase, during which they reside inside the 1.0 μm), flagellate, motile, for hydrolytic enzymes, and for penetrating and resealing dead prey cell, degrading it by secreting enzymes across the Gram-negative deltapro- the prey cell, give access to an intracellular niche, bounded prey cytoplasmic membrane to digest prey macromolecules, teobacteria which invade by the prey-cell outer membrane, where the Bdellovibrio can and taking up the products for Bdellovibrio growth. Bdellovibrio and kill other Gram-nega- ‘dine privately’ on the inner contents of the prey cell without seem to be mostly ‘locked on’ to predatory growth in dilute tive bacteria, entering the competition for nutrients from other bacteria. This contrasts environments and cannot productively switch to HI growth to Bprey cell’s periplasm, replicating within with the ‘eating habits’ of other deltaproteobacteria such survive, but depend on finding prey for replication. During the it and using the contents of that as the myxobacteria which digest prey externally and take free-swimming attack phase, rapid prey location, attachment bacterium as their nutrient source. up digested prey nutrients partly in competition with other and recognition are vital to the successful replication of the Bdellovibrio bacteriovorus HD100 is the bacteria in their surroundings. Bdellovibrio, as they typically have a half-life of about 10 sequenced strain and has a 3.8 Mb gen- hours during starvation in buffered environments. A large ome, indicating that although Bdello- Predatory growth complement of genes for flagellar and chemotaxis systems vibrio have evolved to invade and When growing predatorily, Bdellovibrio exhibit a biphasic life- is seen in the genome to aid movement towards prey-rich ‘eat’ other bacteria, they have not lost style with a free-swimming attack phase and a sessile intra- regions. large numbers of genes, as is the case with truly parasitic bacteria which rely on their hosts. The interaction between Bdellovibrio and other bacteria can be thought of as predatory rather than parasitic as, in most cases, the Bdello- vibrio kill the prey cell within 15 min- utes of entry and do not establish a long- lived parasitic relationship within it. In keeping with its large genome, B. bacteriovorus can exist in two differ- ent growth phases, as host-dependent (HD) cells that require prey for growth and division, and as host-independent (HI) cells, when growing in rich nutri- ent media as might be found in bio- films and sediments in nature. The balance between HD and HI growth in natural environments is not known, but HI growth is a useful tool for saving m Bdellovibrio life cycle, showing predatory (HD) and (rarer) non-predatory mutants for study in the axenic (HI) growth modes. Liz Sockett lab setting. Predatory growth seems to b False-coloured, negatively stained electron micrograph of a be a kind of evolutionary trade-off in B. bacteriovorus bdelloplast. David Milner and Laura Hobley

184 microbiology today nov 08 microbiology today nov 08 185 Bdellovibrio attach to many kinds of surfaces reversibly, We and others are actively engaged in functional analyses have also been isolated from sewage, in the UK, charting the levels of Liz Sockett, Laura Hobley, Andrew including inorganic particles and Gram-positive cells (which of the genes within the B. bacteriovorus HD100 genome, and from the gut flora of humans, resistance particularly in pathogenic Fenton, Richard Woods, Carey are not prey as they do not have a periplasm). How they studying expression patterns and defining roles for them horses and chickens. Bdellovibrio 16S Escherichia coli species. Bdellovibrio Lambert, Chien-Yi Chang, Robert tell prey from ‘junk’ is unknown. There seems to be a in the Bdellovibrio life cycle. We have shown that, although rDNA sequences have been found naturally attack and kill a wide range Atterbury, Rob Till, Marilyn brief recognition period, during which the Bdellovibrio cell Bdellovibrio swim actively using chemotaxis to find prey-rich in a variety of metagenomic studies, of pathogenic Gram-negative bacteria, Whitworth, Mike Capeness, Rowena identifies its prey, attachment betweenBdellovibrio and prey regions, they do not use actively rotating flagella to ‘bore’ including those from marine sediments including Salmonella, E. coli, Proteus, Fung, Rashidah Ahmad, David becomes irreversible, and the Bdellovibrio begins its invasion into prey. We have found that preventing expression of the and even human skin. Bdellovibrio are Pseudomonas, Burkholderia, Serratia Milner, Tom Lerner & Simon King process. A small pore is produced in the outer membrane of Bdellovibrio PilA fibre protein of Type IV pili abolishes prey found strongly associated with natural and others. If applied as ‘living Institute of Genetics, University the prey, through which the Bdellovibrio bacterium seems to entry, showing that pili are involved in productive prey biofilms, and recent studies have antibiotics’, Bdellovibrio would avoid of Nottingham, School of Biology, squeeze. Once inside, the pore is resealed, and modification attachment and or penetration. shown that effective predation occurs many of the shortcomings of phage Medical School, QMC, Derby of the prey’s peptidoglycan causes the rounding of the prey in these naturally occurring bacterial therapy which utilizes bacteriophage Road, Nottingham NG7 2UH, cell and the formation of a structure called a bdelloplast. Where are Bdellovibrio found? communities. as a treatment against bacterial UK (t +44 115 8230325; This is followed by the intraperiplasmic hydrolysis of prey, Bdellovibrio are found throughout nature; wherever there infection. Bdellovibrio are not known e [email protected]) as mentioned above. The Bdellovibrio cell elongates, and are suitable prey to be ‘eaten’, Bdellovibrio are usually found Living antibiotics! to be prey-specific; they infect a variety then septates at multiple fission sites. The multiple progeny eating them! Soil and fresh water samples are often found In July 2008, the Health Protection of Gram-negative hosts, and have no Further reading cells become flagellate, before releasing a final wave of lytic to contain Bdellovibrio, or its closely related cousins Bacterio- Agency published further worrying known specific host recognition sites. Evans, K.J., Lambert, C. & Sockett, enzymes to burst from the confines of the bdelloplast and lyticus and Peredibacter, whilst salt-water samples often yield statistics about the rise of antibiotic- In contrast, bacteriophage attach to R.E. (2007). Predation by Bdellovibrio resistant Gram-negative infections seek out more prey. Bacteriovorax spp., another closely related cousin. Bdellovibrio specific molecular targets, hence are bacteriovorus HD100 requires type IV only effective against a narrow range pili. J Bacteriol 189, 4850–4859. of bacteria, which can in turn become Health Protection Agency Centre resistant by simple point mutations in for Infections (2008). Antimicrobial 1 2 3 genes encoding these protein targets. Resistance and Prescribing in England, In addition, some phage are unable Wales and Northern Ireland, 2008. London to invade cells with capsules, whereas Health Protection Agency. bacterial capsules have been shown to Lambert, C., Morehouse, K.A., be an ineffective barrier to predation Chang, C.Y. & Sockett, R.E. (2006). by Bdellovibrio. Bdellovibrio have been Bdellovibrio: growth and development shown to be unable to enter and infect during the predatory cycle. Curr Opin mammalian cells, which is of great Microbiol 9, 639–644. importance when considering their Sockett, R.E. & Lambert, C. (2004). potential as an antibiotic treatment. Bdellovibrio as therapeutic agents: a This means that they could infect and predatory renaissance? Nat Rev Microbiol kill the pathogenic bacteria causing the 2, 669–675. infection whilst not causing harm to a Stolp, H. & Starr, M.P. (1963). patient. Bdellovibrio bacteriovorus gen. et sp. n., a The potential applications of predatory, ectoparasitic, and bacteriolytic Bdellovibrio offer an exciting avenue microorganism. Antonie Van Leeuwenhoek for further research, and may one 29, 217–248. day form part of a new generation Rendulic, S., Jagtap, P., Rosinus, A. of antimicrobial therapeutics. In the & others (2004). A predator unmasked: future you may visit a doctor and be life cycle of Bdellovibrio bacteriovorus prescribed ‘Bdellovibrio therapy’ to from a genomic perspective. Science combat your infection! 303, 689–692. m Negatively stained electron micrographs of Bdellovibrio bacteriovorus HD100. (1) Free, motile, attack-phase swimming cells hoping to encounter Gram-negative bacterial prey. The cells have long sheathed flagella with an unusual wave-form caused by the presence of several different flagellin proteins making up the flagellum. (2) Attaching to Gram-negative bacterial prey for invasion through the prey outer membrane. (3) Living within bacterial prey forming a bdelloplast where the prey bacterium is beginning to be consumed and the Bdellovibrio is starting to elongate and grow prior to replication. Andrew Fenton, David Milner and Laura Hobley

186 microbiology today nov 08 microbiology today nov 08 187 Bacteriophages: nature’s most successful Phages exist on our planet not only in huge numbers but infinite variety as Graham F. Hatfull describes. experiment

m Coloured electron micrographs of a ou may well be under the biosphere is a stunning 1031. This is a re- samples are analysed, and does not change significantly when What type of viral population has arisen, what do they variety of bacteriophages. From left to impression that the largest markable number, because it suggests comparing coastal, oceanic, surface or deep-water samples. look like, and how different are their genomes? Phages right: SEM of T phages attacking Escherichia coli (Eye of Science / SPL); TEM of lambda number of undiscovered that phages are a numerical majority A simple extrapolation to the total volume of seawater and were among the first ‘invisible’ entities to be observed by phages (CNRI / SPL); TEM of a cluster of species – and the greatest of all biological entities – i.e. there are inclusion of terrestrial counts leads to a total number of electron microscopy, which showed them to be well-defined P1 phages (Biozentrum / SPL); TEM of pool of unknown genes – more phage particles than all other phage particles of 1031. An independent estimate of the total structures containing a protein head (capsid) surround- T phage particles attacking E. coli (Eye of 30 Science / SPL). lie within the considerable biological forms added together. If number of bacteria in the biosphere arrived at 10 , providing ing the genetic material, attached to a tail. While these Ybiodiversity of the tropical rain forests. abundance can be equated with success, some comfort in the validity of these estimations. tailed phages containing double-stranded DNA (dsDNA) are Not so. A compelling argument can be then phages represent the result of perhaps the most common forms, a large variety of different made that the biggest reservoir of un- nature’s most successful experiment! A dynamic population morphotypes have been described, with some spectacular identified genetic information is all It is helpful to understand how this The abundance of phage particles is impressive, but would shapes described recently for viruses of archaeal hosts. The around us, in the global population of abundance is calculated. Samples from be rather less interesting if these were just a large number of genetic material in phages can be either DNA or RNA, either bacteriophages. the environment can be stained with a small number of types. However, there are clues suggesting in single- or double-stranded forms. dyes that cause viruses and bacteria to that this is not the case. First, it has been estimated that there How many phages are there? fluoresce, and the number of particles are approximately 1024 viral infections of bacteria per second Genomics There are two main components to counted using fluorescent microscopy. on a global scale, suggesting that the entire phage population Currently, just over 500 completely sequenced phage gen- this conclusion: the amazing abun- There are two main observations: that turns over every few days – far from being static, the popu- omes are listed in the Genomes section at the National Center dance of phages in the environment viral particles are typically present at lation is highly dynamic, with each cycle of infections having for Biotechnology Information (NCBI). The size of this col- and the emerging picture of their 106–107 per ml seawater, and that there the potential to generate altered or mutant particles. Second, lection has grown considerably over the past 5 years, but is genetic diversity. Over the past few are 5- to 10-fold more viruses than bac- it seems likely that the evolutionary origin of phages is not still dwarfed by the number of sequenced bacterial genomes years it has been calculated that the teria. The viral abundance is broadly too distant from that of their bacterial hosts, so this dynamic (currently ~750), even though these are 100 times larger. total number of phage particles in the similar whether seawater or terrestrial relationship has been going on for at least 2 billion years! While these sequenced phage genomes represent only a

188 microbiology today nov 08 microbiology today nov 08 189 tiny slice of the total phage population, their comparative of the population rather than specific is how the junctions between modules they are compared against databases genomic analysis has provided some fascinating insights and stable population structures. Viral are generated, and although these could such as GenBank, matches revealing into the diversity of the population and the evolutionary metagenomic studies – in which DNA arise from homologous recombina- putative functions are relatively rare, mechanisms generating this diversity. fragments from the total collection of tion between short conserved bound- and typically fewer than 30% of genes There are two general ways of thinking about the genetic viruses in a sample are sequenced – ary sequences, these are not found in newly sequenced phage genomes relationships within the phage population. One is to con- support this view of a highly diverse in most phage genomes. An altern- can be assigned putative functions. sider the similarities between groups of phages that infect phage population. ative explanation is that illegitimate Genomics and bioinformatics are thus different bacterial hosts; the other is to compare genomes recombination occurs at randomly unlikely to provide a comprehensive of phages that infect a common bacterial host. The 500 Mosaicism chosen positions and with randomly understanding of phage gene functions, sequenced phage genomes correspond to about 70 different One of the clearest and most amazing chosen partners, which could be and experimental approaches are bacterial hosts (a small subset of the ~470 bacterial species aspects of phage genomes is their mo- other phage genomes, plasmids or the clearly needed. that have been sequenced), and because phages probably saic architecture. Comparative analysis bacterial chromosome. Most of these Phage genomics are clearly in their exist for the vast majority of bacterial species, this is likely reveals segments or modules that are events will generate genomic trash, infancy. The current state of the field to correspond to a small and highly unrepresentative sample. shared by two or more phages, but but with selection for appropriately- provides a tantalizingly tasty appetizer, Nonetheless, comparisons of these genomes show that they which are flanked by different modules sized genomes that can be packaged but with such a vast landscape of are highly diverse, and phages of one bacterial host will These modules can be groups of genes – into capsids, and for maintenance of a unexplored phages yet to be studied, often have little or no recognizable nucleic acid sequence especially those whose functions need functional set of genes, viable progeny one cannot but feel that the main similarity with phages of other hosts. Although amino acid to work together, such as the virion could arise. The overall process is not course is yet to come. In the next few sequence comparison of predicted gene products can detect structural genes – or single genes. In expected to be efficient or frequent, years, the advent of ultra-high through- more distant relationships, relatively few genes emerge as the mycobacteriophages, this single- but with such a dynamic population put DNA sequencing technologies will having common evolutionary origins. However, it appears gene mosaicism within the non-struc- evolving over such a long period of generate a multitude of new phage as though the more closely related the bacterial hosts, the tural genes is particularly prevalent with time, this would not seem to be a prob- genome sequences, and functional and greater the chance that their phages may share common large groups of contiguous genes hav- lem. Other events such as transposi- structural genomic approaches will genes. For example, phage PA6 of Propionibacterium acnes ing distinct and different evolutionary tion and site-specific recombination help us to elucidate their biology. While contains a number of genes that are shared by phages of the histories. The diversity of phage gen- events will also generate further we may never know for sure what the mycobacteria. Overall, it seems reasonable to suppose that omes suggests that the number of dif- rearrangements, and homologous whole phage population looks like, phages form a continuum of relationships that will only be ferent modules is very large and that recombinationl mediates exchanges at perhaps we can at least learn enough fully understood with a substantial increase in the number of Wildcat only a very small subset have as yet been common gene sequences. to appreciate how much of it we really sequenced genomes. identified. Each individual phage gen- don’t understand. Substantial groups of sequenced genomes have now been ome can thus be viewed as a unique Gene functions accumulated that share common hosts, with more than 20 assembly of modules, and the combina- What do all these phage genes do? genomes for each of Burkholderia, enterobacteria, lactococci, torial possibilities are enormous. While the genes required for virion Graham F. Hatfull mycobacteria, pseudomonads, staphylococci and strepto- structure and assembly can often be Department of Biological Sciences Porky cocci. An emerging theme is that these groups are also Evolutionary mechanisms recognized – especially since they are and Pittsburgh Bacteriophage quite divergent, although there are clusters of phages that The evolutionary mechanisms that give often arranged in common gene Institute, University of Pittsburgh, are more closely related to each other than to others of that rise to these mosaic genome structures orders – along with some recomb- 4249 5th Avenue, Pittsburgh, host. This probably reflects a similar, but perhaps more is not clear, although both homologous ination and DNA replication activities, PA 15260, USA (t +1 412 624 focussed view to that of the phage population as a whole, and illegitimate recombination appear the functions of most other phage 4350; f +1 412 624 4870; with the clusters probably representing unequal sampling Boomer to be involved. One particular mystery genes remains largely unknown. When e [email protected])

m Virion morphology of mycobacteriophage Bxz1. Electron microscopy shows that Bxz1 contains an icosahedral capsid containing a dsDNA genome, and a contractile tail. Graham Hatfull c Mosaicism in mycobacteriophage genomes. Short segments Cjw1 of five mycobacteriophage genomes are shown with the genes represented as coloured boxes. Each gene has been assigned to a phamily (Pham) of related sequences and the Pham number presented above the box, along with the number of genes in that Pham in parentheses; genes of the same Pham are coloured accordingly. Genes without any relatives elsewhere in the collection of 50 completely sequenced mycobacteriophage TM4 genomes are shown as white boxes. Phages Porky, Boomer, Cjw1 and TM4 all contain at least one gene that is related to one in Wildcat in this region, and coloured stripes indicate these relationships. Careful inspection will reveal additional genes shared by some of these phages. Graham Hatfull

190 microbiology today nov 08 microbiology today nov 08 191 Gastric ulcer and dyspepsia were never considered to be caused by an infectious agent before the discovery of H. pylori The SGM (initially called Campylobacter pylori). While bacteria had been occasionally observed in the stomach since the early President, Robin 20th century, this part of the gastrointestinal tract, together with the small intestine, was generally considered to be Weiss, recalls the sterile. Neither did the epidemiology of gastric ulcer disease point towards an infectious agent, although wide variance in geographic prevalence was noted. H. pylori was later year in which three also shown to be the underlying cause of duodenal ulcers, stomach cancer and mucosa-associated lymphoid tumours. important pathogens Warren and Marshall faced an uphill battle to persuade GI specialists that the majority of peptic ulcers had a bacterial aetiology. Barry Marshall resorted to a time-honoured first saw light of day. and dramatic method of testing one of Koch’s postulates on himself. He swallowed a culture of the bacteria and promptly developed severe dyspepsia. He also showed that treatment his year marks the 25th anniversary of three of ulcer patients with inexpensive antibiotics often cured independent discoveries concerning human infect- the illness altogether. For too long the treatment of ulcers by ious diseases. In 1983, Helicobacter pylori was found antibiotics was strongly opposed by pharmaceutical com- to be associated with stomach ulcers by Robin panies which sold far more expensive drugs for the chronic Warren and Barry Marshall, human papilloma virus treatment of the symptoms, e.g. H2-receptor antagonists. (HPV) type 16 was identified as a candidate agent of In contrast to gastric ulcer, cervical carcinoma had long Tcervical cancer by Harald zur Hausen’s group, and human been thought to result from a sexually transmissible agent. immunodeficiency virus (HIV) was first isolated from a In 1842, an astute gentleman of Verona, Domenico Rigoni- c Coloured SEM of Helicobacter pylori patient with symptoms suggestive of the early stages of AIDS Stern, observed that while nuns had an increased incidence bacteria (pink) on human gastric epithelial by Françoise Barré-Sinoussi, Luc Montagnier and colleagues. of breast cancer, they seldom developed cervical cancer, cells (light brown). Science Photo Library

Although these pioneering discoveries were initially greeted whereas the latter was a frequent disease among prostitutes. . Coloured TEM of HPV virions. Centre for with scepticism, each has stood the test of time. When the hunt was on for human cancer viruses following Infections / HPA / Science Photo Library

the discovery of Epstein–Barr virus in Burkitt’s lymphoma in 1964, several investigators implicated herpes simp- lex virus type II as the cause, but the epidemiology was inconclusive. Genital HPV strains were the first viruses to 1983: be discovered through DNA cloning because they were not amenable to classical isolation through cell culture. Zur Hausen cloned HPV-6 and HPV- 11 in vulval papillomas and used an a vintage year HPV-11 probe to pull out HPV-16 and then HPV-18 from malignant cervical carcinoma. Cloning methods were subsequently used to identify many other non-culturable human viruses, for pathogen such as hepatitis C virus, Kaposi’s sarcoma herpesvirus and this year, a novel polyoma virus in Merkel cell carcinoma. The discovery of genital HPVs led discovery to the recent development of two vaccines that prevent infection by the most prevalent cervical HPV strains.

192 microbiology today nov 08 microbiology today nov 08 193 Complete Media Assurance

Culture Media for Harmonised Microbial Limit Tests (Ph. Eur, USP, JP) Oxoid have the full range of culture media for the microbiological examination of non-sterile pharmaceutical products: • Fully validated according to the harmonised MLT methods in the Ph. Eur, USP and JP • Validation package available on request • Complete range for microbial enumeration and tests for specified micro-organisms • Quality Control tested using recommended strains b Coloured TEM of HIV particles (blue and yellow) To find out more contact: Tel: +44 (0) 1256 841144 budding from Fax: +44 (0) 1256 329728 the membrane of Oxoid, Wade Road, Basingstoke, Email: [email protected] a cell. Dr Klaus DEDICATED TO MICROBIOLOGY Hants RG24 8PW www.oxoid.com Boller / Science Photo Library fems half page 9/3/08 12:53 PM Page 1

C M Y CM MY CY CMY K The vaccines are based on virus-like particles containing no which were rapidly introduced for screening tainted blood genomes which self-assemble from recombinant coat protein donations. Treatment with anti-retroviral drugs has proved to and act as efficient immunogens. Hopefully, cervical cancer prolong the length and quality of life, but as with antibiotics, will eventually become a rare curiosity rather than the most drug-resistant strains of HIV emerge. Alas, an efficacious common women’s cancer. vaccine to protect against HIV infection is not yet in sight, 3rd Congress of European Microbiologists Whereas HPV and H. pylori represent ancient human infec- though not for want of trying. tions that have newly emerged to human knowledge, HIV-1 Each of these discoveries 25 years ago was a leap forward is a genuine newcomer, having transferred from chimpanzees in our understanding of persistent infections that lead to within the last 100 years. AIDS was first recognized in 1981 disease in humans, often years after the initial infection event. FEMS 2009 in gay men in the USA who developed Pneumocystis carinii In 2005, Barry Marshall and Robin Warren were awarded the Göteborg, Sweden, June 28 - July 2, 2009 infection or Kaposi’s sarcoma. The appearance in Africa Nobel Prize for the discovery of H. pylori. This year, similar around the same time of what was called ‘slim’ disease recognition has been given to Harald zur Hausen for the Microbes and Man - Interdependence and Future Challenges heralded the seriousness of the HIV pandemic. When HIV-1 discovery of HPV, and to Françoise Barré-Sinoussi and Luc was discovered in May 1983, epidemiologists already knew Montagnier for the discovery of HIV. that the underlying cause of AIDS was an agent transmissible FEMS CONGRESS HIGHLIGHTS KEY AREAS TO BE ADDRESSED: by sex, blood and blood products, and from mother to child. Robin Weiss • Plenary lectures by leading experts in their fields • Biodiversity; Bioremediation; Virology Different investigators had championed various candidate Division of Infection & Immunity, University College • Joint symposia with other international microbiological organizations: • Biofilms in Ecology and Medicine agents, such as leukaemogenic retroviruses, herpesviruses London, 46 Cleveland Street, London W1T 4JF, UK ASM, ESCMID, ISME, IUMS • Clinical Microbiology and Pathogenesis and papilloma viruses, or a fungus in the gut that might (t 0207 679 9554; f 0207 679 9555; e r.weiss@ucl. • Awards: Lwoff Medal; Jensen Award; Congress awards for young scientists • Eukaryotic Microbes release an immunosuppressive product like cyclosporine. ac.uk) • Inauguration of European Academy of Microbiology • Food Microbiology and Marine Microbiology So it was not immediately clear whether Barré-Sinoussi and • Microbial Stress Responses • Career fair for young scientists colleagues had found the genuine culprit – through classical • Microbes in Alternative Energy Generation Further reading • Nordic Midsummerís Night Party propagation in cell culture. However, the French team then Barré-Sinoussi, F., Chermann, J.C., Rey, F., & others (1983). • Molecular Microbiology and Genomics made further isolates from AIDS patients, showed that the Isolation of a T-lymphotropic retrovirus from a patient at risk virus was cytopathic in CD4+ T cells but not other cells, and for acquired immune deficiency syndrome (AIDS).Science 220, noted that it resembled a lentivirus. One year later, Bob Gallo 868–871. Abstract Submission Deadline: CONGRESS ORGANIZERS in the USA made his own claims to the discovery of HIV, but Dürst, M., Gissmann, L., Ikenberg, H. & zur Hausen, H. he had, in fact, confirmed those of the Insitut Pasteur. Gallo (1983). A papillomavirus DNA from a cervical carcinoma and its January 20, 2009 had discovered the first human retroviral pathogen, human prevalence in cancer biopsy samples from different geographic 1-3 rue du Chantepoulet, PO Box 1726 T-cell leukaemia virus in 1980, which in itself was a major regions. Proc Natl Acad Sci U S A 80, 3812–3815. For more information, please visit: CH-1211 Geneva 1, Switzerland milestone. Warren, J.R. & Marshall, B. (1983). Unidentified curved www.kenes.com/fems Tel: +41 22 908 0488, Fax: +41 22 732 2850 The discovery of HIV had an immediate impact on bacilli on gastric epithelium in active chronic gastritis. Lancet i, E-mail: [email protected]. Website: www.kenes.com public health through the development of diagnostic tests 1273–1275.

194 microbiology today nov 08 Composite he Higher Education Academy development of microbiology as a teaching discipline presented in the Profile highlights important educational and recently launched a landmark and its significance for society, for the economy and on intellectual issues. These include the need for the curriculum series of National Subject research in other biosciences. It details the current range to reflect the societal and economic impacts of microbiology Profiles, researched and written of higher education undergraduate and taught postgrad- and to keep pace with the rapid expansion of knowledge National by the Academy’s Subject uate programmes, including their curriculum content and in this field. Alongside this, programmes must meet the Centres. Informed by discipline the key teaching, learning and assessment patterns. Data needs and support the career aspirations of all students Tcommunities and practitioners, each are presented on trends in staffing profiles, student entry by achieving an appropriate balance between discipline- Profile provides an evidence-based profiles, student numbers and graduate destinations. There specific knowledge and transferable skills. And, crucially, Subject overview of higher education provision are also some baseline comparisons with other countries, students must have adequate opportunities to develop skills in a specific discipline, summarizing the including models of provision elsewhere and transferability in practical microbiology, including wherever possible the range of learning experiences available of qualifications. availability of laboratory-based final year research projects. and highlighting areas for develop- A key message is that students wishing to study micro- These are highlighted as priority areas for future development ment. Two Profiles were produced biology at university are offered programmes that are by the HEA Centre for Bioscience. Profile by the HEA Centre for Bioscience – exciting, relevant and diverse in their approaches to teaching, Resource issues are also emphasized, including the need Microbiology and Biochemistry. learning and assessment. The nature of undergraduate for adequate funding per student to support a laboratory- Each Profile was managed by a provision is very varied, and this enables students to choose intensive experience and the availability of appropriate panel comprising representatives a programme that meets their needs in terms of teaching teaching space. Attention is also drawn to the tensions often for from academia, employers, students and assessment methods used, support provided, options faced by academic staff when dividing their time between and learned societies. Sue Assinder available and specialisms taught. Although there has been research and teaching, and the recognition of the latter as (SGM Education Officer) chaired the concern in the sector in recent years about the decrease in an appropriate career option. Microbiology panel and Janet Hurst the number of ‘named’ microbiology programmes on offer, Those involved in producing the Microbiology Profile was a member to represent the various the Profile shows that large numbers of undergraduate hope that it will be a useful reference for both academics and higher microbiology learned societies. The students are still being exposed to a substantial amount students, together with a wide range of other groups such panel used data in the public domain of microbiology teaching. Although any loss of ‘named’ as employers, careers advisors and prospective applicants. where this was available (e.g. centrally programmes is to be regretted from the perspective of It is a starting point for discussion about how university published by funding councils and the maintaining the profile of the discipline, the Profile provides microbiology programmes can best meet the needs of both education results of the National Student Survey). reassuring data about the number of students graduating students and employers and ensure a continued flow of Where new data were required, the with the relevant microbiological knowledge. Data on microbiology graduates that is commensurate with the panel was grateful for the help of SGM graduate destinations show that microbiology degrees demands of the UK economy. It gives academic departments representatives in several academic provide entry to fascinating and varied careers both within information from which to reflect on the appropriateness of departments who provided information and outside the biosciences. their own programmes and provides a foundation that can programmes about their programmes and also The microbiology students surveyed were generally very be updated periodically to enable continual enhancement of allowed their students to be surveyed positive about their experiences. Most reported that their the student learning experience. about their learning experiences. The lecturers were enthusiastic, that their practical and generic The Microbiology and Biochemistry Profiles can be panel also made use of data collected skills had been developed effectively and that they would downloaded from the website of the HEA Centre for in by the SGM, such as the degree recommend their degree programme to others. They were Bioscience (www.bioscience.heacademy.ac.uk/events/themes/ programmes followed by winners of more negative about aspects flagged nationally as concerns sled.aspx). SGM undergraduate prizes. in the annual National Student Survey, such as feedback, The Profile reviews current pro- career guidance and availability of relevant work experience. Sue Assinder microbiology vision in relation to the historical Against this largely positive backdrop, the evidence SGM Education Officer

196 microbiology today nov 08 microbiology today nov 08 197 Science Careers is the key that opens doors. conferences

New for 2009 From 2009, Society meetings will have a new look. The scientific sessions over three and a half days will cover the latest topics in modern microbiology, within a framework of fewer parallel sessions in the mornings, standalone keynote lectures and afternoons packed with workshops, debates, demonstrations and mini-symposia catering for all areas of microbiological science. Poster-viewing will take place over a drink in the evenings. Career development and microbiology education will also be covered. The ever-popular Gala Dinner will retain its Tuesday evening slot. Divisions Scientific programmes will be organized by five Divisions: Prokaryotic Microbiology Eukaryotic Microbiology Virology Education Irish

Each scientific division is divided into four themes Microbial diversity and evolution Fundamental microbiology Translational and applied microbiology Infectious disease

The Education Division covers all aspects of education, training and career development. The Irish Division holds its own meetings in Ireland, but also contributes to the planning process of the main meetings.

Division members are selected to ensure that the appropriate areas of interest are covered. Elections for vacancies will be held annually. Each division is headed by a Chair and Chair-elect, who sit on the Scientific Meetings Committee responsible for making decisions on policy matters and meetings content. The Scientific Meetings Officer, who also has a Deputy, reports to Council. Society members can also make proposals for sessions to the Scientific Meetings Committee. This organizational matrix is shown below:

SCIENTIFIC MEETINGS OFFICER & DEPUTY (Hilary Lappin-Scott & Chris Hewitt)

Opening doors is what we do. We’re the key to connecting with Divisions the industry’s top employers. We’re the experts and source for the latest and most relevant career information across the globe. Virology Eukaryotic Microbiology Prokaryotic Microbiology Education Irish Chair Stuart Siddell Geoff Gadd Petra Oyston* Jo Verran Evelyn Doyle Our newly designed website offers a set of tools that help Chair-elect Mark Harris Neil Gow* Ian Henderson Sue Assinder* John McGrath you unlock career opportunities and your personal potential. Council rep* David Blackbourn Charles Dorman Whether you’re seeking a new job, career advancement in your Themes chosen fi eld or ways to stay current on industry trends, Science Microbial diversity John Walsh Paul Dyer Lucinda Hall David Adams Catherine Adley Careers is your key to a brighter future. & evolution John McCauley Saul Purton Mark Osborn Alan Cann Conor O’Byrne Your Future Awaits. Tony Fooks Tom Richards Ian Head Goura Kudesia John Morrissey Improved Website Features: Malcolm White Lynne Lawrance Gerard Wall » Relevant Job E-mail Alerts Fundamental Ade Whitehouse Adrian Harwood Nick Dorrell Sara Burton Kevin Kavanagh » Improved Resume Uploading microbiology Steve Goodbourn Al Goldman Maggie Smith Martin Adams » Content Specifi c Multimedia Section Lisa Roberts Mick Tuite Steve Busby » Facebook Profi le Jeff Green Translational Martin Cranage Geoff Robson Peter Andrew Job Search Functionality: microbiology Paul Duprex Diane Wilkinson Cath Rees » Save and Sort Jobs John Doorbar Dimitris Charalampopoulos Paul Langford » Track Your Activity Stuart Stocks » Search by Geography Infectious disease Judy Breuer Alan Fairlamb Mark Stevens » Enhanced Job Sorting Deenan Pillay Michael Ginger Paul Everest Katie Jeffery Antonio Di Pietro Dietrich Mack Explore ScienceCareers.org today! Adam Cunningham ScienceCareers.org

microbiology today nov 08 199 Spring09 Harrogate International Centre Autumn09 Heriot-Watt University For up-to-date information www.sgmharrogate2009.org.uk Edinburgh on all future Society events: www.sgm.ac.uk/meetings 30 March–2 April 2009 7–10 September 2009 Organization The organization of SGM Legacy of Fleming – Diagnosing, preventing, controlling and treating Translational microbiology conference programmes is co-ordinated by the Scientific infectious diseases in the modern world The 200th anniversary of the birth of Darwin will be marked by a symposium at this Meetings Officer, Professor meeting, alongside a range of sessions that explore the many ways that microbes can Hilary Lappin-Scott, and Deputy Who should attend? Novel antimicrobials and therapies be put to work, such as in food or drug production, cleaning up the environment, in Scientific Meetings Officer, industry and as model organisms. See www.sgmheriot-watt2009.org.uk for details. Professor Chris J. Hewitt. Antibiotics and the environment This will be the largest gathering of Suggestions for topics for future microbiologists in the UK in 2009. Impact of medical intervention on microbial evolution symposia are always welcome. Attendance is essential for anyone Infection control The administration is carried out who wants to keep up to date with OtherEvents IrishDivision New ways of rapid diagnosis by Mrs Josiane Dunn at SGM modern microbial science. Antibiotics in food preservation 15th Conference of the 22–23 January 2009 Headquarters, Marlborough Where is it? Production, formulation and delivery of antimicrobials (industry session) Federation of Infection Enterobacter sakazakii House, Basingstoke Road, Spencers Wood, Reading RG7 1AG (t 0118 Multi-drug resistant TB Societies University College Dublin, Ireland Located in the heart of historic 988 1805; f 0118 988 5656; Harrogate, gateway to the Yorkshire Mechanisms of resistance (with BSAC) Cardiff City Hall Joint organizers: UCD Centre for e [email protected]). Dales, the International Centre has Antibiotic resistance in staphylococci 2–4 December 2008 Food Safety & SGM Irish Division. excellent facilities. Harrogate is within The human microbiota www.fis2008.co.uk Abstracts easy reach of Leeds, York, Manchester Microbes in history: war wounds Titles and abstracts for all and Newcastle, with convenient rail, 23–24 April 2009 4th Annual Recent presentations are required in air and road transport links. Innovative models and systems for a standard format and should Virology Independent Virology studying microbial pathogenesis be submitted through the The programme will include symposia on Molecular evolution of virus Researchers’ (RIVR) Grants University of Cork, Ireland SGM website by the advertised pathogens, Structural insights into virus biology and Prions, 7 workshops Conference grants are available to Meeting For further details, contact John deadlines. For further information (Pathogenesis | Gene expression | Immunovirology | Epidemiology, evolution and SGM Associate Postgraduate Student Breadsall Priory Hotel, Morrissey (e [email protected]). contact the Administrator. Members. modelling | Entry, trafficking and egress | Virus structure | Plant virology) and near Derby poster sessions. 5–6 January 2009 Deadlines For details of other Irish Division For further details, contact Alain activities, contact Evelyn Doyle Abstract submission Other highlights Kohl (e [email protected]). (e [email protected]). 5 December 2008 New SGM Prize Medal – Professor Stanley Prusiner Earlybird registration Careers and Education Workshops Gala Dinner at the Old Swan Hotel 27 February 2009 Trade Exhibition Prize Lectures Poster Sessions Abstract Book – Dublin meeting The full text of the abstracts book is available as a PDF Go to www.sgmharrogate2009.org.uk for programme details, online registration and abstract submission. on the SGM website.

200 microbiology today nov 08 microbiology today nov 08 201 schoolzone

Schools Membership costs only £10 a year. Benefits include structures (traps). The type of trap produced will depend on the fungal Microbiology Today, advance copies of new teaching resources species involved. The predatory and discounted fees on SGM INSET courses. To join see fungus secretes chemicals that attract the nematode towards it (by www.sgm.ac.uk/membership. Enquiries: [email protected] chemotaxis), leading quickly to its or go to www.microbiologyonline.org.uk for full details of certain death. resources and activities. There are two basic type of traps that have evolved separately.

Adhesive traps Adhesive traps capture their prey by means of an adhesive layer covering Nematode- all or part of the trap. Although the traps are referred to as sticky, they Constricting rings are not sticky like adhesive tape Conidium because the devices don’t get clogged up with debris such as soil. Instead killing fungi the adhesive on the fungal trap binds strongly to sugar compounds on the When we think of predatory The fungi that have developed ways of chemotaxis), as the nematode senses surface of the nematode. utilizing nematodes as their main food this as potential food. This helps to Different kinds of adhesive trap creatures, it tends to be in terms source (nematophagus fungi) can be ensure that attachment takes place. include: divided into two different groups: The fungal spores are either directly networks – the most common ingested by the nematode, where they of tigers stalking other animals in endoparasitic fungi which produce type of trap. They resemble a mesh attach to the gut cuticle, or are sticky spores that infect nematodes of interlocking loops which ramify and adhere to the nematode’s external predatory fungi which catch their through the soil. the jungle. But as Dariel Burdass cuticle. prey with specialized hyphal devices knobs – erect stalks with an Once attached, the spore germinates, describes, fascinating examples adhesive bulb at the end that are producing a germ tube which Endoparasitic nematophagus spaced out along the length of the penetrates the nematode’s cuticle. The of killers and their victims can be fungi hyphae. fungus grows, creating a network of These fungi are obligate parasites, hyphae that produce enzymes which non-constricting rings – composed found on a much smaller scale. which means that they spend almost break down the nematode’s insides of 3 cells that do not change in size all their life cycle inside infected into a nutritional soup. The nematode or shape. They always occur This article explores how certain nematodes and only emerge to dies within 48 hours as a result. 3–10 alongside adhesive knobs. sexually reproduce, i.e. to develop and days after initial infection, the fungus Following adhesion, the nematode’s fungi have adapted, forming disperse their spores. They use the generates aerial hyphae along the fate is sealed. Even if it struggles nematode as their main or only food length of the cadaver. These break m Top. Light micrograph of a nematode captured by the constricting rings of the predatory to break free, the fungal trapping source. fungus Drechslerella anchonia, showing a germinating spore (conidium) with the germ hypha lassoes and sticky pads, to through the cuticle and produce producing a series of constricting rings around the nematode. MycoAlbum CD – George Barron organ, which is firmly bound to the The spores release a chemical which aerial spores which are dispersed by m Bottom. Scanning electron micrograph of a nematode captured by the constricting rings of nematode, will break from the hyphae, capture nematodes for food. attracts the nematodes towards it (by the wind and rain. The process starts the predatory fungus D. anchonia. George Barron & Nancy Allin, University of Guelph, Canada remaining attached to the nematode and initiate infection. all over again. If conditions are not free-living nematodes. They produce What are nematodes? favourable, the fungus can produce traps at intervals along the length of Constricting rings Nematodes are tiny non segmented ‘worms’. They are 100–1,000 µm long, resistant spores within the dead their hyphae that capture, penetrate, which is approximately the width of a human hair. They taper at both ends nematode that allow it to survive until kill and digest a nematode’s contents. This is the most sophisticated of the and are covered by a transparent protective cuticle. They are not related to conditions for growth are suitable. The traps are usually formed in trapping devices and is common in the segmented worms. Nematodes are widespread, occurring in all types of soil, response to the presence of substances species Drechslerella anchonia (formerly Predatory nematophagus produced by the nematodes. Hyphal Arthrobotrys). The nematode wriggles rotten wood and animal dung. Their numbers in a nematode-rich habitat fungi can reach 20 million per m2. Nematodes cannot see and hunt for food using differentiation occurs spontaneously, into the ring hoping to find food, their sense of smell. Over 200 species of fungi use usually very quickly, within a but as it touches the ring it triggers specialized structures to capture few hours, to produce functional a response. Three curved cells at the

202 microbiology today nov 08 microbiology today nov 08 203 end of a short stalk, which make up the closed loop, swell rapidly inwards, within 0.1 seconds crushing the worm like The oyster mushroom Book review SGM at ASE Annual a noose around the neck. Death follows very quickly. Pleurotus ostreatus, the oyster mushroom, produces Germ Stories Conference 2009 Once ensnared, the fungus pierces the nematode’s cuticle a very powerful toxin from special structures on using a narrow penetration peg, which swells inside the its hyphae. This toxin paralyses the nematode, but A. Kornberg 8–10 January, University of Reading host to form an infection bulb that the hyphae grow from. doesn’t kill it. The fungus then sends out specialized University Science Books Fungal enzymes break down the contents of the nematode directional hyphae that penetrate the nematode’s (2007) SGM and the Microbiology in Schools Advisory and the nutrients are translocated elsewhere within the cuticle and digest the contents. £17.99 pp. 72 Committee are joining forces to promote microbiology at hyphal system for growth or spore production. Growth does ISBN 978-1-891389-51-1 the Association for Science Education’s flagship event. not occur at the site of the hyphal trap. Not only can teachers visit us on Stand CS31 in the nematodes can kill their host animal, leading to significant Hurry, hurry to the parade This phase usually takes 1–3 days, before hyphae grow out Exhibition, to see our latest multimedia resource for KS3 financial loss for the farmer. Treatment is almost Of the strangest creatures of the cadaver and sporulate. and GCSE Microbes: the Good, Bad and Ugly, but they can exclusively with drugs that kill or expel the worms. ever made. also hone their practical skills at our drop-in workshop. However, nematodes are now becoming resistant to No legs, no fins, no mouths, This will take place in a lab in the AMS Building, shared Nutrition the drugs, so scientists are looking at other methods of no eyes, with prestigious safety body CLEAPSS. Predatory fungi have evolved these trapping devices to treatment. Little beasties of the tiniest obtain nutrients and give them an edge over other types of One idea that is being tested is the use of the nematode size Under the banner Hands-on Practical Microbiology for organisms in habitats where population densities are high trapping fungus Duddingtonia flagrans. This fungus uses the new GCSEs, experts from MiSAC will demonstrate some essential methods which delegates can try out and consequently competition for resources is fierce. the adhesive net technique to trap and kill nematodes. Germ Stories is a charming anthology of microbiological under their professional guidance. In addition there will The primary function of predatory fungi is wood decay. Researchers are feeding D. flagrans to the animal as spores, verse. Written by the Nobel laureate Arthur Kornberg, be workstations with some simple but effective practical Wood is mainly composed of carbohydrates: cellulose and either directly in their food or in mineral licks. The fungal it comprises 12 poems about bugs, both good and investigations to see. lignocellulose. The carbon to nitrogen ratio (C:N) of wood spores pass through the digestive system of the animal both bad, beautiful and ugly. Originally intended as bedtime is very high at 300:1–1,000:1 or even higher. For good unharmed and without germinating and are deposited stories for his children, they have been updated for his growth to occur, most organisms require a C:N ratio of on the grass in the faeces. The spores then germinate grandchildren (and the 21st century) to include microbes Biology in the Real World: 30:1 to produce nucleic acids, proteins and enzymes. For producing mycelia with hyphal traps that catch and kill such as HIV and Helicobacter pylori. Bringing the Curriculum to Life the nematodes. This significantly reduces the number of predatory fungi nitrogen is the limiting factor for growth. This book is both educational and highly entertaining. 9 January 2009 Nematophagus predatory fungi get their extra nitrogen from nematodes on the pastureland that are able to reinfect the Room 109, Palmer Building, University of Reading grazing animal. The rhyming couplets are interspersed with Roberto digesting the nematode’s biomass. Kolter’s fascinating photographs and accompanying SGM and MiSAC are also sponsoring a speaker on TB This means that predatory fungi are not true saprotrophs Dariel Burdass, SGM explanatory text. The lyrical quality of Kornberg’s writing vaccines in this one-day symposium, which is organized by (which live on dead organic matter) as two phases that run is complemented by Adam Alanz’s enchanting illustrations members of NUCLEUS. in parallel are necessary to supply them with the correct Further sources of information which strike a careful balance between the whimsical and Dr Helen Fletcher, a senior postdoctoral scientist at the nutrients for growth – the predatory parasitic phase and the www.pnas.org/content/104/20/8379.full the scientifically accurate. Nuffield Department of Clinical Medicine, Oxford, will saprotrophic phase. Predatory fungi are facultative parasites. www.uoguelph.ca/~gbarron/MISC2003/feb03.html My only criticism would be that, considering its intended answer the question Why do we need a new vaccine for Deacon J.W. (1997). Modern Mycology, 3rd edn. Oxford: audience, some of the terminology is advanced. I doubt tuberculosis? With 2 million deaths a year from TB and Biological control Blackwell Science. words like ‘microbiocide’, ‘ATP’ and ‘antitoxin’ normally an estimated third of the world’s population infected with Mycobacterium tuberculosis, new vaccines for TB are Experiments are being carried out to see if predatory Jansson, H.-B. & others (1985). Differential adhesion and feature in the average child’s bedtime tales (unless your fungi can be used to control parasitic nematodes that infection of nematodes by the endoparasitic fungus Meria Dad happened to win a Nobel prize in Medicine!), but the urgently needed. Drug treatment and the BCG vaccine have infect grazing animals such as sheep. These gastrointestinal coniospora. Appl Environ Microbiol 49, 552–555. fluidity of his language fully compensates for this. It would failed to control the current epidemic. Dr Fletcher will certainly suit the inner child lurking in an adult biologist talk about MVA85A, a new vaccine designed to boost the and what better way to teach your children the important, protective immune response induced by BCG, and discuss yet difficult, concepts of food hygiene, antibiotic resistance the scientific, clinical and ethical issues surrounding the MiSAC Poster Competition 2009 – and vaccination? development of new TB vaccines. This is one of those tactile books that will survive the The topic will be of particular interest to teachers of KS4 Microbes and Climate Change digital age. A hardback with huge, colourful images and and post-16 biology as factual and ethical issues relating to thick, glossy pages, it invites you to snuggle up with it TB and vaccination figure large in the specifications. This year SGM is sponsoring the annual competition, which asks school under a warm duvet or next to an open fire. It is a book See www.ase.org.uk for further details of all events at the students in two age groups (KS 3 and GCSE) to produce an eye-catching poster to be treasured and would make an ideal Christmas Annual Conference. to illustrate to their peer group one important aspect of the role of microbes in present, for the young or old. climate change. There are cash prizes for both the winning schools and students Please note that anyone wishing to attend any event at the in each category. The closing date for entries is 31 March 2009. Gemma Sims, SGM conference must register, either beforehand or on-site. Checkout www.microbiologyonline.co.uk for details and to download an entry form or email [email protected] for a competition flier and informative factfile about this subject.

204 microbiology today nov 08 microbiology today nov 08 205 gradline

Gradline aims to inform and entertain members in the early 3 Researchers are equipped and supported to be adaptable Commitment to professional development also has and flexible in an increasingly diverse, mobile, global to be personal. Researchers should take control of stages of their career in microbiology. If you have any news research environment. their development and make the most of appropriate opportunities offered by their employers. or stories, or would like to see any topics featured, contact 4 The importance of researchers’ personal and career development, and lifelong learning, is clearly recognized Practical ideas for implementation of the Concordat for Jane Westwell (e [email protected]). and promoted at all stages of their career. research staff: 5 Individual researchers share the responsibility for and See if you can join a mentoring scheme, either as a need to proactively engage in their own personal and mentor or a mentee career development, and lifelong learning. Be proactive about networking 6 Diversity and equality must be promoted in all aspects of Are you represented? Could you join a committee in your A Concordat the recruitment and career management of researchers. institution or a postdoctoral or similar society? 7 The sector and all stakeholders will undertake regular Discuss your career and development in an appraisal with and collective reviews of their progress in strengthening your line manager the attractiveness and sustainability of research careers in to support Explore your career options with a careers advisor. Many the UK. institutions now have one specializing in research staff Attend appropriate transferable skills training courses the career What will the Concordat achieve? Consider how your current skills could be translated to Tristram Hooley and Tennie Videler The Concordat encourages institutions to embed other careers support for researchers and maximize their potential both from Vitae, look at the new Concordat within research roles and beyond. Managers of researchers You can find out more about the Concordat and related development developments by visiting the Vitae website at www.vitae. and ask what it will mean in practice for (such as PIs) are encouraged to look for opportunities to develop their staff by mentoring them and giving them ac.uk/policy-practice/ research staff and PIs. more responsibilities. Typically this might be done through of researchers appraisals, professional development courses and access Tristram Hooley to tailored advice. Senior Manager, Stakeholders and Networks, What is Vitae? can support your work; visit the Vitae website to find out Personal developmental activity often impacts the success of Vitae (e [email protected]) more. The website includes dedicated sections dealing with projects; it can increase the effectiveness of researchers and Tennie Videler Vitae (www.vitae.ac.uk) is a national organization professional development and careers for research staff. We help keep motivation and vision within a longer term career Programme Manager, Researchers (e tennie. championing the professional and career development of also offer a regular newsletter for supervisors and managers context. [email protected]) researchers. Funded by Research Councils UK (RCUK) and of research and regular events and courses to help you get managed by CRAC: The Career Development Organization, to grips with issues and access a network of colleagues with Vitae builds on previous work by the UK GRAD Programme whom you can share ideas and practice. SGM Meeting at Harrogate, Spring 2009 for Experimental Biology, SEB and UKHERD to involve all stakeholders in supporting the (www.sebiology.org). With an early professional development of researchers. Through national Workshop for early career microbiologists – Personality at work The Concordat background in biological sciences activities, and the work of eight regional Hubs, Vitae research and publishing, she is now works with higher education institutions, researchers and The 2008 Concordat to support the career development of 1915, Monday 30 March 2009 a qualified careers coach and has employers for real and positive change. researchers was launched in June. It is a statement of key Delivered by Sarah Blackford (Society for Experimental Biology) worked as a careers consultant within Vitae’s vision is for the UK to be world-class in supporting principles for the support and management of researchers university careers services and, more and their careers, agreed by Universities UK and major the professional development of researchers and researcher Have you ever wondered why there personality elements which describe recently, with the SEB for over 10 funders of research in the UK. It recognizes that permanent careers. are some people you get on with you or that you recognize in your years. Sarah is a qualified MBTI (Myers research or academic positions are limited. The Concordat The programme has four key aims: and others you don’t? Why it is that friends or colleagues and will attempt Briggs Type Indicator) practitioner and could deliver real progress but its success depends on some people just don’t seem to be to demonstrate the importance of uses it as a basis for self-awareness in Championing the development and implementation of researchers and their managers re-examining the ways they thinking along the same wavelength considering personality in your day- the career development programmes effective policy work. as you or seem disorganized or to-day working life and for your career she runs which are specifically Enhancing higher education provision through sharing The Concordat’s key principles are: dispassionate? development and planning. As well designed for postgraduates and practice and resources postdoctorals. 1 Recognition of the importance of recruiting, selecting and In this session, you will learn about as being informative, the session will Providing access to development opportunities and retaining researchers with the highest potential to achieve a well-known personality inventory, take a light-hearted and interactive The session will be followed by buffet resources excellence in research. the MBTI (Myers Briggs Type approach giving you the insights and drinks. Building an evidence base to support the researcher 2 Researchers are recognized and valued by their employing Indicator), and how it can help to as well as the practical uses for this This event is restricted to postgraduate development agenda organization as an essential part of their organization’s decipher between different personality fascinating instrument. students and first postdocs attending As a researcher or manager of researchers, Vitae offers human resources and a key component of their overall types. The session will give you the Sarah Blackford is the Education & the conference and pre-registration is you access to a range of information and services that strategy to develop and deliver world-class research. opportunity to recognize some of the Public Affairs Officer for the Society essential.

206 microbiology today nov 08 microbiology today nov 08 207 addresses

council08–09 Enhancing the Officers Members President – Prof. Robin Weiss Prof. Mike R. Barer undergraduate Division of Infection and Immunity, University College London, Infection, Immunity and Inflammation, University of Leicester, 46 Cleveland Street, London W1T 4JF Medical Sciences Building, PO Box 138, University Road, t–0207 679 9554;–f–0207 679 9555;–e–[email protected] Leicester LE1 9HN t–0116 252 2933;–f–0116 252 5030;–e–[email protected] experience Treasurer – Prof. Colin R. Harwood School of Cell and Molecular Biosciences, University Dr David J. Blackbourn Each year, the SGM Vacation Studentship scheme funds of Newcastle Medical School, Framlington Place, , Cancer Research UK Institute for NE2 4HH Cancer Studies, Edgbaston, Birmingham B15 2TT more than 40 undergraduate research projects lasting 6–8 t–0191 222 7708;–f–0191 222 7736 t–0121 415 8804;–f–0121 414 4486 weeks during the summer before the students enter their final e–[email protected] e–[email protected] year. Summer students gain valuable practical experience and General Secretary – Dr Ulrich Desselberger Prof. Neil A. R. Gow School of Medical Sciences, Institute of Medical Sciences, an insight to microbiology research. Jane Westwell caught Dept of Medicine, University of Cambridge, Level 5, Addenbrooke’s Hospital, Cambridge CB2 2QQ University of Aberdeen, Aberdeen AB25 2ZD t–01224 555879;–f–01224 555844;–e–[email protected] up with three students from the 2007 cohort. t–01223 763403;–e–[email protected] or [email protected] Dr Richard M. Hall Li Yen Mah – University of Manchester Anna Janowicz – Scientific Meetings Officer – Prof. Hilary M. Lappin-Scott Biological Reagents and Assay Development (BR&AD), (supervised by Dr Christian Heintzen) University of Glasgow GlaxoSmithKline R&D, New Frontiers Science Park – North Site Dept of Biosciences, University of Exeter, Geoffrey Pope (supervised by Dr Robert Davies) SC1, H31/1-047 (Mail Code H31111), Third Avenue, Harlow, Li Yen’s project looked at VVD – a photoreceptor and Building, Exeter EX4 4QD Essex CM19 5AW repressor of light-signalling in the model eukaryotic Anna studied two different ethanol- f–01392 263434;–e–[email protected] microbe Neurospora crassa that also plays a role in producing micro-organisms – t–0127 962 7172;–f–0127 962 7014 modulating light-resetting of the organism’s circadian clock. Zymomonas mobilis and Saccharomyces International Secretary – Prof. George P. C. Salmond e–[email protected] The aim of her project was to identify domains within VVD cerevisiae, determining which one Dept of Biochemistry, University of Cambridge, Tennis Court Dr Kim R. Hardie Road, Building O, Downing Site, Cambridge CB2 1QW that are important for resetting of the circadian clockwork. would be most suitable for large- University of Nottingham, Centre for Biomolecular Sciences, t–01223 333650;–f–01223 766108 After the project Li Yen commented, ‘I am very inspired by scale bioethanol production. Anna University Park, Nottingham NG7 2RD e–[email protected] Dr Heintzen’s and his team’s hard work, and this experience enjoyed the opportunity to learn t–0115 846 7958;–f–0115 586 7950 has instilled in me the passion to pursue a career in scientific much more about real-life research Education Officer – Dr Susan J. Assinder e–[email protected] research.’ work than during routine laboratory Director of Education, Liverpool School of Tropical Medicine, Prof. Mark Harris classes. She found the studentship Pembroke Place, Liverpool L3 5QA Li Yen has been accepted by the Beatson Institute of Institute of Molecular & Cellular Microbiology, Faculty of Cancer Research in Glasgow to pursue a PhD studying how good preparation for her industrial t–0151 705 2515;–e–[email protected] placement at the University of South Biological Sciences, , Leeds LS2 9JT autophagy is regulated, and how this might integrate with Editor, Microbiology Today – Dr Matt Hutchings t–0113 343 5632;–e–[email protected] apoptosis to cause tumour cell death. Her long-term aim is Bohemia in the Czech Republic which School of Biological Sciences, University of East Anglia, to be a principal investigator in a university. started a month after she completed Dr Paul A. Hoskisson the studentship. Anna commented, Norwich Research Park, Norwich NR4 7TJ Strathclyde Institute of Pharmacy & Biomedical Sciences, ‘I think that all students of biological t–01603 592257;–e–[email protected] University of Strathclyde, 204 George Street, Glasgow G1 1XW Leanne Allum – Cardiff University sciences should have an opportunity like Editor-in-Chief, Microbiology – Prof. Charles J. Dorman t–0141 548 2819;–e–[email protected] (supervised by Professor Lynn Boddy) this to find out what real research is like Dept of Microbiology, Moyne Institute, Trinity College, Dr Catherine O’Reilly and whether it is a good choice for them or Leanne’s project focused on investigating isolates of the Dublin 2, Ireland Dept of Chemical and Life Sciences, Waterford Institute of not. It reassured me that this is something endangered oak polypore Piptoporus quercinus for evidence t–+353 1 608 2013;–f–+353 1 679 9294;–e–[email protected] Technology, Cork Road, Waterford, Ireland of inbreeding. Samples came from different areas of I want to do in future. It also provided Editor-in-Chief, JGV – Prof. Richard M. Elliott t–+353 51 302858;–f–+353 51 378292;–e–[email protected] Windsor Great Park, Germany and Wales and early results a good insight into what to do if things from Leanne’s project indicated that the species may be go awry, which is a helpful experience Centre for Biomolecular Sciences, School of Biology, University Prof. Petra C. F. Oyston highly inbred. Before the project started Leanne hadn’t been regardless of what field you go into!’ of St Andrews, North Haugh, St Andrews, Fife KY16 9ST TL Molecular Bacteriology, Dstl, B07A Microbiology, Porton t–01334 463396;–e–[email protected] sure that a career in science was for her but afterwards she Anna returned to Glasgow recently to Down, Salisbury SP4 0JQ t–01980 613641;–f–01980 614307;–e–[email protected] observed, ‘The placement definitely made me want to continue complete her MSc. She plans to apply Editor-in-Chief, JMM – Prof. Charles W. Penn working in labs as I loved the hands on experience.’ Leanne was for a position as a trainee clinical School of Biosciences, University of Birmingham, Edgbaston, Dr Gary Rowley pleased to graduate with an upper second class honours microbiologist and continue research Birmingham B15 2TT School of Biological Sciences, University of East Anglia, degree and aims to find a lab-based role near her home in in this field with a view to one day t–0121 414 6562;–f–0121 414 5925 Norwich NR4 7TJ Wiltshire. leading her own research team. e–[email protected] t–01603 592889;–e–[email protected]

208 microbiology today nov 08 microbiology today nov 08 209 obituary

launching the most productive and highly cited era of his hair was always well cut and brushed. With his wife Sue, and Professor Chris Thurston tragically short career. In collaboration with excellent post- later their daughter Anna, they lived in beautifully restored doctoral researchers and his long-standing friend David period houses. His office at QEC was very organized; neat Wood (HRI) and funded by competitive research council examples of his curious, rather spidery handwriting were (29.06.1944–18.07.2008) grants, Chris tackled the cloning and characterization of genes carefully filed. encoding proteins involved in the degradation of cellulose, a In the College community, Chris will probably be best Chris Thurston died after a long illness at the Royal Hospital for Neuro- process critical to the commercial production of the mush- remembered for his outstanding contributions to College room. Laccase (polyphenol oxidase) received the most management through services to at least 20 Committees disability in London. He had suffered profound brain damage following attention since it is an abundant glycoprotein that constitutes and Boards during his 31 years at QEC/King’s. In 1975–76, a major heart attack 8 years ago and remained in care for almost all this 2% of mycelial protein during vegetative growth. Chris also he represented the Academic Board of QEC on the College time. Chris was a polymath, an adventurous and successful researcher and published significant papers onA. bisporus proteinases, xylan- Council, and was later a major driving force in the University ase and peroxidases and, in particular, the cellulases that of London Board of Studies. He was instrumental in some an accomplished teacher, administrator and communicator. During his enable growth on crystalline cellulose as carbon source; four of the most tumultuous mergers and reorganizations the academic career, conducted almost entirely in the cellulose-growth specific cel( ) genes were isolated and charac- University has seen. He was a member of the joint Working Colleges, he played a major role in the development of microbiology and terized and their regulation elucidated. These papers (e.g. Party for the merger of QEC, Chelsea College and King’s Yagüe et al., 1997, Microbiology 143, 239–244; Smith et al., College (1983–85) and played a similar role from 1994 higher education in London. Chris always made a big impression: he was 1998, Microbiology 144, 1063–1069) illustrate beautifully on the Academic Planning Team for the King’s/UMDS unusually articulate, humorous and generous. Chris’s concise and precise writing and a clarity of thought merger. He was Deputy Head of the Division of Biosphere and expression. This topic occupied Chris until his illness, Sciences from 1988 to 1991 and retained a high profile in Chris was a London microbiologist through and through, but be appointed to a permanent academic position without a generating en route his most highly cited paper, a valuable Divisional management in its successor, Life Sciences. He not a Londoner by birth. Born in Norfolk, he went to King PhD; indeed, Chris took the place of Mr John Birch in John review in Microbiology (Thurston, 1994, 140, 19–26; 578 worked tirelessly with Marian Simmonds on ‘The Cornwall Edward VI School in Norwich, where he was Head of House, Pirt’s group, and Brian Bainbridge, Don Kelly and Tony Trinci citations to date). It is quite typical of Chris’s modesty that this House Project’ to plan and bring to fruition the move of and active in school rowing, drama and the choir. Chris were all appointed before award of their PhDs. Nevertheless, review acknowledges David Wood as follows: ‘…from whom the Kensington scientists to Waterloo, generating through a was also a Norwich Cathedral chorister. After his arrival in PhD or not, Chris made quite an impression as an extremely I have learned greatly about laccases and other fungal enzymes; PFI the current home of Biomedical and Health Sciences – University College London (UCL) as an undergraduate, Chris bright yet sociable new colleague at QEC. he is not however responsible for any errors or omissions – the Franklin-Wilkins Building. His work for the project never left the capital to work, apart from a sabbatical period One of the defining characteristics of Chris’s research career they simply reflect my imperfect learning’. planning team involved innumerable plans, measurements, (1979–80) with Bob Schmidt at the Virginia Polytechnic was his enthusiasm for tackling technically and intellectually Chris served the SGM with dedication and distinction. He and company representatives, not to mention a great deal of Institute, Blacksburg, USA. difficult projects. Those topics would be challenging now, was for many years (1987–92) an Editor of the Journal of hassle. These were trying times, yet Chris remained incredibly Chris had entered UCL to read microbiology, but in the but truly daunting in the 1970s and 1980s. Chris stuck with General Microbiology (the predecessor of Microbiology) and resilient, exuberant and professional in all his dealings. He Department of Botany. Microbiology departments were very the intransigent C. fusca for over 15 years. However, for most served as Professional Affairs Officer (1993–98). made trips overseas to inspect laboratories already designed thin on the ground, so Chris obtained his degree under a of the 1980s, he became fascinated by another, apparently His inclination to incisive thought and reasoning and his and furnished by tendering companies: a trip to California hybrid scheme jointly administered by UCL and Queen unrelated, line of research on the design and fabrication of love of precise measurements and instrumentation were was memorable for his hotel room, which was accessed by Elizabeth College London (QEC), where microbiology was redox-mediated electrochemical sensors using whole micro- reflected in Chris’s many other interests. He greatly admired a high walkway – unsuited to his vertigo. Today’s Franklin- well established. Chris stayed at UCL to do a PhD on the alga organisms. In collaboration with Peter Bennetto (Chemistry optically and mechanically fine cameras and we enjoyed Wilkins Building on the South Bank is largely based on the Chlorella fusca under the supervision of Philip Syrett. When Department), Jeremy Mason, John Stirling (Biochemistry), many long debates on the relative merits of rangefinder, large scheme that he helped to generate for disposition of the Syrett was appointed to a chair at Swansea, Ian Morris acted Sibel Roller and Gerard Delaney, over a dozen papers, chapters format and SLR cameras. I suspect that Chris would not have office, social, teaching, library and research space. as supervisor. and patents were generated. The two most cited (Roller et al., objected to the assertion that he treasured the photographic Chris was a thorough, systematic teacher and examiner yet It may seem extraordinary to 21st century young scientists 1984, J Chem Tech Biotechnol 134B, 3–12; Delaney et al., apparatus as much as the images. He appreciated fine Eastern with no sense of self-importance. His intellect never got in that, while still working for a PhD, Chris was appointed in ibid. 13–27; 79 and 90 citations, respectively) quantify the carpets, wines, whiskies (and was a founding member of the the way. Keith Gull remembers Chris accepting with good 1969 to the first lectureship in Biochemistry at QEC in leafy reduction by diverse bacteria of dyes and show how an appro- exclusive QEC Malt Whisky Society), cigars (for a while) and grace a prank involving the removal of his office door (yes, (and trendy) Kensington. In 1970, having obtained his PhD, priate combination of microbe, mediator dye and oxidizable food (offering, for example, a postdoctoral colleague a dinner the removal of the office door) and hiding it in a basement he transferred to the Microbiology Department, an influential, substrate can generate significant, anodic electrode potentials. party recipe for watercress, date and orange salad). In these room for a week! vigorous and congenial consortium. The Department was Subsequent papers described electrochemical bioreactors worldly pleasures, as in his published research output, Chris Chris was, in Sue Thurston’s words, curious, kind and established in 1961 from a Bacteriology Department that had for treatment of carbohydrate wastes and effluents and valued quality over quantity. At lunchtimes, in QEC days, he contented. He was a fine gentleman and an accomplished existed since 1914. At the time of Chris’s move there, the application of the principle to biosensors and a sucrose fuel would walk through the lanes of Holland Park adjacent to scientist. The plethora of his accomplishments endeared him Department comprised John Pirt (the only Professor and cell to achieve efficient biomass conversions. the College, discussing work, life and experiments with a few to so many. Their loss and sorrow must be compounded by Head of Department), together with ‘Simos’ Anagnostopoulos, Throughout, the science was the motivating force for close colleagues. Chris had a rare regard for an appropriate the nature of his long illness. Brian Bainbridge, Michael Bazin, Don Kelly, Ted Mathison Chris, but he wanted to share the excitement too and so took work/life balance. and Tony Trinci. (Shortly after, in 1975, this author joined to great pains to explain his work to others – at home, over the Chris was humorous, a mine of information and an observer Robert Poole, The University of Sheffield replace Don Kelly). Of these lecturers, six became university snooker table and to his many colleagues and friends. Equally, of small detail. He loved The Times crosswords. Chris also professors – remarkable then, less remarkable now. Equally he was an excellent listener and always curious to learn what had style. In a decade where many of his colleagues paraded I am very much indebted to Sue Thurston, Keith Gull, Janet Hurst, remarkable was the peripatetic electric typewriter that was others were doing and how they were doing it. dubious sartorial taste (and I dare not mention by name which Joy Poole, Sibel Roller, John Stirling, Tony Trinci and Ann Wood for the used by all staff except John Pirt, who had both typewriter In 1992, he published his first paper on the molecular colleagues), Chris favoured highly polished, brown brogue recollections, constructive comments and invaluable information received and a secretary to use it. It was certainly not remarkable to genetics of the commercial mushroom, Agaricus bisporus, shoes and tailored, crisp shirts, and his trademark, reddish during the writing of this obituary.

210 microbiology today nov 08 microbiology today nov 08 211 hotoffthepress

Science writer Meriel Jones takes a look at Bugs and colon cancer The authors have been experimenting with Enterococcus HIV by numbers faecalis, a minor inhabitant of the colon but one that can some recent papers in SGM journals which Allen, T.D., Moore, D.R., Wang, X., Casu, V., May, R., cause DNA damage and promote chromosomal instability by Hogue, I.B., Bajaria, S.H., Fallert, B.A., Qin, S., Reinhart, T.A. Lerner, M.R., Houchen, C., Brackett, D.J. & Huycke, M.M. releasing reactive oxygen species. They wanted to know how & Kirscher, D.E. (2008). The dual role of dendritic cells in the highlight new and exciting developments in (2008). Dichotomous metabolism in Enterococcus faecalis the colon responded to this threat. They have discovered that, immune response to human immunodeficiency virus type 1 induced by haematin starvation modulates colonic gene although the colon tissue looks perfectly normal under the infection. J Gen Virol 89, 2228–2239. microbiological research. expression. J Med Microbiol 57, 1193–1204. microscope, the activity of several genes altered rapidly once Trying to understand exactly why HIV-1 invariably causes The colon is home to around 1011 bacteria per gram of the bacteria released oxidizing chemicals. Looking in more a lethal infection has highlighted our lack of understanding contents. For many years, scientists have argued about detail, the researchers proved that E. faecalis could activate the of many of the complex interactions in the human immune Getting into shape whether the presence of this vast microbial horde is always in NF-κB signalling pathway in white blood cells – this signal system. Cells have dual roles, as targets for disruption by the best interests of its human host. Specifically, the idea that can promote tumours. HIV-1 and as essential components in an immune response to Pul, Ü., Lux, B., Wurm, R. & Wagner, R. (2008). Effect of some bacteria are involved in sporadic colorectal cancer has After checking 5,000 genes, the researchers identified 42 that counter the infection. Hogue et al. have tried a new approach upstream curvature and transcription factors H-NS and LRP been around, but unproven, for decades. The major difficulties increased or decreased in expression. Several were involved to this problem by creating a mathematical model to describe on the efficiency of Escherichia coli rRNA promoters P1 and with making any progress are that most of the microbes have in the immune response, while 9 were implicated in stress how HIV-1 and cells interact in a human lymph node. P2 – a phasing analysis. Microbiology 154, 2546–2558. not been identified and the interaction between bacteria and responses and a further 10 in control of whether the cell In the decades since HIV-1 was identified, much data have The double helix structure of DNA is one of the great icons the surface of the colon has many unknown features. should divide or die. Looking into the roles of these genes in been recorded on how the numbers of viral particles and of the 20th century. However, DNA has additional structural To make progress, scientists in Oklahoma, USA, have more detail brought out the message that E. faecalis affects a different types of human cells change throughout an infection. features. As well as the exact sequence of the nucleotide concentrated on bacteria that are known to damage DNA since single response network that contains NF-κB signalling and Myeloid dendritic cells (DCs) in the lymph nodes activate bases, the shape of the DNA molecule is important. Each this could start the genetic changes required for cancer. The several genes that have been implicated in cancer biology. T-cells to defend against HIV-1. One type of T-cell, CD8+, comparatively large DNA molecule folds to fit into the cell, damage is caused by highly reactive forms of oxygen known as The argument about the role of bacteria in colon cancer has has the main protective role against HIV-1 infections through but regions remain available for use at a moment’s notice, superoxide, hydroxyl radicals and hydrogen peroxide which thus moved forward with implication of specific mechanisms killing infected cells and releasing antiviral factors. Another controlled by proteins and DNA structure. The DNA bases diffuse from some bacteria when they are stressed and into the through which E. faecalis can increase the susceptibility of T-cell type, CD4+, is also important in the body’s defences, ahead of every gene are important for regulating when each is surrounding animal or human tissues. colon cells to DNA damage. but is attacked by the virus. DCs can thus promote immunity switched on or off by proteins binding at a region called the as a link between the virus and T-cell defences, but are also promoter. DNA curvature and regulatory proteins act together used by HIV-1 to boost infection. It is difficult to study DCs to regulate the efficiency with which genes are used, but many Novel bone disease mycobacterium more detailed tests that recorded the sequence of several directly because they reside within lymph nodes which cannot of the exact details are unknown. genes from the bacteria showed some differences from all be examined easily. The advantage of a mathematical model Bang, D., Herlin, T., Stegger, M., Andersen, A.B., Torkko, P., known species. In addition, some results from growth on in this situation is that it may predict factors that govern the Researchers in Düsseldorf, Germany, have been studying how Tortoli, E. & Thomsen, V.O. (2008). Mycobacterium arosiense various laboratory media and an analysis of the fatty and infection and which are easier to test experimentally. DNA and proteins interact at two promoters in Escherichia sp. nov., a slowly growing, scotochromogenic species causing mycolic acids from the cells matched with several different coli. The P1 and P2 promoters both regulate production of In the first few weeks of infection there is usually a large osteomyelitis in an immunocompromised child. Int J Syst species. a structural RNA molecule required as part of the protein Evol Microbiol 58, 2398–2402. amount of virus in the body and substantial immune system synthesis machinery. The DNA upstream of P1 is curved, Putting all the information together, the researchers have activity. This stabilizes into a long-term chronic infection while there is a complete lack of curvature upstream of P2. To The most well known Mycobacterium species is M. tuberculosis, convincing evidence for a new species that is closely related to that can last years, characterized by much lower numbers of test the relative importance of DNA structure and proteins, the infections of which can result in the disease tuberculosis. M. intracellulare, but very clearly different from it. They have virus particles. Eventually, for unknown reasons, this stable researchers changed the DNA bases in the promoter region Closely related species that cause different, rarer diseases can named it M. arosiense after the Latin name of Aarhus, the city state breaks down, CD4+ cell counts decrease, the levels of to vary the amount of curvature. Regardless of curvature, the now be distinguished using molecular genetic and chemical in Denmark where it was first identified. virus increase, and the patient experiences the debilitating gene could always be switched on, but the level of activity was analyses. Several have been identified as the cause of infections symptoms of AIDS. All the mechanisms proposed for this highest when the inside of the curved section of DNA and the in children’s bones, although most of these infections have change imply that DCs are of key importance, but for several start of the gene were in the same plane. fortunately not been severe. However, treatments with different reasons. antibiotics to kill the bacteria are quite prolonged and the The equations were designed using information from human Proteins called transcription factors are normally involved disease can recur. One recent serious infection in a 7-year- patients and similar immunodeficiency viral infections in regulating gene activity through modulating interactions old girl, who had inherited a problem with her immune in primates. The idea was to have terms for documented with the RNA synthesis system. The researchers went on system, was caused by what turned out to be a novel species significant interactions between HIV-1, DCs, CD4+ and CD8+, to test the effect of three E. coli transcription factors called of bacteria. She responded well to therapy with a mixture of concentrating on DCs. The model was good at simulating H-NS, LRP and FIS in conjunction with the curved DNA antibiotics for over a year, with no signs of recurrence of the the numbers of each type of cell in a healthy human lymph molecules. FIS activates P1 promoters while LRP and H-NS infection after a further 18 months. However, she probably node, and in showing how HIV-1 infection results in T-cell inhibit transcription from them. The subtle effects seen with remains at life-long risk from non-tuberculous mycobacteria. depletion. Using mathematical methods for uncertainty and the differently curved molecules differed between P1 and P2, Staff working at the International Reference Laboratory of sensitivity analysis allowed the testing of different hypotheses indicating that these two promoters are regulated differently, Mycobacteriology and National Center for Antimicrobials and about the roles of DCs. The way that DCs simultaneously with P1 being more strongly inhibited. Infection Control at Copenhagen in Denmark, along with infect and alert CD4+ cells seemed to be crucial in establishing From these results it is evident that the combined effects of colleagues at other laboratories in Denmark, Finland and Italy, infection. Later on, failure of proper DC function has a greater DNA curvature and several transcription factors cause the studied the bacteria in detail because their features did not effect on pathogenesis of the disease than the loss of CD4+. different levels of activity of each gene, but much more work correspond exactly to any known species. The yellow-coloured One practical outcome of this modelling is to suggest that is needed before accurate predictions can be made for every bacterial cells grew slowly and looked like typical clinically m Coloured scanning electron micrograph of a T-cell (orange) infected treatments that improve DC functions could be valuable in gene. significant mycobacteria under the microscope. However, with HIV viruses (blue). Eye of Science / Science Photo Library improving the outcome of HIV-1 infections.

212 microbiology today nov 08 microbiology today nov 08 213 goingpublic

There are many ways of publicizing research and informing people about microbiology. Talking to the Science, media is one and Lucy Goodchild shows that with the right training, this can be a positive experience. media &

When I ask scientists if they will speak Jack Gilbert from Plymouth Marine to the media, I am sometimes met Laboratory. ‘This is increasingly making with a negative response. ‘No way, important in light of the need to engage they’ll get my science wrong/misquote the public more completely in our current me/interview me like Jeremy Paxman output and design of future work.’ would.’ So what is the reality of science your point: Science journalists often have a in the media and how can scientists background in science. Although make sure they are treated and they might not all be microbiologists represented fairly? (but some are!), they are able to SGM To get the right idea, on Monday 7 July understand scientific concepts much 2008, six scientists with specialist areas more than they are given credit ranging from HIV research on primates for. The vast majority of scientific to investigating plankton that produce reporting is responsible and accurate, media DMS in the ocean came along to and journalists do their best to check Marlborough House for media training. facts and get comments from experts. The tutor, Myc Riggulsford from The scientist’s role in this process is the Walnut Bureau, provided some twofold: to supply the media with training valuable insights into the minds of useful material on which to base the media and helped the participants stories, and to comment on other explained clearly. The same goes for overcome their reservations about people’s research. radio and TV interviews – talk to the speaking to journalists and publicizing When presenting science (or interviewer as if you were talking to their research. anything else for that matter) to the a non-scientist friend at the pub. A These days, research councils make print media, reading age must be minute of jargon and acronyms on public engagement a condition considered. Believe it or not, all the the radio is not very entertaining! This of their funding and many people content in a broadsheet newspaper doesn’t mean you have to compromise think scientists have a responsibility is aimed at a reading age of 12–13. your scientific accuracy, you just have to communicate their research, So language should be kept simple to make the research accessible and particularly if they have been publicly and scientific concepts should be understandable. ‘Science concepts may funded. A great way to do this is to promote their science to the media. This can be done in all sorts of ways, from distributing a press release to organizing a TV or radio interview. Although every researcher will have a press officer, either working for their research institute or for an organization like the SGM, understanding how the media works will certainly help the scientist get more involved in the process and feel more comfortable speaking to journalists. ‘The value of understanding the way the media machine functions is key to providing an accurate and yet wide-reaching portrayal of our research’, said Dr Photos.com / Jupiter microbiology today nov 08 215 be difficult to explain to the public in SGM likes to encourage the personal some cases, but big fancy words do not help science communication’, said Dr New media update developments of early career microbiologists. By Ernest Asilonu from Genzyme Ltd. If you are asked to comment on Microbe Talk – www.sgm.ac.uk/news/poscast.cfm supporting the activities of Sense about Science, somebody else’s research, or on an In the September episode Dr Louis Magnarelli, Director of The Connecticut emerging news story, the key is speed. Agricultural Experiment Station in the USA, talks to us about diagnosing our members can attend their workshops. Sarah Journalists work to exceptionally West Nile virus. tight deadlines and will usually need A new test for West Nile virus in horses that could be modified for use with Maddocks went on one. feedback within minutes rather than humans and wildlife may help track the spread of the disease, according to days. They are often after ‘soundbites’, an article in the September issue of the Journal of Medical Microbiology. short quotes that can be added to a story to give it a different perspective. New launch for micropod – At the SGM we get lots of calls from www.micropodonline.com/podcast.html reporters asking to be put in touch with an expert. When this happens, Episode 10 has arrived! This month we have a special bumper launch edition Standing up for Science I search our experts database to find of micropod for you. Not only do we have a fabulous new jingle, but we’re people who are happy to speak to also twice the length of the normal podcast! But don’t worry, it’s not just the media. As an SGM expert, there twice as much Lucy and Lucy, it’s more interviews, news and two topics.... yes TWO topics! media workshop are plenty of opportunities for you to get involved with microbiology We’re talking (and listening to) music with an interview with Dr Carl Winter in the media. We publicize research and his amazing food safety songs. presented at our meetings, as well We also talk about genetic modification, Lucy G interviews Dr John Heritage Sense about Science, a charitable trust that counters misrepresentation of science as findings published in our four and finds out exactly what GM means. Then Lucy H has a chat with Professor in the media (www.senseaboutscience.org.uk), recently ran a workshop aimed at journals. We produce two podcasts, Nigel Poole about the media and GM and his experiences of getting early career scientists inviting them to Stand up for Science. Co-ordinated by the Micropod and Microbe Talk, which genetically modified tomatoes onto supermarket shelves. Voice of Young Science network (VoYS), this workshop introduced PhD students include interviews with specialists and postdocs from a range of disciplines, to the media and confronted the related on a diverse range of topics, from SGM now has groups on Facebook and MySpace! issues facing scientists today. astrobiology to STIs. And finally, Held at the Institute of Biology headquarters in London, the workshop began by there are opportunities to respond Join in for news about the Society and event updates, as well as discussions introducing Science and the Media. Groups of participants discussed the changing to consultations and review books. and interesting microbiology stories! roles and image of science and scientists in the public domain. Case studies If you would like to be added to Facebook page – www.new.facebook.com/groups/create.php?customize where science had been misrepresented were offered and discussed with a panel our database, or would like more &gid=27768262231#/group.php?gid=27768262231 of scientists who were experts in their field, with prior experience of media information, please email press@sgm. MySpace page – http://groups.myspace.com/SocGenMicro interaction. ac.uk Then science in the media was covered from a reporter’s point of view with The training included tips on how to lively debate from a panel of journalists (Daily Mirror, BBC radio and The Times). write a news story, information about ‘the main message for me was that George’s, University of London said, The panel explained how they approach scientific stories and the importance of how newspapers work, what to wear dealing with the media does not have to ‘the media training day was great balancing news and entertainment with conveying science. This made participants on TV and even some practice radio be ‘scary’ and instead of avoiding it we and I guess the main point that I took appreciate the importance of good communication between the scientific interviews. The participants found should be more ready to embrace it as home was get your message over community and the media. the day very helpful and are already a means of getting science out there to cogently even if it means responding to making use of what they learnt. Dr the public. At the end of the training I an oblique question with the answer The day rounded off with a ‘nuts and bolts’ discussion in which members of the Mike Dempsey from Manchester felt significantly more confident in terms that you want to give rather than VoYS offered practical advice on getting your voice heard in scientific debates Metropolitan University is using the of dealing with the media. As scientists, where the interviewer may be trying including the difficulties involved, areas of misunderstanding and ensuring that techniques for writing abstracts. ‘The we are trained to write and give to take you. The knowledge gained ‘good’ science is communicated to the public. main message I took from the training presentations in a particular style which from the training has definitely Having no prior involvement with the media and viewing it with some pessimism, was to make sure the key point is in is not appropriate outside the confines increased my confidence in engaging the Sense about Science workshop has helped me to develop a more informed the first sentence.’ This is also a great of our scientific environment. In terms with the media.’ attitude. I appreciate the importance of the media in conveying science to help for press officers, who look for of the future, the knowledge gained SGM will be running media training the public and the role that scientists can play in this to ensure that accurate potential stories by searching through from the training has given me the skills, events annually, so if you would information is published. This workshop would be advantageous for all scientific abstracts. I hope, to interact more confidently and like to be invited to the next one, researchers, regardless of their experience, who want to stand up for science and Clinical scientist Dr Siobhan O’Shea positively with the media.’ please email Lucy at l.goodchild@ eliminate its misrepresentation. from St Thomas’ Hospital Trust said, Professor Martin Cranage from St sgm.ac.uk Sarah Maddocks, University of Bristol AbleStock.com / Jupiter

216 microbiology today nov 08 microbiology today nov 08 217 reviews

If you would like your name to be added to our database of would have depleted the food supply, decomposers is also not acknowledged role of microbiology in food poisoning so much concise information, in such potentially causing herbivores to starve. sufficiently. and food-borne infections. Part 2 is a well-designed format to aid effective Although initially this would have concerned with food hygiene in the learning. I can well imagine professional book reviewers, please complete the book reviewer interests I would certainly recommend this provided carnivores with easy prey, they prevention of food poisoning. The final hygiene trainers delving into this book book to anyone interested in dinosaurs form at www.sgm.ac.uk. A classified compendium of reviews too would eventually have starved. part is divided into chapters on the time and time again. and prehistoric life in general. It contribution of food poisoning and Some of the chapters begin with a has changed the way I imagine the While I was very enthusiastic to include from 1996 to the present is also available on the website. hygiene in specific settings. description of a fictional (but possible) Cretaceous and the extinction of the the book for our Environmental Health scenario. Although some of these dinosaurs and I am sure it will open up The first section covers the core aspects, students, whether to use it as a core text paint a vivid picture, they can distract new avenues of thought in this area. in 7 chapters, and introduces the on a food microbiology degree course What Bugged the the reader from the story and are reader to major food-borne pathogens, is less strong. Nevertheless, I would Lucy Goodchild, SGM Dinosaurs? Insects, sometimes difficult to read because their sources and diversity. Infections, certainly recommend it as a supporting Disease, and Death in they are so packed full of adjectives. intoxications and prions are covered. text, and essential background reading. The reason for this is that the chapters the Cretaceous Nonetheless, they show the enthusiasm Hobbs’ Food Poisoning The chapter on parameters controlling the authors have for the subject, as do bacterial growth includes preservation are light on reference material in and Food Hygiene some chapters, and the UK focus. By G. Poinar Jr & R. Poinar the numerous personal anecdotes in the 7th Edition as well as food spoilage. The chapter Published by Princeton University text. on epidemiology includes interesting, This is a two-edged sword, since the Press (2008) Edited by J. McLauchlin & C. Little well-illustrated examples of outbreaks. UK emphasis is of great benefit to The extinction of the dinosaurs is £17.95 pp. 264 Published by Hodder Arnold The final chapter is on water-borne environmental health students; however, hotly debated, primarily swinging ISBN 0-69112-431-5 Education (2007) disease and sewage/sludge disposal. it is of less international relevance. between two schools of thought: that £19.99 pp. 412 As already stated, since many of the At the end of the day, the cover price I was intrigued by dinosaurs as a child. the extinction happened quickly ISBN 0-34090-530-2 authors are from government agencies, of £19.99 makes this a formidable They were so majestic and powerful, (catastrophists) versus slowly the reader benefits from the inclusion information per pound book; it is part of a fantasy world I could never (gradualists). The arguments are This may be a little different from a of information on policy development, definitely going to be well-thumbed quite imagine. This book attempts explained well at the end of the book, normal review, but I’ll start at the end; standards and legislation. for my lecture presentations. to answer the question of how they although some clarification may have whether to recommend the book? Well, became extinct. George and Roberta been useful earlier in the text. I was so struck by the book’s layout and The second part has 12 chapters Stephen Forsythe, Nottingham Trent Poinar propose that microbes played design, that within 30 minutes I had focussed on food hygiene. The opening University Readers with little prior knowledge an important role in the demise of the added it to our list of recommended chapter is on personal hygiene of the of palaeontology may find some dinosaurs at the end of the Cretaceous. texts for our Environmental Health food handler, and the chapter’s progress Reviews on the web chapters hard-going – continuous Their evidence centres around three degree courses, and requested our to food preparation, manufacture, the Reviews of the following books are references (with no explanations) to amber deposits made between 135 and ears and nose would have been much libraries to purchase additional copies! retail trade. Cleaning and disinfection, available on the website at www.sgm. types of dinosaurs, time periods and 80 million years ago which provide more accessible. and pest control are dealt with in ac.uk/pubs/micro_today/reviews.cfm prehistoric trees can stagnate the flow I already have a number of earlier a plethora of fossilized insects that separate chapters. Whereas the majority The amber deposits suggest that of the narrative. Appendix C is a useful versions of ‘Hobb’s’, although I confess Environmental Genomics have recently been found to contain of the book is UK-orientated, there biting midges were quite common in resource for readers not trained in that editions 4 to 6 had escaped my Legionella Molecular Microbiology pathogenic microbes. The process is one chapter on food hygiene in the Cretaceous. Morphologically, the the science, as it shows the problems notice. I therefore cannot comment Microcosm: E. coli and The New Science of fossilization is selective and an developing countries, and another on fossilized creatures are related to reptile associated with palaeontological on how this version compares with of Life incomplete record causes problems. food hygiene in the wilderness. However, the authors explain how the biters, so the authors suggest they may evidence and evaluating the fossil record. the previous edition. Neverthess, the MicroRNAs From Basic Science to evidence supports their hypothesis. have fed on dinosaurs. They suggest Unfortunately, an incoherent order layout of this version is first thing The third, and final part, gives the Disease Biology that an allergic reaction to a bite could makes an otherwise comprehensive which strikes you; the use of colour for reader an interesting insight into the By comparing insects fossilized Chemical Communication among Bacteria have led to scratching, which can cause reference list difficult to use. headings in the text, tables and figures, relevance of food poisoning and hygiene in amber to those that exist today, High-Pressure Microbiology bacterial and fungal infections and and the use of colour photos. This in various sector groups. The areas palaeontologists can determine the Insects are central to this book, with a Food-Borne Viruses: Progress and could be life-threatening. The amber makes the book pleasing to browse range from healthcare, ships, aircraft, likelihood of pathogens being present. whole chapter dedicated to explaining Challenges deposits also provided researchers through, and captivates your attention. seaports, as well as the environmental In an ‘intricate case of detective work’, how they managed to survive when all Structural Proteomics: High-Throughput with evidence of a Cretaceous malarial Some notable pictures are those of the health, medical and veterinary the Poinars first discovered pathogenic the dinosaurs died out. In my opinion, Methods parasite, Paleohaemoproteus, which microbial flora of hands after handling practitioners. microbes in a fossilized sand fly, along the story of the microbes is somewhat could have caused a fatal infection cloths, etc.; super for getting the Food-borne Diseases with vertebrate blood cells. Today, neglected and some mistakes creep Christine Little and Jim McLauchin in dinosaurs. Black flies carried the message across. Avian Influenza Virus blood-sucking insects are a major in. A chapter on insects as sanitary should be congratulated on such a well malarial parasite Leucocytozoon and Microbial Ecology of Aerial Plant source of disease. The authors suggest engineers explains how, without insects It is a multiauthored book, with many constructed text on the broad subjects mosquitoes, horseflies, ticks and fleas Surfaces that things were not so different in the to decompose excrement and cadavers, of the writers from the UK Health that are encompassed in the subject of may also have transmitted disease. Viral Therapy of Cancer Cretaceous. Dinosaurs had surprisingly the Cretaceous world would have been Protection Agency (HPA), and Food food poisoning. Inevitably, with such The authors suggest that emerging thin scales with small openings, and the almost uninhabitable. The authors Standards Agency. Therefore, the a range of topics and authors, there is Campylobacter, 3rd edn contagious diseases may have spread spaces between scales offered them even applaud termites for their good job information is authoritative, and likely to be some overlap, as occurs with Referenced Review Questions in among dionsaur populations. less protection against insects. Even if at keeping things clean, but do not advantage has been taken to frequently the topic of food poisoning outbreaks Pharmacogenomics the skin proved difficult to penetrate, Dinosaurs may also have been affected refer to their essential endosymbionts! include data from the HPA in the in chapters 6 and 32. But this is a Paramecium Genetics and Epigenetics the areas around the mouth, eyes, by microbes indirectly. Plant diseases The important role of microbes as figures and tables. Part 1 covers the minor issue for a book which can give Fundamentals of Biofilm Research

218 microbiology today nov 08 microbiology today nov 08 219 Howard Gest explodes

what he considers to be

the myth of ‘unculturable’

bacteria. commentScotoma in contemporary microbiologytitle The eminent neurologist Dr Oliver Sacks writers on this disease state that the causative provide appropriate chemical and physical describes scotoma as involving the deletion agent cannot be cultivated outside the animal conditions. Whether or not the requirements of what was originally perceived, a loss of body’. They went on to demonstrate that can be satisfied in the laboratory depends on knowledge, a loss of insight … a regression Mycobacterium pseudotuberculosis can be many factors, which include the knowledge, to less perceptive explanations. ‘All these grown in pure culture by adding extracts skill, and patience of the investigator … not only beset neurology but are surprisingly of dead cells of Mycobacterium phlei. This There is no doubt that studies on nucleic acid common in all fields of science. They raise was one of the earliest researches showing sequences of bacterial species are enlarging the deepest questions about why such lapses requirements of many bacteria for our understanding of species relationships occur.’ A scotoma has apparently afflicted ‘essential’ growth factors, later identified and evolutionary patterns. But justification many molecular biologists, and others, in this instance to be a form of vitamin K. for pursuing such research hardly needs to who maintain that most (>95%) of bacteria In support of the myth of be based on the myth that the ‘molecular living in nature are ‘unculturable’ in the unculturability, it is repeatedly claimed approach’ is necessary because many species laboratory. This view is frequently used as that ‘only a fraction of less than 1% of are ‘unculturable’.’ a crutch to justify molecular metagenomics bacteria on or in natural sources can be In my opinion, the study of pure as the panacea for understanding the recovered as colonies on standard laboratory cultures remains the most reliable source complexities of bacterial ecology. media.’ This, of course, is a vague and of basic information for understanding the The myth of unculturability is repeated inadequate criterion of culturability. As properties and evolutionary relationships so often that it has penetrated to semi- indicated by Twort & Ingram, it is not of the vast majority of bacteria, as well as popular science writing. In a recent issue news to knowledgeable microbiologists the dynamics of changes they catalyse in of the American Scientist, Dorit asks ‘Why that the definition of nutritional the biosphere. did it take so long to acknowledge our inner requirements of bacteria is often difficult microbe? The answer stems, in part, from the and requires lengthy laboratory studies. Howard Gest fact that most bacteria cannot be grown in To illustrate the point, I have posted Distinguished Professor Emeritus the laboratory. Consequently, until recently, several more significant examples from of Microbiology, Professor History microbiologists could not identify – let alone the literature on the web at http://hdl. and Philosophy of Science, Indiana understand – microbes that refused to live in handle.net/2022/3149 University, Bloomington, IN 47405, the world of Petri dishes and culture flasks.’ My critique of the myth of USA (e [email protected]) The myth of ‘unculturability’ persists ‘unculturability’ on the internet is because it is promoted by scientists who ‘dedicated to the pioneering microbiologists have little experience in growing fastidious who isolated pure cultures of microbes Further reading bacteria or knowledge of past investigations responsible for (a) infectious diseases of Sacks, O. (1995). Scotoma: forgetting and neglect in science. In Hidden Histories in which nutritional idiosyncracies of animals and plants, and (b) the cyclic of Science, pp. 141–179. Edited by R.B. numerous types of organisms were defined transformations of major chemical elements Silvers. New York: New York Review Book. by intensive studies. For over a century, on the Earth. Their characterization of Bulloch, W. (1938). The History of a legion of microbiologists has provided the biological, physiological, and genetic Bacteriology. Oxford University Press. numerous examples of bacteria that have properties of these organisms paved the Dorit, R. (2008). All things small and great. complex growth requirements that are way for current research.’ The careers and Am Sci 96, 284–286. not satisfied by simple concoctions of contributions of more than 300 of the yeast extract and similar supplements. early pioneers are profiled in William Gest, H. (1993). Bacterial growth and reproduction in nature and in the An interesting case in point: in 1910, Bulloch’s 1938 classic book The History of laboratory. ASM News 59, 542–543. F.W. Twort undertook to isolate the agent Bacteriology. Back in 1993, I summarized responsible for tuberculosis of cattle. The the problem under discussion as Twort. F.W. & Ingram, G. (1911). Proc R Soc LXXXIV, 517–542. disease was causing great losses of cattle in follows: ‘The requirements for growth and Britain and Europe. In a classic 1911 paper, reproduction of extant species of bacteria Please note that views expressed in Comment do not Twort and his colleague Ingram noted, ‘All are obviously met in environments that necessarily reflect official policy of the SGM Council. Please note that views expressed in Comment do not m Tek Image / Science Photo Library necessarily reflect official policy of the SGM Council.

220 microbiology today nov 08