prokaryote taxonomy online: challenges ahead

1
Sir — As pointed out in your Opinion article “Anyone for neutrons?” (Nature 417, 883; 2002), the European Spallation Source (ESS) user meeting in May was an impressive demonstration of the lively activity of European neutron users. Five propositions for hosting the site of the ESS were presented, with backing from regional and/or national authorities. It was surprising and regrettable to note the absence of a proposal for a French site. France has a long and deep tradition in the field of scientific use of neutron beams. It hosts the most powerful neutron source in the world, the Institut Laue Langevin (Grenoble), and a modern and well- equipped national source, the Laboratoire Léon Brillouin (Saclay). The French user community has declared its scientific interest in the ESS project on several occasions, and the French Neutron Users Society (www.sfn.asso.fr) has fully approved the goal of a new-generation neutron source in the next decade. A French team is heavily involved in the design and evaluation of the ESS. Despite this commitment, no French site was proposed at Bonn, reflecting the obstacles raised by the diverging approaches of its national bodies (the Ministry of Research and Technology, and the two major funding agencies, the CEA and the CNRS). Moreover, the absence of high-level decision-makers representing French authorities at Bonn appeared as a sign of indifference. It may be difficult in France at the moment to support large research infrastructures, and the financial climate may be unfavourable. But this does not excuse sacrificing the future. One cannot make progress by sticking to fixed schemes of funding and maintaining a conservative outlook on the merits of neutron science. The Bonn meeting showed the multi- disciplinary and scientific potential of the ESS project. The present sources are needed to assure continuity, and to maintain and complete the training of the scientists who will run and use the source when it is completed. As is usual in the case of any large- facility project, the construction phase of the ESS would require funding beyond the level of current functioning. But, considering the rapid expansion of the areas of science that will benefit from the new facility, the running costs will surely be reasonable. F. Leclercq (president)*, H. Mutka (vice- president)†, Société Française de la Neutronique *LASIR UMR 8516 du CNRS, 13 rue de Toul, F-59046, Lille Cedex, France Institut Laue Langevin, BP 156, F-38042 Grenoble Cedex 9, France correspondence NATURE | VOL 419 | 5 SEPTEMBER 2002 | www.nature.com/nature 15 French users need European neutrons Big projects may not be popular at present, but policy-makers must think of the future. Shared knowledge can combat malaria Sir — Andrew Clark in his excellent News and Views article “Malaria variorum” (Nature 418, 283–285; 2002) discusses the extent of genetic variability exhibited in populations of Plasmodium falciparum, the causative agent of the most lethal form of malaria, and the implications for vaccine development and for the emergence of drug resistance. He concludes that a shared resource of P. falciparum isolates is needed to address the problem and to advance our understanding of the evolution of this species. We agree. The Malaria Research and Reference Reagent Resource Center (MR4) was established in 1998, partly to provide the resources available to malaria researchers worldwide that Clark discusses, and is managed by the American Type Culture Collection (ATCC). Under contract to the National Institute of Allergy and Infectious Diseases (NIAID), MR4 makes reagents available free of charge to registered individuals worldwide (see www.malaria. mr4.org). Further information can be found at the NIAID website (www.niaid. nih.gov/dmid/malaria/malrep/default.htm). MR4 currently has more than 450 reagents, including numerous isolates, strains and species of Plasmodium and Anopheles mosquitoes as well as antibodies, antigens, DNA libraries and primers and microarray chips. Training programmes, workshops and technology transfer to malaria-endemic regions are also important components of MR4. We encourage researchers to collaborate with MR4 to develop and support the needs of the community, as well as to contribute resources that can thereby be made more widely available. Yimin Wu*, M. John Rogers† *MR4/Protistology, ATCC, 10801 University Boulevard, Manassas, Virginia 20110, USA National Institute of Allergy and Infectious Diseases, 6610 Rockledge Drive, Bethesda, Maryland 20892, USA Prokaryote taxonomy online: challenges ahead Sir — Following calls for online taxonomic databases encompassing all organisms living on Earth 1–4 , we wish to point out that extensive taxonomic information on the prokaryotes is already available online. The Approved Lists of Bacterial Names, including names and their nomenclatural history, are on a website that is updated bimonthly (www.bacterio.cict.fr). On 9 July 2002 the lists named 5,866 species, classified in 1,104 genera, Archaea and Bacteria combined. Comprehensive information on prokaryote taxonomy is in two handbooks, The Prokaryotes and Bergey’s Manual of Systematic Bacteriology, both published by Springer-Verlag. The former is published online (www.link.springer.de/link/service/books/ 10125), and the database of the second edition of the latter (www.cme.msu.edu/ bergeys) exists in electronic form, so could easily be made available on the web if the publisher gives permission. In the case of the prokaryotes, obstacles virtually unknown to the botanist and the zoologist must be overcome to achieve the goals mentioned by Gewin and others. First, the species concept for bacteria is still not well-defined 5,6 . Second, sequencing of 16S ribosomal RNA genes collected from terrestrial and aquatic environments shows that the number of known prokaryotic species probably forms only a fraction of 1% of the number in nature. Morphological diversity is small, and therefore digital images of type specimens are of little help in online taxonomic databases. The lack of innovative culturing techniques and of well-trained taxonomists to study the isolates are of great concern. Some of the most abundant prokaryotes on Earth defy microbiologists’ attempts to isolate them. Here lies one of the major challenges to future taxonomists. Aharon Oren*, Erko Stackebrandt† *Institute of Life Sciences and Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroderweg 1b, D-38124 Braunschweig, Germany 1. Godfray, H. C. J. Nature 417, 17–19 (2002). 2. Lee, M. S. Y. Nature 417, 787–788 (2002). 3. Gewin, V. Nature 418, 362–363 (2002). 4. Bisby, F. A. et al. Nature 418, 367 (2002). 5. Cohan, F. M. Syst. Biol. 50, 513-524 (2001). 6. Stackebrandt, E. et al. Int. J. Syst. Evol. Microbiol. 52, 1043–1047 (2002). © 2002 Nature Publishing Group

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Page 1: Prokaryote taxonomy online: challenges ahead

Sir — As pointed out in your Opinionarticle “Anyone for neutrons?” (Nature417, 883; 2002), the European SpallationSource (ESS) user meeting in May was animpressive demonstration of the livelyactivity of European neutron users. Fivepropositions for hosting the site of the ESSwere presented, with backing fromregional and/or national authorities.

It was surprising and regrettable to notethe absence of a proposal for a French site.France has a long and deep tradition in thefield of scientific use of neutron beams. Ithosts the most powerful neutron source inthe world, the Institut Laue Langevin(Grenoble), and a modern and well-equipped national source, the LaboratoireLéon Brillouin (Saclay). The French usercommunity has declared its scientificinterest in the ESS project on severaloccasions, and the French Neutron UsersSociety (www.sfn.asso.fr) has fully

approved the goal of a new-generationneutron source in the next decade. AFrench team is heavily involved in thedesign and evaluation of the ESS.

Despite this commitment, no Frenchsite was proposed at Bonn, reflecting theobstacles raised by the divergingapproaches of its national bodies (theMinistry of Research and Technology, andthe two major funding agencies, the CEAand the CNRS). Moreover, the absence ofhigh-level decision-makers representingFrench authorities at Bonn appeared as asign of indifference.

It may be difficult in France at themoment to support large researchinfrastructures, and the financial climatemay be unfavourable. But this does notexcuse sacrificing the future. One cannotmake progress by sticking to fixed schemesof funding and maintaining a conservativeoutlook on the merits of neutron science.

The Bonn meeting showed the multi-disciplinary and scientific potential of theESS project. The present sources areneeded to assure continuity, and tomaintain and complete the training of thescientists who will run and use the sourcewhen it is completed.

As is usual in the case of any large-facility project, the construction phase of the ESS would require funding beyondthe level of current functioning. But,considering the rapid expansion of theareas of science that will benefit from the new facility, the running costs willsurely be reasonable.F. Leclercq (president)*, H. Mutka (vice-president)†, Société Française de laNeutronique *LASIR UMR 8516 du CNRS, 13 rue de Toul, F-59046, Lille Cedex, France†Institut Laue Langevin, BP 156, F-38042 Grenoble Cedex 9, France

correspondence

NATURE | VOL 419 | 5 SEPTEMBER 2002 | www.nature.com/nature 15

French users need European neutronsBig projects may not be popular at present, but policy-makers must think of the future.

Shared knowledge cancombat malariaSir — Andrew Clark in his excellent Newsand Views article “Malaria variorum”(Nature 418, 283–285; 2002) discusses the extent of genetic variability exhibitedin populations of Plasmodium falciparum,the causative agent of the most lethal form of malaria, and the implicationsfor vaccine development and for theemergence of drug resistance. Heconcludes that a shared resource of P. falciparum isolates is needed to address the problem and to advance ourunderstanding of the evolution of thisspecies. We agree.

The Malaria Research and ReferenceReagent Resource Center (MR4) wasestablished in 1998, partly to provide theresources available to malaria researchersworldwide that Clark discusses, and ismanaged by the American Type CultureCollection (ATCC). Under contract to theNational Institute of Allergy and InfectiousDiseases (NIAID), MR4 makes reagentsavailable free of charge to registeredindividuals worldwide (see www.malaria.mr4.org). Further information can befound at the NIAID website (www.niaid.nih.gov/dmid/malaria/malrep/default.htm).MR4 currently has more than 450reagents, including numerous isolates,strains and species of Plasmodium andAnopheles mosquitoes as well asantibodies, antigens, DNA libraries andprimers and microarray chips.

Training programmes, workshops andtechnology transfer to malaria-endemicregions are also important components ofMR4. We encourage researchers tocollaborate with MR4 to develop andsupport the needs of the community, aswell as to contribute resources that canthereby be made more widely available.Yimin Wu*, M. John Rogers†*MR4/Protistology, ATCC, 10801 UniversityBoulevard, Manassas, Virginia 20110, USA†National Institute of Allergy and InfectiousDiseases, 6610 Rockledge Drive, Bethesda,Maryland 20892, USA

Prokaryote taxonomyonline: challenges aheadSir — Following calls for online taxonomicdatabases encompassing all organismsliving on Earth1–4, we wish to point outthat extensive taxonomic information onthe prokaryotes is already available online.The Approved Lists of Bacterial Names,including names and their nomenclaturalhistory, are on a website that is updatedbimonthly (www.bacterio.cict.fr). On 9 July 2002 the lists named 5,866 species,classified in 1,104 genera, Archaea andBacteria combined. Comprehensiveinformation on prokaryote taxonomy is intwo handbooks, The Prokaryotes andBergey’s Manual of Systematic Bacteriology,both published by Springer-Verlag. Theformer is published online(www.link.springer.de/link/service/books/

10125), and the database of the secondedition of the latter (www.cme.msu.edu/bergeys) exists in electronic form, so couldeasily be made available on the web if thepublisher gives permission.

In the case of the prokaryotes, obstaclesvirtually unknown to the botanist and thezoologist must be overcome to achieve thegoals mentioned by Gewin and others.First, the species concept for bacteria is stillnot well-defined5,6. Second, sequencing of16S ribosomal RNA genes collected fromterrestrial and aquatic environmentsshows that the number of knownprokaryotic species probably forms only afraction of 1% of the number in nature.Morphological diversity is small, andtherefore digital images of type specimensare of little help in online taxonomicdatabases. The lack of innovative culturingtechniques and of well-trained taxonomiststo study the isolates are of great concern.Some of the most abundant prokaryoteson Earth defy microbiologists’ attempts toisolate them. Here lies one of the majorchallenges to future taxonomists.Aharon Oren*, Erko Stackebrandt†*Institute of Life Sciences and Moshe Shilo MinervaCenter for Marine Biogeochemistry, The HebrewUniversity of Jerusalem, 91904 Jerusalem, Israel†Deutsche Sammlung von Mikroorganismen undZellkulturen GmbH, Mascheroderweg 1b, D-38124 Braunschweig, Germany1. Godfray, H. C. J. Nature 417, 17–19 (2002). 2. Lee, M. S. Y. Nature 417, 787–788 (2002). 3. Gewin, V. Nature 418, 362–363 (2002).4. Bisby, F. A. et al. Nature 418, 367 (2002).5. Cohan, F. M. Syst. Biol. 50, 513-524 (2001). 6. Stackebrandt, E. et al. Int. J. Syst. Evol. Microbiol. 52, 1043–1047

(2002).

© 2002 Nature Publishing Group