Letter a call to action for the International Committee on Systematics of Prokaryotes



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Letter
A call to action for the International Committee on Systematics of Prokaryotes
Iain C. Sutcliffe1*, Martha E. Trujillo2, William B. Whitman3 and Michael Goodfellow4
1School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK

2Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain

3Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA

4 School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
* Corresponding author: Sutcliffe, I.C. (iain.sutcliffe@northumbria.ac.uk)

We have followed with great interest the letters to Trends in Microbiology from Gribaldo and Brochier-Armanet [1] and Garrity and Oren [2] concerning the need to improve the framework for prokaryotic systematics, notably with respect to the rules of nomenclature at the Domain and Phylum levels as these currently lack formal standing in the International Code of Nomenclature of Prokaryotes (ICNP, [3]). We agree that this debate is necessary and urgent, noting that this issue has been considered at meetings of the International Committee on Systematics of Prokaryotes (ICSP), the body which provides governance over the interpretation and implementation of the ICNP. It is therefore of considerable concern that we note the closing comments of Garrity and Oren [2] that ”in spite of the good intentions [of the ICSP], little progress was made: the ad hoc committee appointed in 2005 never met, and the funding for the workshop discussed in 2008 was not secured”. This statement is symptomatic of larger structural deficiencies within the ICSP as historically constituted. We therefore encourage the ICSP to continue to address this subject, in the process revitalising itself so as to be able to more quickly address concerns such as these, and offer some suggestions as to how this might be achieved.

Prokaryotic systematists are currently naming ca. 600 new species each year [4,5,6]. This impressive level of activity, driven in part by the application of 16S rRNA gene sequence analyses, has greatly improved our understanding of the breadth of prokaryotic diversity and it is clear that there are at least 30 recognisable phyla within the Domain Bacteria [2,7] (see http://www.bacterio.cict.fr/classifphyla.html). Moreover, many more as yet uncultivated taxa that are presently recognised only as distinct 16S rRNA ‘phylotypes’ are likely to merit phylum classification upon characterisation. Similarly, there are at least four phyla recognisable within the Domain Archaea [1].

The increasing clarity regarding this taxonomic framework now presents the ICSP with a great opportunity to consolidate its leadership on prokaryotic systematics and to re-energise its subcommittees. Currently, the ICSP has 29 subcommittees (see http://www.the-icsp.org/), the origins of which appear ad hoc and historic. Some address issues relating to the nomenclature and taxonomy of specific genera, others focus on particular families, suborders, classes or functional groupings. Consequently, only a tiny fraction of prokaryotic diversity (and less than 10 of the >30 well established prokaryotic phyla) currently fall within the remits of the established taxonomic subcommittees. Moreover, although some subcommittees are commendably active, nearly half of them appear to be quiescent. We suggest therefore that the remits of the taxonomic subcommittees be reappraised to ensure that they reflect the full extent of prokaryotic diversity and are constituted in a proactive rather than responsive manner.



Now is a time of unparalleled opportunity in systematics, and the ICSP has the chance to provide leadership to develop taxonomic concepts and practices in the light of changes that have revolutionised biology over the past 10 to 15 years, in particular developments in genomic sciences and the contemporaneous establishment of the internet as a platform for information collection, exchange and analysis [4,5,6]. To stimulate this process we wish to make the following constructive suggestions.

  1. The ICSP is encouraged to review its structure and membership. The overall aim should be to reinvigorate the committee membership and to create an infrastructure (i.e. subcommittees) that more accurately reflects present understanding of prokaryotic diversity. This may require reviewing the current statutes governing formation (or standing down) of subcommittees. For this purpose, we suggest that the ICSP hold a meeting within the next 12 months in order to review its membership, allow the election of new officers and appoint the ad hoc committees proposed below. Indeed, we note that the ICSP appears to be in breach of Article 3 of its statutes, which requires that “Plenary Meetings shall be held at intervals of not more than four years” ([3]; http://www.ncbi.nlm.nih.gov/books/NBK8815/). For the purposes of this meeting, we request that all members of ICSP committees and its subcommittees, as well as other parties with a demonstrated interest in systematics, be able to participate as Co-opted Members, with the ability to vote as set forward in the statutes (Article 2). We note that the statutes do not require that ICSP meetings be held in concert with those of the IUMS (Article 3.1), and we suggest that this next meeting be either a dedicated meeting or, alternatively, a meeting held in conjunction with one of the major meetings of a member society of the IUMS in 2013.

  2. Prior to the meeting, the Executive Secretary of the ICSP is asked to continue the current practise of requesting nominations for Full Members from each member society of IUMS (as required by Article 2 of the statutes). To enable members of the societies to know who their representatives are and which societies are represented, we suggest that the ICSP should report on the results of this process (e.g. by announcements on its website and via the International Journal of Systematic and Evolutionary Microbiology). This might also allow the changing demographic of taxonomy [6] to become better reflected in the membership of the ICSP.

  3. The ICSP should continue to review its statutes [3], which are currently cryptic and arcane. We believe that, as noted above, the manner in which subcommittees with specific remits are constituted still needs attention. The procedures for the election of officers to the ICSP should be made more straightforward and transparent. Revision of the statutes should also allow the ICSP to fully utilise modern telecommunications for meetings of its committees, subcommittees and commissions. We understand that some progress has been made in this area but would encourage the ICSP to continue this process, if necessary through the appointment of an ad hoc committee to further review its statutes.

  4. We also suggest that the ICSP establish a new ad hoc committee to review the basis by which minimal standards for specific taxa are defined, taking full account of the accelerating impact of whole genome sequencing on systematics [5,6,8] and hopefully reflecting our view that “excessive standards directly contradict the spirit of the Code [ICNP]” [8]. This would help improve the present situation wherein there are currently minimal standards covering the classification of only a tiny fraction of the known microbial taxa [5]. The same committee could consider the issue of the rules of nomenclature at the Domain and Phylum level raised in earlier letters [1,2].

  5. The ICSP should consider establishing an ad hoc committee to review the best implementation of a database driven approach to the reporting and storage of taxonomic data, including a curated database of validly published names [9]. This committee should also review the impact of online publishing on the publication process and formats for descriptions of new microbial taxa.

  6. To promote its activities, the ICSP should continue to seek permanent funding, either through royalty income from its publications or from the member associations of the IUMS. The funding needed is not large but will be necessary for the ICSP to fulfil its responsibilities both to itself and to the wider microbiological community.

We, and others, have written recently of the pressing need for the prokaryotic systematics community to modernise and revitalise its practices, particularly given the extraordinary and exciting progress that has and is being made in the field of microbial genomics [4,5,6,8]. It is our view that if the ICSP does not take urgent action to modernise its structures and activities along the lines outlined above, then there is a grave danger that prokaryotic systematists will be left to operate in an arbitrary and marginalised manner that will ultimately threaten a return to the chaotic situation that prevailed in the 20th century, before the introduction of the ICNP and the Approved Lists of Bacterial Names [3,10]. The broader microbiological community needs to be involved in this process, not least bioinformaticists, genomic scientists and molecular biologists, as was done with considerable success by ad hoc subcommittees set up under the aegis of the International Committee of Systematic Bacteriology, the body that predated the ICSP [11,12, 13].

These comments and suggestions are made in a constructive and collegiate spirit, for the overall good of the discipline of systematics and are not intended as criticisms of individuals. Nevertheless, we hope that the ICSP will accept these comments and respond appropriately.


References


  1. Gribaldo, S. and C. Brochier-Armanet (2012).Time for order in microbial systematics. Trends in Microbiology 20, 209-210.




  1. Garrity, G.M. and A. Oren (2012). Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics. Trends in Microbiology 20, 353-354.




  1. Lapage S.P. et al. (1992). International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C.




  1. Rosselló-Mora, R. (2012). Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environmental Microbiology 14, 318-334.




  1. Sutcliffe I.C., Trujillo M.E. and M. Goodfellow (2012). A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie van Leeuwenhoek 101, 13-20.



  1. Tamames, J. and Rosselló-Mora, R. (2012). On the fitness of microbial taxonomy. Trends in Microbiology 20, 514-516.




  1. Oren A. (2010). The phyla of prokaryotes – cultured and uncultured. In Molecular Phylogeny of Microorganisms (Oren, A. and Papke, R.P., eds.) pp 85-107. Caister Academic Press, UK.




  1. Whitman W.B. (2011). Intent of the nomenclatural Code and recommendations about naming new species based on genomic sequences. Bulletin of BISMIS 2, 135-139.




  1. Watson, D.R.W. and Young, J.M. (2007). Proposals that the International Committee on Systematics of Prokaryotes establish a public database of validly published names and that the Bacteriological Code be amended to change the prescription for citation of validly published names. International Journal of Systematic and Evolutionary Microbiology 57, 1167–1168.




  1. Skerman, V.B.D., McGowan, V. and Sneath, P. H. A. (eds.) (1980). Approved Lists of Bacterial Names. International Journal of Systematic Bacteriology 30, 225–420.



  1. Stackebrandt, E. et al. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology 52, 1043–1052.



  1. Wayne, L.G. et al. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 37, 463-464.



  1. Murray, R.G.E. et al. (1990). Report of the ad hoc committee on approaches to taxonomy within the proteobacteria. International Journal of Systematic Bacteriology 40, 213-215.


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