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Minutes |
Session 1 – Closed meeting
Minute 1. Call to order.
The meeting was called to order at 9 : 00 on 11 July 2004 by the Chairman, J. M. Bradbury.
Minute 2. Record of attendance.
The members present were A. Blanchard, J. M. Bradbury (Chairman and Acting Secretary), J. Frey, R. Harasawa, R. F. Rosenbusch. J. G. Tully and R. F. Whitcomb. Ex-officio members present were D. G. Pitcher of the Health Protection Agency (UK), M. K. Davidson and J. K. Davis, Director and Curator, respectively, of the Mollicutes Collection at Purdue University, West Lafayette, IN, USA, and K. B. Waites, Chair of the Board of the International Organization of Mycoplasmology (IOM) International Research Programme on Comparative Mycoplasmology (IRPCM). A. Bertaccini attended as an alternate for G. Firrao. D. R. Brown, G. M. Garrity, G. E. Gasparich, J. Glass, T. F. Knight Jr and K. S. Wise were invited to attend in order to participate in some of the discussions. Apologies for absence were received from J. Bové, G. Christiansen, G. Firrao, K.-E. Johansson (Secretary), B. C. Kirkpatrick, H. C. Neimark, J. D. Pollack, S. Razin, K. Sachse and D. Taylor-Robinson.
Minute 3. Report of the Chairman.
J. M. Bradbury welcomed the attendees and thanked Dr D. Krause and the organising committee of the 15th International Congress of the IOM for making arrangements for the subcommittee meetings and providing a meeting room. A newly elected member, A. Blanchard, was welcomed. J. A. Robertson, who had resigned from the subcommittee during the last biennium, was thanked for her valuable contributions, particularly in the area of ureaplasma taxonomy. The resignation of K.-E. Johansson as Secretary had been received prior to the meeting and was acknowledged with regret. His important contributions to taxonomy and phylogeny would be greatly missed as would his efficient support as Secretary, although he will remain on the subcommittee as an Advisory member.
Five novel ‘Candidatus Phytoplasma’ species were described in the previous biennium in the class Mollicutes. These were ‘Candidatus Phytoplasma castaneae’ associated with chestnut witches'-broom disease, ‘Candidatus Phytoplasma phoenicium’ associated with an emerging lethal disease of almond trees, ‘Candidatus Phytoplasma oryzae’ associated with rice yellow dwarf disease, ‘Candidatus Phytoplasma ziziphi’, associated with jujube witches'-broom disease and ‘Candidatus Phytoplasma ulmi’ associated with elm yellows. Several other descriptions are already in press and available online. Mycoplasma testudineum, isolated from the respiratory tract of the desert tortoise, was also described and Eperythrozoon ovis, an epierythrocytic agent of haemolytic anaemia in sheep and goats, was reassigned to the genus Mycoplasma as Mycoplasma ovis comb. nov. The Chairman also welcomed the publication by the Phytoplasma group of the IRPCM Phytoplasma/Spiroplasma Working Team of the new description for the novel genus ‘Candidatus Phytoplasma’.
During the last biennium K.-E. Johansson determined the 16S rRNA gene sequences of all members of the genus Acholeplasma and T. F. Knight Jr determined those of the genera Entomoplasma and Mesoplasma. This completes the sequencing for the entire spectrum of the currently recognized species of Mollicutes.
The nomenclature of the ruminant mycoplasmas is still under debate but R. A. J. Nicholas and colleagues will write a proposal to classify Mycoplasma bovigenitalium and ovine/caprine serogroup 11 as a single species.
With considerable help from J. G. Tully, the Mollicutes contribution for the International Committee of Prokaryotes (ICSP) website (http://www.the-icsp.org/subcoms/mollicutes.htm) was completed and a link is now available from the IOM website. The site contains information on all the recognized taxa, on subcommittee membership, Minutes of past meetings and minimum standards documents.
The Chairman drew attention to the difficulties arising from the recent amendment to Rule 27 of the Code requiring deposition of cultures of newly described species in two independent culture collections in two different countries. This item is addressed again in Minutes 4, 8 and 12 below.
Minute 4. ICSP information.
G. M. Garrity presented information on the ICSP and its Code of Nomenclature. He reported that the recent changes to Rule 27, referred to above, had also caused difficulties for workers on other bacteria, for example the spirochetes. He explained that the subcommittees are covered by the Statutes of the ICSP, which in turn are governed by the International Union of Microbiological Societies (IUMS). If the IOM were to become a voting member of IUMS then it could have more say in the affairs of these bodies and the Rules that are made. Comments on changes to the Code and to the Statutes can be introduced for discussion at upcoming meetings (the next being in San Francisco in 2005). He urged members of the subcommittee to keep up with ICSP actions, which are published in the International Journal of Systematic and Evolutionary Microbiology following the IUMS Congress, because an updated Code has not been published since 1992. It was difficult to determine the best course of action to take on Rule 27 because a ‘Request for an Opinion’ could delay matters for up to 3 years, depending on the cycle of the Congresses. On another matter, and having read the minutes of the subcommittee's 2000 meeting, he pointed out that, although subspecies divisions are governed by the Code, the classification of serotypes, pathovars etc. do not come under the Code and can be very useful in some circumstances.
Minute 5. Spiroplasma taxonomy.
Phylogenetic trees presented at the 2002 subcommittee meeting by G. E. Gasparich have now been published [Gasparich et al., Int J Syst Evol Microbiol 54 (2004), 893–918]. In writing the paper the authors used terminology that would satisfy both the eukaryote and prokaryote systematists. G. E. Gasparich pointed out that, although this study was a comprehensive analysis, it used only 16S rRNA gene sequences and she viewed it as a good starting point for asking questions about diversity, pathogenicity and other issues. The molecular data tied in well with much other data on morphology, biochemistry and serology.
R. F. Whitcomb reported that F. French's laboratory were in the process of characterizing many novel species of Spiroplasma. Also, G. E. Gasparich and D. R. Brown had characterization programmes underway so that it was very important that the minimum standards were revised to aid this and similar ventures.
Minute 6. Phytoplasma taxonomy.
The Phytoplasma taxonomy group of the IRPCM Phytoplasma/Spiroplasma Working Team published the description of the genus ‘Candidatus Phytoplasma’, a taxon proposed for the wall-less non-helical prokaryotes that colonize plant phloem and insects [Int J Syst Evol Microbiol 54 (2004), 1243–1255]. The subcommittee commended the efforts of those involved in preparing this important document.
Minute 7. Ureaplasma taxonomy.
There has been a reduction in activity in this field in the last biennium but revisions have been made to the forthcoming Bergey chapter by the authors J. A. Robertson and D. Taylor-Robinson, which will contain much useful information.
Minute 8. Mycoplasma and haemoplasma taxonomy.
J. G. Tully indicated that the main problem concerned the classification of Eperythrozoon and Haemobartonella within the genus Mycoplasma. The priority of the name Eperythrozoon had again been raised in the literature [Uilenberg et al., Exp Appl Acarol 32 (2004), 301–312]. The Judicial Commission was expected to deal with this problem.
The amendments to Rule 27, which requires deposition of each novel species in two repositories, was discussed in the light of the above description of a comb. nov., since these organisms have never been cultured. G. M. Garrity believed that it was a matter of interpretation of the Rules as to whether the comb. nov. designation would be accepted or whether the organism would be designated Candidatus. He also explained that the Judicial Commission acts only on matters of nomenclature and not on taxonomy. Furthermore the result of a Request for an Opinion is only published if it is agreed by the Commission. When the Commission rejects such a request, the reason is not given. Thus the failure of the Commission to act may reflect the simple fact that the proposal addressed a taxonomic rather than a nomenclatural issue.
Minute 9. Bergey's Manual of Systematic Bacteriology.
J. G. Tully explained that, although the contributions on the mollicutes for Volume 3 were submitted at the end of 2002, problems with Volume 2 had pushed back the date of publication. Therefore the authors had updated the various sections. G. M. Garrity, in his capacity as Editor of Bergey's Manual, indicated that the Manual will be prepared electronically and can therefore be updated and modified up to the time that the galley proofs are produced (hopefully December 2004) for publication in summer 2005. The Chairman, on behalf of the subcommittee, and G. M. Garrity, on behalf of Bergey's Trust, acknowledged the very considerable contributions made by J. G. Tully to the forthcoming volume and to its predecessors.
Minute 10. The Minimum Standards Document.
Although the document could not be revised in detail within this forum, R. F. Whitcomb raised some issues requiring discussion. In addition to determining the 16S rRNA gene sequence of potential novel species, a phylogenetic tree should be constructed. Since a BLAST search does not necessarily identify the closest relatives of a potential novel species, a tree is the most efficient way to identify them. It will be important to reduce the labour of serological testing by first identifying to which clade a potential novel species belongs and then restricting serology to species within this phylogenetic group.
The requirement for production of species-specific antiserum (inadvertently omitted from the 1995 minimum standards document) was discussed. As indicated above, antisera will be needed in future research to test potential novel species with their closest relatives and with other species from the same host. The majority opinion was that sufficient antiserum should be prepared by the worker(s) describing the novel species to provide reagents for such future studies. There will be strong encouragement to submit antiserum to the Mollicutes collection when depositing a new type strain. Many diagnostic laboratories have phased out serology in favour of PCR methods, but it was agreed that serology is still crucial for determination of novel species.
It was reported that DNA–DNA reassociation studies were being carried out by K. Miles at the Central Veterinary Laboratories (UK). The subcommittee expressed its gratitude to her for continuing these critical tests, which are still needed in bacterial taxonomy [Stackebrandt et al., Int J Syst Evol Microbiol 52 (2002), 1043–1047]. It was also recognized that sequencing of complete genomes is becoming less expensive, and that this could eventually provide a very useful tool for classification.
Tests for absence of reversion to L-phase bacteria are currently included in the minimum standards document [Int J Syst Bacteriol 45 (1995), 605–612] but it was agreed that establishing the 16S rRNA gene sequence would circumvent this need. It was also agreed that filtration of a putative novel species through 450 nm (and possibly 220 nm) pore size filters is a very important initial step to ensure purity of the culture, but that quantitation of the process is unnecessary.
R. F. Whitcomb argued against the need to prepare ultrathin sections of new organisms to demonstrate lack of a cell wall because the 16S rRNA gene sequences will suffice to assign the organism to the class Mollicutes. J. M. Bradbury pointed out the value of ultrathin sections for revealing attachment organelles in members of the genus Mycoplasma. The subcommittee agreed that preparation of such sections would be especially relevant for the pneumoniae group and should be strongly encouraged.
It was generally agreed that the establishment of G+C content and genome size, although difficult for the average laboratory, should also be strongly encouraged. Nevertheless workers should be aware that the presence of transposons can give confusing G+C values and that genome sizes may appear to differ when determined by different methods. D. G. Pitcher suggested that, since the exact size of several mollicute genomes is now known, one of these should always be included as a control for the method. With regard to G+C content, J. Glass suggested that it could be useful to determine statistically whether any particular well-conserved genes might accurately reflect the overall chromosomal content.
R. F. Whitcomb proposed that formal thanks should be recorded to four people for their substantial efforts to provide the basic data now underpinning mollicute classification. They are K.-E. Johansson and T. F. Knight Jr for establishing the 16S rRNA gene sequences, J. G. Tully for the serology and P. Carle for establishing genome sizes.
Minute 11. The polyphyly within the Mollicutes.
R. F. Whitcomb indicated that in all phylogenetic reconstructions Asteroleplasma anaerobium does not belong in the Mollicutes. However, as only 75 % of the 16S rRNA gene has been sequenced it would be premature to propose reclassification of this organism.
The evolution of the mycoides phylogenetic group from the spiroplasmas by way of the Entomoplasmataceae makes this group very distinct from the other mycoplasma groups and its hosts are restricted to ruminants, suggesting a relatively recent adaptation to a vertebrate host. Other mycoplasmas appear to be monophyletic (originating from a single common ancestor). R. F. Whitcomb had raised this problem at the 2002 subcommittee meeting, with the possibility of creating a subgenus for each of these distinct groups. The subgenus proposal was formulated as a compromise between those subcommittee members who felt that it would be appropriate to change the genus name of one of the two phylogenetic groups, and those who felt that no change was necessary. The subcommittee felt that a change of genus name was unacceptable because of the large number of economically important pathogenic species in both groups. G. M. Garrity pointed out that a proposal could be submitted for name changes but if such changes might prove hazardous (for example changing the names of a human or veterinary pathogen) then objections would probably be raised on the grounds of nomen periculosum and the proposal would be rejected.
After much deliberation it was agreed that the Weisburg phylogenetic groups, which had been conserved by K.-E. Johansson in subsequent analyses, provided a useful working nomenclature to differentiate the mycoides group from the other phylogenetic groups of the genus Mycoplasma. The use of this system should be encouraged amongst mycoplasmologists. It was considered that, if such groups were useful, then the mycoplasma community would automatically adopt them.
Minute 12. Deposition of strains in culture collections.
D. G. Pitcher described the demise of the UK National Collection of Type Culture's Mycoplasma Unit. The fact that this repository was, at the time of the meeting, no longer accepting mycoplasma cultures, had dramatically highlighted the problems associated with changes in Rule 27 of the Code, now requiring deposition of novel species in two independent collections in two countries. Currently only two collections are willing to accept depositions and both are in the USA.
Exhaustive attempts had been made by various mycoplasmologists to locate a culture collection outside the USA that would accept mollicutes but the curators of several prestigious culture collections had claimed a lack of expertise in handling these microrganisms. It appeared that the Japanese National Biological Resource Centre (NBRC) would accept only plant mollicutes. The subcommittee strongly regretted the overall situation and observed that advances in mycoplasma taxonomy were already being stifled as a consequence.
There followed extensive discussion of this problem and possible ways to circumvent it but the final conclusion was for the subcommittee to press for a change to Rule 27. Other groups of workers (e.g. spirochaetologists) were having similar problems. It was pointed out that the situation forced upon such groups seems to be in contravention of Principle 1 paragraph 4 of the amended Bacteriological Code, which states that ‘Nothing in this Code may be construed to restrict the freedom of taxonomic thought or action’.
Minute 13. The use of the term Candidatus.
D. G. Pitcher expressed concern that some authors were submitting descriptions of Candidatus species when insufficient effort had been made to culture the organism in vitro. Although the Candidatus status is not covered by the Code, it would be useful to have basic rules for such descriptions and a requirement that some material (perhaps DNA) be deposited somewhere. Furthermore some authors designate a type strain, although this should more accurately be a reference strain. The subcommittee agreed that the ICSP should be aware of these problems and hoped that they would initiate modification of the original proposal by Murray and Schleifer [Int J Syst Bacteriol 44 (1994), 174–176].
In terms of ‘Candidatus Phytoplasma’ species, the laboratories of A. Bertaccini in Bologna, Italy and A. Blanchard in Bordeaux, France maintain strains that are readily available to the scientific community. The phytoplasmas are propagated in plants and workers need to be aware that such strains are not necessarily genetically stable over the years. For example, A. Blanchard indicated that the genome size of a Stolbur phytoplasma strain has already decreased by more than 100 kbp during propagation.
Minute 14. The gyrB gene as a phylogenetic tool.
T. F. Knight Jr in his work on the entomoplasma and mesoplasma phylogeny was concerned that several of these species had identical 16S rRNA gene sequences. Therefore he chose another marker, the gyrB gene, for sequencing and has now deposited these sequences for all the entomo- and mesoplasmas. The trees drawn from these sequences are quite different to those derived from the 16S rRNA gene data; in particular the clusters do not correlate. This suggests that several more genes need to be sequenced, preferably in the protein regions rather than in the ribosomal regions, and it also suggests that the mollicute phylogeny may well become more confused until more data have accumulated. With regard to selecting a suitable set of genes, he cited the paper by Søgaard et al. [Infect Genet Evol 1 (2002), 277–285] as a useful pointer. J. Glass pointed out that within another few years the complete genomes of some 25–30 mollicutes should be known and should permit better decisions on suitable genes. Current data show that 169 genes in Mollicutes are highly conserved.
Minute 15. Sequencing of the 16S–23S rRNA spacer region as a tool in taxonomy.
M. K. Davidson reported that F. Kong is compiling a database of the 16S–23S rRNA spacer region sequences of the type strains of the mollicutes. In order to serve the mycoplasma community the database would be accessible via the IOM website, probably in the IRPCM section. K. B. Waites raised concerns about the accessibility of the information to non-IOM members; this was to be discussed at the ensuing IRPCM Board Meeting.
Minute 16. The implication of horizontal gene transfer for systematics.
A. Blanchard stated that newer data indicate that meaningful phylogenetic analyses can be done using a core of genes. J. Glass reported that he had had extensive discussions on horizontal gene transfer in bacteria with colleagues at The Institute for Genomic Research who believed that it was not a major issue. The mollicute genomes sequenced so far show little evidence of transfer from outside the mollicutes, although transposons may have had such an origin. He felt that the influence on systematics, even among the wider taxa, may have been exaggerated in some of the literature. A. Blanchard pointed out that there are a few well-documented examples of transfer occurring, for example the transfer of the gyrase gene from bacteria to the archaea [Gadelle et al., Bioessays 25 (2003), 232–242]. K. S. Wise believed that horizontal transfer in the mollicutes is probably inhibited by strong restriction systems.
Minute 17. Liaison with the International Research Programme for Comparative Mycoplasmology (IRPCM).
The IRPCM Chair, K. B. Waites, commented on the value of having subcommittee information on the IRPCM page of the IOM website. J. M. Bradbury explained that the ICSP now had its own website which lists subcommittee members and their contact details. It also has the dates of meetings, reference to the minutes of previous meetings and to minimum standards documents. In addition it has details of all taxa. There is already a link on the IOM website, but this would be made more prominent.
A matter of concern to both the taxonomy subcommittee and the IRPCM Board was the schedule of future meetings. One proposal for a much abbreviated Congress in 2008 would make it difficult to hold these meetings. Unlike the IRPCM, the subcommittee has no operating budget. There was strong feeling amongst members that the current arrangements should be continued, with the local Congress hosts scheduling the meetings. There then followed discussion as to whether the Chairman or a designated alternative could attend the plenary session of IUMS and whether the IOM should consider joining the IUMS.
Minute 18. Future meeting schedule.
The next subcommittee meeting is scheduled to take place alongside the 16th International Congress of the IOM, which is to be held in Cambridge, UK in July 2006.
Minute 19. Election of officers and membership changes.
J. G. Tully tendered his resignation but agreed to remain as an Advisory Member. D. R. Brown, G. E. Gasparich, K. Miles, T. F. Knight Jr and A. Bertaccini were elected as new members with D. R. Brown to be the new Secretary. The Chairman was elected to another term of office.
Minute 20. Current membership.
The current membership of the subcommittee is as follows: J. M. Bradbury (Chairman; UK), D. R. Brown (Secretary; USA), A. Bertaccini (Italy), A. Blanchard (France), J. M. Bové (France), G. Christiansen (Denmark), G. Firrao (Italy), J. Frey (Switzerland), G. E. Gasparich (USA), R. Harasawa (Japan), B. C. Kirkpatrick (USA), T. F. Knight Jr. (USA), K. Miles (UK), H. C. Neimark (USA), J. D. Pollack (USA), S. Razin (Israel), R. F. Rosenbusch (USA), K. Sachse (Germany) and R. F. Whitcomb (USA). Advisory members are K.-E. Johansson (Sweden), D. Taylor-Robinson (UK) and J. G. Tully (USA). Ex-officio members are S. Levisohn (IOM IRPCM Chair), M. K. Davidson and J. K. Davis (USA), and D. G. Pitcher (UK).
Minute 21. Any other business.
M. K. Davidson sought approval from the subcommittee to form an Advisory Committee for the Mollicutes Collection, now located at Purdue University. The Committee would include the immediate Past Chair of the IOM, the Chair of the IRPCM and the Chair of the taxonomy subcommittee and would meet alongside the biennial IOM Congress. Subcommittee members have given their unanimous support to this proposal.
Minute 22. Adjournment.
The meeting was adjourned at 13 : 30 on 11 July 2004.
Session 2 – Open meeting
Minute 23. Call to order.
The meeting was called to order at 10 : 30 on 16 July 2004 by the Chairman, J. M. Bradbury. Approximately 150 IOM members attended this meeting and subcommittee members present were A. Blanchard, J. Frey, R. F. Rosenbusch, J. G. Tully and R. F. Whitcomb. Ex-officio members present were D. G. Pitcher, M. K. Davidson, J. K. Davis and K. B. Waites.
Minute 24. Summary of Session 1.
J. M. Bradbury reminded IOM members of the structure and function of the ICSP and its taxonomy subcommittees and then summarized the more important items that had been discussed in Session 1. Questions received from the IOM membership addressed the problems of deposition of type strains and the nomenclature of the ruminant mycoplasmas.
Minute 25. Next meeting.
The next meeting will be held in Cambridge, UK in July 2006.
Minute 26. Adjournment.
J. M. Bradbury thanked all those who attended the meeting and those who contributed to the discussions. She thanked K.-E. Johansson for his help in preparation for the meeting. The meeting was adjourned at 11 : 00 on 16 July 2004.
This article has been cited by other articles:
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  R. A. J. Nicholas, Y.-C. Lin, K. Sachse, H. Hotzel, K. Parham, L. McAuliffe, R. J. Miles, D. P. Kelly, and A. P. Wood Proposal that the strains of the Mycoplasma ovine/caprine serogroup 11 be reclassified as Mycoplasma bovigenitalium Int J Syst Evol Microbiol, January 1, 2008; 58(1): 308 - 312. [Abstract] [Full Text] [PDF]
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