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Minutes |
Minute 1. Call to order.
The meeting was held at the University of Essex, Wivenhoe Park, Colchester, UK. The chairman, Dr A. Ventosa, opened the meeting at 18 : 15.
Minute 2. Record of attendance.
The subcommittee members present were Drs A. Ventosa (Chairman, Subcommittee on the taxonomy of Halobacteriaceae and Subcommittee on the taxonomy of Halomonadaceae), A. Oren (Secretary, Subcommittee on the taxonomy of Halobacteriaceae), R. H. Vreeland (Secretary, Subcommittee on the taxonomy of Halomonadaceae), D. R. Arahal, V. Bejar, M. L. Dyall-Smith, C. D. Litchfield, Y. Ma and H. Stan-Lotter. Apologies were received from Drs R. R. Colwell, A. Gambacorta, W. D. Grant, M. Kamekura, M. R. Mormile, Y. H. Park, E. Quesada, F. Rodríguez-Valera and B. J. Tindall. In addition, the meeting was attended by A. Antunes, H. Banciu, S. DasSarma, M. Enache, E. A. Galinski, C. M. González-Domenech, A. Gramain, J. E. Hallsworth, B. J. Jones, I. Llamas Company, S. McCready, T. J. McGenity, E. Majewski, R. Mancinelli, F. Martinez-Checa, M. Miezeiewski, T. Papke, G. Popescu-Teodosiu, S. Sabet, T. Takashina and J. Wiegel.
Minute 3.
The chairman A. Ventosa presented a short obituary in memory of Dr Milos Kocur, the former curator of the Czech Collection of Micro-organisms, who had passed away in September 2006. Dr Kocur was the first chairman of the ISCB Subcommittee on the taxonomy of Halobacteriaceae and contributed much to the study of halophilic micro-organisms.
Minute 4. Approval of agenda.
The agenda of the meeting was approved.
Minute 5. Minutes of previous meetings.
The minutes of the meetings of the Subcommittee on the taxonomy of Halobacteriaceae held in San Francisco, USA, 25 July 2005 [Oren & Ventosa, Int J Syst Evol Microbiol 55 (2005), 2637–2638] and of the Subcommittee on the taxonomy of Halomonadaceae held in San Francisco, USA, 25 July 2005 [Vreeland & Ventosa, Int J Syst Evol Microbiol 56 (2006), 2021–2022] were approved.
Minute 6. New taxa within the family Halobacteriaceae.
All attendees received handouts listing currently accepted and validly published names associated with new taxa in both families. The new names associated with taxa within each individual family were reviewed by A. Oren. As of August 2007, the family Halobacteriaceae contained 26 genera and 85 species. Reports on the following new taxa were presented:
Halorubrum tibetense sp. nov. [Fan et al., Int J Syst Evol Microbiol 54 (2004), 1213–1216], with type strain AS 1.3239T, JCM 11889T.
Halorubrum arcis sp. nov. [Xu et al., Int J Syst Evol Microbiol 55 (2005), 1069–1072], with type strain CGMCC 1.5343T, JCM 13916T.
Haloterrigena saccharevitans sp. nov. [Xu et al., Int J Syst Evol Microbiol 55 (2005), 2539–2542], with type strain AS 1.3730T, JCM 12889T.
Halovivax gen. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 765–770], with type species Halovivax asiaticus.
Halovivax asiaticus sp. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 765–770], with type strain CGMCC 1.4248T, CECT 7098T.
Halococcus hamelinensis sp. nov. [Goh et al., Int J Syst Evol Microbiol 56 (2006), 1323–1329], with type strain JCM 12892T, ACM 5227T.
An emended description of the genus Natronorubrum was given [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1515–1517].
Natronorubrum aibiense sp. nov. [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1515–1517], with type strain CGMCC 1.4299T, JCM 13488T.
Halostagnicola gen. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 1519–1524], with type species Halostagnicola larsenii.
Halostagnicola larsenii sp. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 1519–1524], with type strain CGMCC 1.5338T, CECT 7116T, DSM 17691T, JCM 13463T.
Halorubrum ezzemoulense sp. nov. [Kharroub et al., Int J Syst Evol Microbiol 56 (2006), 1583–1588], with type strain CECT 7099T, DSM 17463T.
Halorubrum lipolyticum sp. nov. [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1631–1634], with type strain CGMCC 1.5332T, JCM 13559T.
Halorubrum aidingense sp. nov. [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1631–1634], with type strain CGMCC 1.2670T, JCM 13560T.
Haloterrigena longa sp. nov. [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1837–1840], with type strain CGMCC 1.5334T, JCM 13562T.
Haloterrigena limicola sp. nov. [Cui et al., Int J Syst Evol Microbiol 56 (2006), 1837–1840], with type strain CGMCC 1.5333T, JCM 13563T.
Halobacterium jilantaiense sp. nov. [Yang et al., Int J Syst Evol Microbiol 56 (2006), 2353–2355], with type strain CGMCC 1.5337T, JCM 13558T.
Halorubrum orientale sp. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 2559–2563], with type strain CECT 7145T, JCM 13889T, CGMCC 1.6295T.
Natrinema ejinorense sp. nov. [Castillo et al., Int J Syst Evol Microbiol 56 (2006), 2683–2687], with type strain CECT 7144T, JCM 13890T, CGMCC 1.6202T.
Haladaptatus gen. nov. [Savage et al., Int J Syst Evol Microbiol 57 (2007), 19–24], with type species Haladaptatus paucihalophilus.
Haladaptatus paucihalophilus sp. nov. [Savage et al., Int J Syst Evol Microbiol 57 (2007), 19–24], with type strain JCM 13897T, DSM 18195T, ATCC BAA–1313T, KCTC 4006T.
Haloarcula amylolytica sp. nov. [Yang et al., Int J Syst Evol Microbiol 57 (2007), 103–106], with type strain CGMCC 1.5335T, JCM 13557T.
Haloquadratum gen. nov. [Burns et al., Int J Syst Evol Microbiol 57 (2007), 387–392], with type species Haloquadratum walsbyi.
Haloquadratum walsbyi sp. nov. [Burns et al., Int J Syst Evol Microbiol 57 (2007), 387–392], with type strain JCM 12705T, DSM 16854T.
Haloferax prahovense sp. nov. [Enache et al., Int J Syst Evol Microbiol 57 (2007), 393–397], with type strain JCM 13924T, DSM 18310T.
Halococcus qingdaonensis sp. nov. [Wang et al., Int J Syst Evol Microbiol 57 (2007), 600–604], with type strain CGMCC 1.4243T, JCM 13587T.
Haloferax larsenii sp. nov. [Xu et al., Int J Syst Evol Microbiol 57 (2007), 717–720], with type strain CGMCC 1.5347T, JCM 13917T.
Natronorubrum sulfidifaciens sp. nov. [Cui et al., Int J Syst Evol Microbiol 57 (2007), 738–740], with type strain CGMCC 1.6307T, JCM 14089T.
Haloplanus gen. nov. [Elevi Bardavid et al., Int J Syst Evol Microbiol 57 (2007), 780–783], with type species Haloplanus natans.
Haloplanus natans sp. nov. [Elevi Bardavid et al., Int J Syst Evol Microbiol 57 (2007), 780–783], with type strain DSM 17983T, JCM 14081T.
Halovivax ruber sp. nov. [Castillo et al., Int J Syst Evol Microbiol 57 (2007), 1024–1027], with type strain CGMCC 1.6204T, DSM 18193T, JCM 13892T.
Halopiger gen. nov. [Gutiérrez et al., Int J Syst Evol Microbiol 57 (2007), 1402–1407], with type species Halopiger xanaduensis.
Halopiger xanaduensis sp. nov. [Gutiérrez et al., Int J Syst Evol Microbiol 57 (2007), 1402–1407], with type strain CECT 7173T, CGMCC 1.6379T, JCM 14033T.
Haloterrigena hispanica sp. nov. [Romano et al., Int J Syst Evol Microbiol 57 (2007), 1499–1503], with type strain DSM 18328T, ATCC BAA-1310T.
Descriptions of the following novel species are in press in Int J Syst Evol Microbiol: Halorubrum ejinorense sp. nov., Halalkalicoccus jeotgali sp. nov., Halorubrum litoreum sp. nov., Halococcus thailandensis sp. nov., Natronococcus jeotgali sp. nov.
Minute 7. New taxa within the family Halomonadaceae.
As of August 2007 the family Halomonadaceae contained 5 genera and 57 species. Reports on the following new taxa were presented:
The name Halomonas campaniensis sp. nov. [Romano et al., Syst Appl Microbiol 28 (2005), 610–618], with type strain DSM 15293T, ATCC BAA-966T, has been validly published [Validation List no. 106, Int J Syst Evol Microbiol 55 (2005), 2235–2238].
Chromohalobacter nigrandesensis sp. nov. [Prado et al., Int J Syst Evol Microbiol 56 (2006), 647–651], with type strain CECT 5315T, DSM 14323T.
Pseudomonas beijerinckii Hof 1935 was reclassified as Chromohalobacter beijerinckii comb. nov., with type strain DSM 7218T, ATCC 19372T, NCIMB 9041T, and an emended description of the species was given [Peçonek et al., Int J Syst Evol Microbiol 56 (2006), 1953–1957].
Halomonas indalinina sp. nov. [Cabrera et al., Int J Syst Evol Microbiol 57 (2007), 376–380], with type strain CECT 5902T, LMG 23625T.
Halomonas gomseomensis sp. nov. [Kim et al., Int J Syst Evol Microbiol 57 (2007), 675–681], with type strain KCTC 12662T, DSM 18042T.
Halomonas janggokensis sp. nov. [Kim et al., Int J Syst Evol Microbiol 57 (2007), 675–681], with type strain KCTC 12663T, DSM 18043T.
Halomonas salaria sp. nov. [Kim et al., Int J Syst Evol Microbiol 57 (2007), 675–681], with type strain KCTC 12664T, DSM 18044T.
Halomonas denitrificans sp. nov. [Kim et al., Int J Syst Evol Microbiol 57 (2007), 675–681], with type strain KCTC 12665T, DSM 18045T.
Halomonas avicenniae sp. nov. [Soto-Ramírez et al., Int J Syst Evol Microbiol 57 (2007), 900–905], with type strain CECT 7193T, CCM 7396T.
Halomonas gudaonensis sp. nov. [Wang et al., Int J Syst Evol Microbiol 57 (2007), 911–915], with type strain LMG 23610T, CGMCC 1.6133T.
Halomonas shengliensis sp. nov. [Wang et al., Int J Syst Evol Microbiol 57 (2007), 1222–1226], with type strain LMG 23897T, CGMCC 1.6444T.
Chromohalobacter salarius sp. nov. [Aguilera et al., Int J Syst Evol Microbiol 57 (2007), 1238–1242], with type strain CECT 5903T, LMG 23626T.
Halomonas saccharevitans sp. nov. [Xu et al., Int J Syst Evol Microbiol 57 (2007), 1619–1624], with type strain CGMCC 1.6493T, JCM 14606T, LMG 23976T.
Halomonas arcis sp. nov. [Xu et al., Int J Syst Evol Microbiol 57 (2007), 1619–1624], with type strain CGMCC 1.6494T, JCM 14607T, LMG 23978T.
Halomonas subterranea sp. nov. [Xu et al., Int J Syst Evol Microbiol 57 (2007), 1619–1624], with type strain CGMCC 1.6495T, JCM 14608T, LMG 23977T.
Descriptions of the following new taxa are in press in Int J Syst Evol Microbiol: Halomonas sabkhae sp. nov., Modicisalibacter gen. nov. (including an emended description of the family Halomonadaceae), Modicisalibacter tunisiensis sp. nov., Chromohalobacter japonicus sp. nov., Halomonas kribbensis sp. nov., Halotalea gen. nov. (including an emended description of the family Halomonadaceae), Halotalea alkalilenta sp. nov.
Minute 8. Reclassification of existing taxa.
A. Ventosa explained the reclassification of Pseudomonas beijerinckii Hof 1935 as Chromohalobacter beijerinckii comb. nov. and the emendation of the species description [Peçonek et al., Int J Syst Evol Microbiol 56 (2006), 1953–1957].
Minute 9. Placement of the genus Zymobacter within the Halomonadaceae.
Following the question of in which publication had the genus Zymobacter been formally placed in the family Halomonadaceae (see Minute 8 of the open meeting of the ICSP Subcommittee on the taxonomy of Halomonadaceae held in San Francisco, USA, 25 July 2005 [Vreeland & Ventosa, Int J Syst Evol Microbiol 56 (2006), 2021–2022]), it was reported that the genus Zymobacter was placed in the family Halomonadaceae by Dobson & Franzmann [Int J Syst Bacteriol 46 (1996), 550–558].
Minute 10. Minimal standards for the Halomonadaceae.
A paper presenting the recommended minimal standards for describing new taxa of the family Halomonadaceae, co-authored by the majority of the members of ICSP Subcommittee on the taxonomy of Halomonadaceae (D. R. Arahal, R. H. Vreeland, C. D. Litchfield, M. R. Mormile, B. J. Tindall, A. Oren, V. Bejar, E. Quesada & A. Ventosa) is now in press in Int J Syst Evol Microbiol. D. R. Arahal presented and explained the document and emphasized the subcommittee's hope that new descriptions will at least conform to these standards. He stressed the intention that the minimal standards should also serve as a guide for reviewers and editors, as well as for authors describing new taxa within the family.
Minute 11. Minimal standards for the Halobacteriaceae.
The current minimal standards document for the family Halobacteriaceae dates from 1997 [Oren et al., Int J Syst Bacteriol 47 (1997), 233–238]. It may be desirable to re-evaluate the document and update it. A working group consisting of A. Ventosa (chairman), M. L. Dyall-Smith, C. D. Litchfield, A. Oren, H. Stan-Lotter and R. H. Vreeland was established for this purpose.
Minute 12. Naming novel species of the families Halobacteriaceae and Halomonadaceae.
At the request of E. Quesada, A. Oren discussed the problems often connected with the finding of new names for novel species. He explained the possibilities and the current attempts to reduce the creation of ‘geographical’ names (‘localimania’, as termed by H. G. Trüper [Int J Syst Evol Microbiol 55 (2005), 1753]). This expedient is becoming more important with the explosive growth of novel species in these two families. The subcommittee reminded all attendees that geographical naming should avoid attempts to make political statements. The subcommittee also reminded authors to beware of closely sounding or spelled geographical names as these may become confusing. Honourific names (those developed to honour someone) should be restricted to scientists associated with the taxon and those making great contributions to the overall field. Authors are reminded that while there are no rules governing the use of such names, past practice has been that the individual being honoured is not listed as a coauthor of the manuscript. He recommended that authors consult H. G. Trüper or J. Euzéby if suggestions are needed for new names.
Minute 13. Report of the ad-hoc committee for the identification of genes relevant to multilocus gene comparison studies of Halobacteriaceae.
Following the discussions in Ljubljana in 2004, an ad-hoc committee was appointed consisting of M. Kamekura, C. Daniels, S. DasSarma, W. F. Doolittle, M. L. Dyall-Smith, and B. J. Tindall. Thus far, this committee has not been active. M. Kamekura expressed the wish to retire from the ad-hoc committee. A new ad-hoc committee was established, consisting of T. Papke (chairman), S. DasSarma and M. L. Dyall-Smith, to make suggestions for a suitable set of genes for multilocus gene typing of the family Halobacteriaceae.
Minute 14. Impact of genome sequencing in current systematics of halophilic Archaea and Bacteria.
A. Ventosa commented that thus far the genomes of no more than six halophilic Archaea and four halophilic Bacteria have been sequenced. He stressed upon the subcommittee the necessity to have information available for a large number of halophiles, to search for funding for more genomes to be sequenced and to prepare a list of type species to be sequenced with high priority. Further discussions on this topic were held at a roundtable session in Colchester, during the Halophiles 2007 meeting, on 5 September 2007.
Minute 15. Potential use of DNA microarrays for identification of halophiles.
H. Stan-Lotter commented that conventional techniques for the determination of DNA–DNA relatedness, required in many cases for the description of novel species, are complicated and expensive and suggested that microarray techniques are more convenient for this purpose. There was a consensus that currently these microarray-based techniques are not sufficiently standardized and calibrated against the earlier methods. It was concluded that therefore such techniques should not be used to delineate species until the methods are better established. J. Wiegel asked to what extent DNA–DNA relatedness determination for phylogenetically closely related species is obligatory for the description of novel species. There are no strict rules here and much depends on the degree of similarity of the new isolate with the type strains of earlier established species.
Minute 16. Abbreviation of names of genera within the family Halobacteriaceae.
The joint subcommittee meeting agreed on the recommendation of the use of three-letter abbreviations for genera of the family Halobacteriaceae as follows: Haladaptatus (Hap.), Halalkalicoccus (Hac.), Haloarcula (Har.), Halobacterium (Hbt.), Halobaculum (Hbl.), Halobiforma (Hbf.), Halococcus (Hcc.), Haloferax (Hfx.), Halogeometricum (Hgm.), Halomicrobium (Hmc.), Halopiger (Hpg.), Haloplanus (Hpn.), Haloquadratum (Hqr.), Halorhabdus (Hrd.), Halorubrum (Hrr.), Halosimplex (Hsx.) Halostagnicola (Hst.), Haloterrigena (Htg.), Halovivax (Hvx.), Natrialba (Nab.), Natrinema (Nnm.), Natronobacterium (Nbt.), Natronococcus (Ncc.), Natronolimnobius (Nln.), Natronomonas (Nmn.) and Natronorubrum (Nrr.). Use of three-letter abbreviations is recommended only in cases when the use of one-letter abbreviations may give rise to confusion. Authors describing new genera are asked to propose appropriate three-letter abbreviations in the genus descriptions.
Minute 17. Validation of names of taxa effectively published outside the International Journal of Systematic and Evolutionary Microbiology.
B. J. Jones asked what kind of quality control exists on the validation of names previously effectively published in journals other than IJSEM. A. Oren explained the current procedure, as described by Tindall et al. [Int J Syst Evol Microbiol 56 (2006), 2715–2720]. It is the responsibility of the authors to submit names properly for validation to IJSEM and not the task of the subcommittee or anyone else to pursue such validation. The current procedures for accepting names for validation in IJSEM focus primarily on certification that type strains have been submitted to at least two permanent culture collections located in different countries. Editors handling requests for validation also examine the manuscripts to ensure that they meet IJSEM standards; however, emphasis was placed on the fact that this is not a second review of the research. Rejections of requests for validation may only occur on purely technical grounds, rejections are not disseminated to other journals or published in IJSEM. Rejected requests would usually only require corrections by the submitting authors.
Minute 18. Database of private collections of Halomonadaceae.
A. Antunes asked whether any progress had been made with the establishment of a database with an inventory of strains maintained in ‘private’ collections. R. H. Vreeland admitted that no such database has been set up yet and he hopes to start working on this in the near future. Dr Vreeland stated that while program systems have been identified, the funding necessary to purchase such programs, maintain security and host the site is not trivial and is not yet available.
Minute 19. Requirement for multiple strains for the proposal of novel species of Halobactericeae and Halomonadaceae.
J. Wiegel asked whether description of new taxa can be based on a single isolate. There have been attempts in the past to make the availability of a larger number of isolates obligatory for the establishment of species. However, the rules of the International Code of Nomenclature of Prokaryotes allow such descriptions to be based on a single strain. It is always recommended, however, that multiple isolates are compared so that the description is based on as many strains as possible. Appropriate type strains should also be included in testing as quality controls.
Minute 20. Next meeting of the subcommittees.
The next meeting of both subcommittees will be held in association with the International Union of Microbiological Societies meetings to be held in Istanbul, Turkey, from 4 to 8 August 2008.
Minute 21. Adjournment.
The meeting was adjourned at 19 : 45 on 3 September 2007.
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