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. 2017 Aug 31;67(10):4279–4283. doi: 10.1099/ijsem.0.002296

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Halobacteria and Subcommittee on the taxonomy of Halomonadaceae. Minutes of the joint open meeting, 11 July 2017, Valencia, Spain

David R Arahal 1, Aharon Oren 2,*, Antonio Ventosa 3
PMCID: PMC5845653  PMID: 28857024

Minute 1. Call to order

The meeting was held at the Feria de Valencia Convention and Exhibition Centre, Valencia, Spain. The chairman, Dr A. Ventosa, opened the meeting at 09:05.

Minute 2. Record of attendance

The subcommittee members present were Drs A. Ventosa (Chairman, Subcommittee on the Taxonomy of Halobacteria and Subcommittee on the Taxonomy of Halomonadaceae), A. Oren (Secretary, Subcommittee on the Taxonomy of Halobacteria), D. R. Arahal (Secretary, Subcommittee on the Taxonomy of Halomonadaceae), M. A. Amoozegar, V. Bejar and F. Rodríguez-Valera. Apologies were received from H.-L. Cui, M. L. Dyall-Smith, R. R. de la Haba, M. Kamekura, Y. Ma, H. Minegishi, R. Montalvo-Rodriguez, M. R. Mormile, R. T. Papke, H. Stan-Lotter, B. J. Tindall and R. H. Vreeland. X.-W. Xu. R. Hahnke (Germany) served as alternate for B. J. Tindall. In addition, the meeting was attended by R. Cojoc (Romania), M. Enache (Romania), S. A. S. Fazerli (Iran) and I. Gomoiu (Romania).

Minute 3. Appointment of secretary

A. Oren (Secretary, Subcommittee on the Taxonomy of Halobacteria) and D. R. Arahal (Secretary, Subcommittee on the Taxonomy of Halomonadaceae) were appointed joint secretaries of the joint subcommittee meeting.

Minute 4. Approval of agenda

The agenda of the meeting was approved.

Minute 5. Minutes of previous meeting

The minutes of the joint meeting of the Subcommittee on the taxonomy of Halobacteriaceae and Subcommittee on the taxonomy of Halomonadaceae held in San Juan, Puerto Rico [Oren and Ventosa, Int J Syst Evol Microbiol 66 (2016), 4291–4295] were unanimously approved.

Minute 6. Report of the chairman

A. Ventosa explained the work of the ICSP subcommittees on taxonomy.

Minute 7. New taxa within the class Halobacteria

As of May, 2017, the class Halobacteria contained three orders, six families, 57 genera and 233 species whose names have standing in the nomenclature (genus name, recommended three-letter abbreviation and number of species): Halobacterium (Hbt. 4 – not including Hbt. piscisalsi), Haladaptatus (Hap. 4), Halalkalicoccus (Hac. 3), Halanaeroarchaeum (Haa. 1), Halapricum (Hpr. 1), Halarchaeum (Hla. 6), Haloarchaeobius (Hab. 5), Haloarcula (Har. 9), Halobaculum (Hbl. 3), Halobellus (Hbs. 8), Halobiforma (Hbf. 3), Halobium (Hbm. 1), Halocalculus (Hcl. 1), Halococcus (Hcc. 9), Haloferax (Hfx. 12), Halogeometricum (Hgm. 4), Halogranum (Hgn. 4), Halohasta (Hht. 2), Halolamina (Hlm. 6), Halomarina (Hmr. 2), Halomicroarcula (Hma. 3), Halomicrobium (Hmc. 3), Halonotius (Hns. 1), Haloparvum (Hpv. 2), Halopelagius (Hpl. 3), Halopenitus (Hpt. 3), Halopiger (Hpg. 6), Haloplanus (Hpn. 6), Haloprofundus (Hpd. 1), Haloquadratum (Hqr. 1), Halorhabdus (Hrd. 2), Halorientalis (Hos. 3), Halorubellus (Hrb. 3), Halorubrum (Hrr. 36), Halorussus (Hrs. 4), Halosarcina (Hsn. 0 – its two species were transferred to Halogeometricum), Halosiccatus (Hsc. 1), Halosimplex (Hsx. 4), Halostagnicola (Hst. 4), Halostella (Hsl. 1), Haloterrigena (Htg. 10), Halovarius (Hvr. 1), Halovenus (Hvn. 3), Halovivax (Hvx. 4), Natrialba (Nab. 6), Natribaculum (Nbl. 2), Natrinema (Nnm. 7), Natronoarchaeum (Nac. 3), Natronobacterium (Nbt. 2), Natronococcus (Ncc. 4), Natronolimnobius (Nln. 2), Natronomonas (Nmn. 3), Natronorubrum (Nrr. 6), Salarchaeum (Sar. 1), Salinarchaeum (Saa. 1), Salinigranum (Sgn. 2), Salinirubrum (Srr. 1).

The number of Halococcus species listed does not include Halococcus formicarii Takahashi 1951 which is a scale insect named under the International Code of Zoological Nomenclature.

Reports on the following new taxa with validly published names and emendation of existing taxa were presented, as published between May 2016 and May 2017:

  • Haloparvum gen. nov. [Chen et al., Int J Syst Evol Microbiol 2016;66 : 2332], with type species Haloparvum sedimenti. Recommended three-letter abbreviation: Hpv.

  • Haloparvum sedimenti sp. nov. [Chen et al., Int J Syst Evol Microbiol 2016;66 : 2333], with type strain DYS4 (=CGMCC 1.14998=JCM 30891).

  • Halanaeroarchaeum gen. nov. [Sorokin et al., Int J Syst Evol Microbiol 2016;66 : 2380], with type species Halanaeroarchaeum sulfurireducens. Recommended three-letter abbreviation: Haa.

  • Halanaeroarchaeum sulfurireducens sp. nov. [Sorokin et al., Int J Syst Evol Microbiol 2016;66 : 2380], with type strain HSR2 (=JCM 30661=UNIQEM U935).

  • Haloarculaceae fam. nov. [Gupta et al., Int J Syst Evol Microbiol 2016; 66 : 2464 (Validation List no. 170); effective publication: Antonie van Leeuwenhoek 2016; 109 : 582], with type genus Haloarcula.

  • Halococcaceae fam. nov. [Gupta et al., Int J Syst Evol Microbiol 2016;66 : 2464 (Validation List no. 170); effective publication: Antonie van Leeuwenhoek 2016;109 : 583], with type genus Halococcus.

  • Halorhabdus rudnickae sp. nov. [Albuquerque et al., Int J Syst Evol Microbiol 2016;66 : 2464 (Validation List no. 170); effective publication: Syst Appl Microbiol 2016;39 : 103], with type strain WSM-64 (=DSM 29498=CECT 8673).

  • Halorubraceae fam. nov. [Gupta et al., Int J Syst Evol Microbiol 2016;66 : 2464 (Validation List no. 170); effective publication: Antonie van Leeuwenhoek 2016;109 : 583], with type genus Halorubrum.

  • Halostella gen. nov. [Song et al., Int J Syst Evol Microbiol 2016;66 : 2745], with type species Halostella salina. Recommended three-letter abbreviation: Hsl.

  • Halostella salina sp. nov. [Song et al., Int J Syst Evol Microbiol 2015;66 : 2745], with type strain CBA1114 (=JCM 30111=KCTC 4206).

  • Halorubrum pallidum sp. nov. [Chen et al., Int J Syst Evol Microbiol 2016;66 : 2985], with type strain PJ61 (=CGMCC 1.15212=JCM 30955).

  • Salinigranum salinum sp. nov. [Wang et al., Int J Syst Evol Microbiol 2016;66 : 3019], with type strain YJ-50–52 (=CGMCC 1.12572=JCM 30033).

  • Halolamina litorea sp. nov. [Xu et al., Int J Syst Evol Microbiol 2016;66 : 3762 (Validation List no. 171); effective publication: Microbiol China 2016, 905], with type strain YJ-41 (=CGMCC 1.12859=JCM 30237).

  • Halobium gen. nov. [Mori et al., Int J Syst Evol Microbiol 2016;66 : 3803], with type species Halobium palmae. Recommended three-letter abbreviation: Hbm.

  • Halobium palmae sp. nov. [Mori et al., Int J Syst Evol Microbiol 2016;66 : 3803], with type strain 2a_47_2 (=InaCC Ar34=NBRC 111368).

  • Halomarina salina sp. nov. [Xu et al., Int J Syst Evol Microbiol 2016;66 : 4301 (Validation List no. 172); effective publication: Antonie van Leeuwenhoek 2016 : 124], with type strain ZS-57-S (=CGMCC 1.12543=JCM 30039).

  • Halopiger djelfimassiliensis corrig. [Hassani et al., Int J Syst Evol Microbiol 2016;66 : 4301 (Validation List no. 172); effective publication: Standards Genomic Sci 2013 : 171], with type strain IIH2 (=CSUR P3035=DSM 27506).

  • Halopiger goleimassiliensis corrig. [Hassani et al., Int J Syst Evol Microbiol 2016;66 : 4301 (Validation List no. 172); effective publication: Standards Genomic Sci 2014 : 966], with type strain IIH3 (=CSUR P3036=DSM 27562).

  • Halopiger thermotolerans sp. nov. [Minegishi et al., Int J Syst Evol Microbiol 2016;66 : 4979], with type strain SR-441 (=JCM 19583=KCTC 4248).

  • Haloparvum alkalitolerans sp. nov. [Kondo et al., Int J Syst Evol Microbiol 2016;66 : 5317], with type strain MK62-1 (=JCM 30442=KCTC 4214).

  • Haloprofundus gen. nov. [Zhang et al., Int J Syst Evol Microbiol 2017;67 : 14], with type species Haloprofundus marisrubri. As the authors had not indicated a recommended three-letter abbreviation for the genus name, the subcommittee recommended Hpd.

  • Haloprofundus marisrubri sp. nov. [Zhang et al., Int J Syst Evol Microbiol 2017;67 : 14], with type strain SB9 (=CGMCC 1.14959=JCM 19565).

  • Halorussus salinus sp. nov. [Xu et al., Int J Syst Evol Microbiol 2017;67 : 529 (Validation List no. 174); effective publication: Arch Microbiol 2016, 960], with type strain YJ-37-H (=CGMCC 1.12571=JCM 30032).

  • Halobaculum roseum sp. nov. [Chen et al., Int J Syst Evol Microbiol 2017;67 : 822], with type strain D90 (=CGMCC 1.15501=JCM 31273).

  • Haloterrigena mahii sp. nov. [Ding et al., Int J Syst Evol Microbiol 2017;67 : 1337], with type strain H13 (=BCRC 910151=NBRC 111885).

  • Halorubrum trueperi sp. nov. [Chen et al., Int J Syst Evol Microbiol 2017;67 : 1569], with type strain Y73 (=CGMCC 1.15503=JCM 31271).

Papers describing the following new taxa were in press in the IJSEM as of 31 May 2017:

  • Natrinema soli sp. nov. [Amoozegar et al., Int J Syst Evol Microbiol 2017;67, in press], with type strain 5–4 (=IBRC M 11063=LMG 29247).

  • Natronoarchaeum persicum sp. nov. [Naghoni et al., Int J Syst Evol Microbiol 2017;67, in press], with type strain WIIAL99 (=IBRC M 11062=LMG 29814).

The following names of members of the Halobacteria were effectively but not validly published as of 31 May 2017:

The following emended descriptions were published outside the IJSEM:

  • Emended description of Halobacteriaceae Gibbons 1974 (Approved Lists 1980) emend. Gupta et al. 2016, 1521 [Gupta et al., Antonie van Leeuwenhoek 2016;109 : 1621–1523].

  • Emended description of Haloferacaceae Gupta 2015 emend. Gupta et al. 2016 : 1523 [Gupta et al., Antonie van Leeuwenhoek 2016;109 : 1621–1523].

A recently published paper [Amoozegar, Siroosi, Atashgahi, Smidt and Ventosa, Microbiology 163 (2017), 623–645] provides a good overview of the current status of the systematics of the Halobacteria.

Minute 8. New taxa within the family Halomonadaceae

As of May 2017 the family Halomonadaceae contained 12 genera (name and number of species with validly published names): Halomonas (90); Aidingimonas (1); Carnimonas (1); Chromohalobacter (8); Cobetia (5); Halotalea (1); Kushneria (6); Larsenimonas (2); Modicisalibacter (1); Pistricoccus (1), Salinicola (6); Zymobacter (1), total 123 species.

Reports on the following new taxa with validly published names were presented, as published between May 2016 and May 2017:

  • Halomonas urumqiensis sp. nov. [Zhang et al., Int J Syst Evol Microbiol 2016;66 : 1967], with type strain BZ-SZ-XJ27 (=CGMCC 1.12917=JCM 30202).

  • Larsenimonas suaedae sp. nov. [Xia et al., Int J Syst Evol Microbiol 2016;66 : 2956], with type strain ST307 (=CGMCC 1.8902=DSM 22428).

  • Halomonas sediminicola sp. nov. [Lee et al., Int J Syst Evol Microbiol 2016;66 : 3869], with type strain CPS11 (=KACC 18262=NBRC 110636).

  • Halomonas lutescens sp. nov. [Wang et al., Int J Syst Evol Microbiol 2016;66 : 4702], with type strain Q1U (=CGMCC 1.15122=KCTC 42517).

  • Pistricoccus gen. nov. [Xu et al., Int J Syst Evol Microbiol 2017;67 : 1096 (Validation List 175); effective publication: Antonie van Leeuwenhoek 109 (2016) 1598] with type species Pistricoccus aurantiacus.

  • Pistricoccus aurantiacus sp. nov. [Xu et al., Int J Syst Evol Microbiol 2017;67 : 1096 (Validation List 175); effective publication: Antonie van Leeuwenhoek 109 (2016) 1599] with type strain SS9 (=KCTC 42586=MCCC 1H00111).

  • Halomonas alkalicola sp. nov. [Tang et al., Int J Syst Evol Microbiol 2017;67 : 1549], with type strain 56-1-4-10aEn (=CICC 11012 s=DSM 103354).

Papers describing the following new taxa were in press in the IJSEM as of 30 May 2017:

  • Halomonas aestuarii sp. nov. [Koh et al., Int J Syst Evol Microbiol 2017;67, in press], with type strain Hb3 (=JCM 31415=KCTC 52253).

The following new names of members of the Halomonadaceae were effectively but not validly published as of 30 May 2017:

  • Halomonas xiaochaidanensis sp. nov. [Liu et al., Arch Microbiol 2016;198 : 764], with type strain CUG 00002 (=CCTCC AB 2014152=KCTC 42685).

  • Halomonas massiliensis sp. nov. [Seck et al., New Microbe and New Infect 2016;14 : 20], with type strain Marseille-P2426 (=CSUR P2426).

  • Halomonas saudii sp. nov. [Bibi et al., New Microbe and New Infect 2017;15 : 43], with type strain Saudii DR2 (=CSUR P2512).

The following emended descriptions were published outside the IJSEM:

Minute 9. Families and orders in the class Halobacteria

Since the discussions in the previous meeting of the subcommittee about the splitting of the class Halobacteria into a number of orders and families as proposed by Radhey Gupta and coworkers (Int J Syst Evol Microbiol 2015;65 : 1050–1069; Antonie van Leeuwenhoek 2016;109 : 565–587), an erratum to the latter paper was published (Antonie van Leeuwenhoek 2016;109 : 1521–1523) in which the genus Natronomonas was transferred from the Halobacteriaceae to the Haloarculaceae and the genus Halogranum assigned to the family Haloferacaceae, the descriptions of the families Halobacteriaceae and Haloferacaceae were emended and corrected descriptions of the families Haloarculaceae and Halorubraceae were presented.

Based on the data presented in these papers by Gupta and coworkers and on further analyses by A. Oren and A. Ventosa of the 16S rRNA gene sequences of members of genera not used in Gupta’s phylogenomic analyses, the genera within the class Halobacteria can be assigned as follows to orders and families:

A. Oren read messages received from B. J. Tindall, R. T. Papke and M. Kamekura. B. J. Tindall commented: ‘Like all names the work of Gupta and colleagues needs to stand the test of time. Differing opinions may accept all or only some of these proposals and lead to either names being treated as synonyms or to the definitions attached to the names also changing. In essence this is a principle behind the use of different data sets (popularly called the polyphasic approach) and something underlying the workings of the International Code of Nomenclature of Prokaryotes’ and ‘sometimes one forgets that and sometimes relying on a limited data set can either revolutionize our way of thinking or in some cases be counter-productive. However, only time and careful evaluation puts all this in perspective’. R. T. Papke wondered to what extent the groups proposed by Gupta et al. are stable, especially when considering the indels, as it is not clear how many indels disagree with his groupings. Moreover, the effects of horizontal gene transfer and homologous recombination within and between lineages is largely unknown. It may be wise to wait until the work can be confirmed and verified by other groups to get a stronger consensus on the matter, resulting in more taxonomic stability. Moreover, not all type strains of the species within the class Halobacteria have yet been sequenced. The analyses by Gupta et al. are a good starting point, but more work must be done to confirm the proposed reclassification of the group. F. Rodríguez-Valera stated that his studies on gene alignments largely confirmed the divisions proposed by Gupta et al. M. Kamekura commented that the type of analysis on which Gupta et al. based their conclusions is too complicated for routine studies by most workers in the field.

The subcommittee strongly recommends that each description of new species within the Halobacteria be accompanied by the deposition of good-quality genomic data so that all new taxa can be included in comparative phylogenomic analyses.

Minute 10. Phenotypic testing of strains of Halobacteria

A letter was received from H. Minegishi and M. Kamekura about the often poor quality of the polar lipid data in descriptions of new taxa within the class Halobacteria. Based on the proposed minimal standards, any description of a new species should include a characterization of polar lipids, with special emphasis on the pattern of the glycolipids present. Many recently published descriptions contain statements such as ‘polar lipids were unidentified glycolipids’ or ‘sulfated mannosyl glucosyl archaeol was detected’ without indicating to which type of sulfated diglycosyl diether lipid this refers. ‘Identification’ is often based on two-dimensional thin-layer chromatography (TLC) without proper comparison with the authentic glycolipids. It is recommended to first use one-dimensional TLC with the same solvent system used in references and to compare Rf values with those of the authentic glycolipids. Two-dimensional TLC is a good tool to separate PGS from PGP-Me. B. J. Tindall added in an email to the members of the subcommittee that a standard ‘single mix’ reagent works equally well as the two-stage α-naphthol spray reagent for detection of glycolipids. Similarly, it would be useful to confirm the presence of different diethers by TLC of the hydrolysed lipids. B. J. Tindall also commented that he had noted that over the years chemotaxonomic data have been published on members of the class Halobacteria that do not bear up to closer scrutiny. This phenomenon also applies to some of the data published on members of the family Halomonadaceae. R. Hahnke stressed the need for more in-depth characterization of physiological properties and chemotaxonomic studies of the genera and species within the class Halobacteria, and he suggested that it may be worthwhile to organize a course to teach advanced methods for the characterization of the lipids and other chemotaxonomic properties to be applied in taxonomic studies of the group. He further commented that for descriptions of new members of the Halobacteria growth must be tested over a wide range of salt concentrations, including in the lower range, and that activity of extracellular enzymes such as amylase and protease must be tested also at the highest salt concentrations enabling growth as such enzymes may not be active in the lower salinity range.

Minute 11. Treatment of the Halobacteria and the Halomonadaceae in Bergey’s Manual

As of 1 July 2017, updated or newly prepared chapters had been published in Bergey's Manual of Systematics of Archaea and Bacteria, published online by John Wiley and Sons:

The genera: Haladaptatus (Oren), Halanaeroarchaeum (Sorokin, Yakimov, Kublanov and Oren), Halapricum (Roh), Haloarchaeum (Minegishi), Halobellus (Cui), Halobiforma (Xu and Oren), Halogranum (Cui, Xu and Oren), Halohasta (Oren), Halolamina (Cui), Halomarina (Inoue and Kogure), Halomicroarcula (Echigo), Halomicrobium (Oren), Halonotius (Oren), Halopelagius (Cui, Xu, Wu and Oren), Haloplanus (Oren), Haloquadratum (Rodríguez-Valera, Martin-Cuadrado and Bolhuis), Halorhabdus (Antunes, Ferrer and Yarza), Halorientalis (Cui), Halorubellus (Cui), Halorussus (Cui), Halosarcina (Oren), Halosimplex (Vreeland and Cui), Natribaculum (Zhang and Oren), Natronoarchaeum (Shimane), Natronolimnobius (Itoh), Salarchaeum (Shimane), Salinarchaeum (Cui), Salinigranum (Cui), Salinirubrum (Cui).

Updated or newly written chapters on the higher taxa have been accepted for publication and are currently in production: (class-level) Halobacteria (Oren, Ventosa and Kamekura), (order-level) Halobacteriales (Oren, Ventosa and Kamekura), Haloferacales (Oren and Ventosa), Natrialbales (Oren and Ventosa), (family-level) Halobacteriaceae (Oren, Ventosa and Kamekura), Halococcaceae (Oren and Ventosa), Haloferacaceae (Oren and Ventosa), Halorubraceae (Oren and Ventosa), Haloarculaceae (Oren and Ventosa), Natrialbaceae (Oren and Ventosa).

The following updated genus-level chapters have been accepted for publication and are currently in production: Halobacterium (Oren and Ventosa), Halobaculum (Oren), Halococcus (Oren).

An updated chapter on the genus Haloarcula (Ventosa) is currently in preparation, and so are new genus-level chapter on Halalkalicoccus (Ventosa and Sánchez-Porro), Haloarchaeobius (Ventosa and Amoozegar), Halocalculus (Minegishi), Haloparvum (Chen), Halopenitus (Ventosa and Amoozegar), Halopiger (Ventosa and de la Haba), Halosiccatus (Amoozegar), Halostagnicola (Ventosa and Sánchez-Porro), Halostella (Roh), Halovarius (Amoozegar), Halovenus (Ventosa and Amoozegar), Halovivax (Ventosa and de la Haba).

We hope that the editors of Bergey’s Manual will send out invitations for the preparation of updated chapters for the remaining genera of the class Halobacteria based on the chapters published in the 2nd edition of Bergey’s Manual of Systematic Bacteriology.

The chairman and the secretary of the Subcommittee on the taxonomy of Halomonadaceae will inquire with the editors of Bergey’s Manual about the possibility to start soon with the updating of the older chapters (the family Halomonadaceae, the genera Halomonas, Carnimonas, Chromohalobacter and Zymobacter) and the preparation of chapters for the 8 new genera added in recent years.

Minute 12. Next meeting of the subcommittees

The next joint meeting of both subcommittees is scheduled to be held in association with the Halophiles 2019 conference, scheduled to be held in Cluj, Romania, in June 2019.

Minute 13. Any other business

D. R. Arahal called for nominations for a new member of the ICSP Subcommittee on the taxonomy of Halomonadaceae following the retirement of E. Quesada.

Minute 14. Adjournment

The meeting was adjourned at 10 : 00 on 11 July 2017.

David R. Arahal, Secretary; Aharon Oren, Secretary and Antonio Ventosa, Chairman.

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