Genome‑based classification of the family Natrialbaceae and description of four novel halophilic archaea from three saline lakes and a saline-alkaline land.
Haloterrigena
Halovalidus
Natrialbaceae
Natronococcus
Novel halophilic archaea
Journal
Extremophiles : life under extreme conditions
ISSN: 1433-4909
Titre abrégé: Extremophiles
Pays: Germany
ID NLM: 9706854
Informations de publication
Date de publication:
22 Oct 2024
22 Oct 2024
Historique:
received:
30
07
2024
accepted:
07
10
2024
medline:
22
10
2024
pubmed:
22
10
2024
entrez:
22
10
2024
Statut:
epublish
Résumé
The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amino acid identity (AAI) (≤ 76%) proposed to differentiate genera within the family Natrialbaceae, Halobiforma, and Natronoglomus should be merged with Natronobacterium and Halomontanus, respectively. Beyond these, four novel halophilic archaeal strains, CCL63
Identifiants
pubmed: 39436425
doi: 10.1007/s00792-024-01366-y
pii: 10.1007/s00792-024-01366-y
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
47Subventions
Organisme : National Natural Science Foundation of China
ID : 32070003
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Japan KK.
Références
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. https://doi.org/10.1186/1471-2164-9-75
doi: 10.1186/1471-2164-9-75
Chalita M, Kim YO, Park S, Oh HS, Cho JH, Moon J, Baek N, Moon C, Lee K, Yang J, Nam GG, Jung Y, Na SI, Bailey MJ, Chun J (2024) EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol 74:006421. https://doi.org/10.1099/ijsem.0.006421
doi: 10.1099/ijsem.0.006421
pubmed: 38888585
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu X-W, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
doi: 10.1099/ijsem.0.002516
pubmed: 29292687
Corral P, Gutiérrez MC, Castillo AM, Domínguez M, Lopalco P, Corcelli A, Ventosa A (2013) Natronococcus roseus sp. nov., a haloalkaliphilic archaeon from a hypersaline lake. Int J Syst Evol Microbiol 63:104–108. https://doi.org/10.1099/ijs.0.036558-0
doi: 10.1099/ijs.0.036558-0
pubmed: 22345136
Cui H-L, Dyall-Smith ML (2021) Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Mar Life Sci Technol 3:243–251. https://doi.org/10.1007/s42995-020-00087-3
doi: 10.1007/s42995-020-00087-3
pubmed: 37073340
pmcid: 10077297
Cui H-L, Zhou P-J, Oren A, Liu S-J (2009) Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 13:31–37. https://doi.org/10.1007/s00792-008-0194-2
doi: 10.1007/s00792-008-0194-2
pubmed: 18836684
Cui H-L, Gao X, Yang X, Xu X-W (2010) Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 14:493–499. https://doi.org/10.1007/s00792-010-0329-0
doi: 10.1007/s00792-010-0329-0
pubmed: 20824294
Cui C, Han D, Hou J, Cui H-L (2023) Genome-based classification of the class Halobacteria and description of Haladaptataceae fam. nov. and Halorubellaceae fam. nov. Int J Syst Evol Microbiol 73:005984. https://doi.org/10.1099/ijsem.0.005984
doi: 10.1099/ijsem.0.005984
Cui H-L, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR, Minegishi H, Montalvo-Rodriguez R, Oren A, Sanchez-Porro C, Ventosa A, Vreeland RH (2024) Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 74:006290. https://doi.org/10.1099/ijsem.0.006290
doi: 10.1099/ijsem.0.006290
pubmed: 38456846
pmcid: 10999741
de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A (2021) Phylogenomics of haloarchaea: the controversy of the genera Natrinema-Haloterrigena. Front Microbiol 12:740909. https://doi.org/10.3389/fmicb.2021.740909
doi: 10.3389/fmicb.2021.740909
pubmed: 34690986
pmcid: 8530250
Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. https://doi.org/10.1186/s13059-019-1832-y
doi: 10.1186/s13059-019-1832-y
pubmed: 31727128
pmcid: 6857279
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/bf01734359
doi: 10.1007/bf01734359
pubmed: 7288891
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
doi: 10.1111/j.1558-5646.1985.tb00420.x
pubmed: 28561359
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
doi: 10.1099/ijs.0.64483-0
pubmed: 17220447
Gupta RS, Naushad S, Baker S (2015) Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 65:1050–1069. https://doi.org/10.1099/ijs.0.070136-0
doi: 10.1099/ijs.0.070136-0
pubmed: 25428416
Hezayen FF, Tindall BJ, Steinbüchel A, Rehm BHA (2002) Characterization of a novel halophilic archaeon, Halobiforma haloterrestris gen. nov., sp. nov., and transfer of Natronobacterium nitratireducens to Halobiforma nitratireducens comb. nov. Int J Syst Evol Microbiol 52:2271–2280. https://doi.org/10.1099/ijs.0.02324-0
doi: 10.1099/ijs.0.02324-0
pubmed: 12508897
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280. https://doi.org/10.1093/nar/gkh063
doi: 10.1093/nar/gkh063
pubmed: 14681412
pmcid: 308797
Kim M, Oh H-S, Park S-C, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351. https://doi.org/10.1099/ijs.0.059774-0
doi: 10.1099/ijs.0.059774-0
pubmed: 24505072
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054
doi: 10.1093/molbev/msw054
pubmed: 27004904
pmcid: 8210823
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404
doi: 10.1093/bioinformatics/btm404
pubmed: 17846036
Li S-Y, Xin Y-J, Bao C-X, Hou J, Cui H-L (2022) Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil. Extremophiles 26:6. https://doi.org/10.1007/s00792-021-01255-8
doi: 10.1007/s00792-021-01255-8
Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:e73. https://doi.org/10.1093/nar/gku169
doi: 10.1093/nar/gku169
pubmed: 24589583
pmcid: 4005636
Mao Y-L, Wang B-B, Yin X-M, Hou J, Cui H-L (2024) Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang plateau. Syst Appl Microbiol 47:126500. https://doi.org/10.1016/j.syapm.2024.126500
doi: 10.1016/j.syapm.2024.126500
pubmed: 38417236
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2021) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50:D801–D807. https://doi.org/10.1093/nar/gkab902
doi: 10.1093/nar/gkab902
pmcid: 8728197
Minh BQ, Nguyen MAT, von Haeseler A (2013) Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 30:1188–1195. https://doi.org/10.1093/molbev/mst024
doi: 10.1093/molbev/mst024
pubmed: 23418397
pmcid: 3670741
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185. https://doi.org/10.1093/nar/gkm321
doi: 10.1093/nar/gkm321
pubmed: 17526522
pmcid: 1933193
Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A, Hugenholtz P (2022) GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50:D785–D794. https://doi.org/10.1093/nar/gkab776
doi: 10.1093/nar/gkab776
pubmed: 34520557
Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Davín AA, Waite DW, Whitman WB, Parks DH, Hugenholtz P (2021) A standardized archaeal taxonomy for the genome taxonomy database. Nat Microbiol 6:946–959. https://doi.org/10.1038/s41564-021-00918-8
doi: 10.1038/s41564-021-00918-8
pubmed: 34155373
Serrano S, Mendo S, Caetano T (2022) Haloarchaea have a high genomic diversity for the biosynthesis of carotenoids of biotechnological interest. Res Microbiol 173:103919. https://doi.org/10.1016/j.resmic.2021.103919
doi: 10.1016/j.resmic.2021.103919
pubmed: 34942349
Shu W-S, Huang L-N (2022) Microbial diversity in extreme environments. Nat Rev Microbiol 20:219–235. https://doi.org/10.1038/s41579-021-00648-y
doi: 10.1038/s41579-021-00648-y
pubmed: 34754082
Sorokin DY, Merkel AY, Messina E, Yakimov MM, Itoh T, Mesbah NM, Wiegel J, Oren A (2020) Reclassification of the genus Natronolimnobius: proposal of two new genera, Natronolimnohabitans gen. nov. to accommodate Natronolimnobius innermongolicus and Natrarchaeobaculum gen. nov. to accommodate Natronolimnobius aegyptiacus and Natronolimnobius sulfurireducens. Int J Syst Evol Microbiol 70:3399–3405. https://doi.org/10.1099/ijsem.0.004186
doi: 10.1099/ijsem.0.004186
pubmed: 32374250
Sorokin DY, Elcheninov AG, Bale NJ, Sinninghe Damsté JS, Kublanov IV (2024) Natronoglomus mannanivorans gen. nov., sp. nov., beta-1,4-mannan utilizing natronoarchaea from hypersaline soda lakes. Front Microbiol 15:1364606. https://doi.org/10.3389/fmicb.2024.1364606
doi: 10.3389/fmicb.2024.1364606
pubmed: 38533326
pmcid: 10963439
Sun Y-P, Wang B-B, Zheng X-W, Wu Z-P, Hou J, Cui H-L (2022) Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius. Int J Syst Evol Microbiol 72:005598. https://doi.org/10.1099/ijsem.0.005598
doi: 10.1099/ijsem.0.005598
Sun J-H, Lu F, Luo Y-J, Bie L-Z, Xu L, Wang Y (2023) OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 51:W397–W403. https://doi.org/10.1093/nar/gkad313
doi: 10.1093/nar/gkad313
pubmed: 37114999
pmcid: 10320085
Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxomic purposes. Int J Syst Evol Microbiol 60:249–266. https://doi.org/10.1099/ijs.0.016949-0
doi: 10.1099/ijs.0.016949-0
pubmed: 19700448
Walsh D, Bapteste E, Kamekura M, Doolittle W (2004) Evolution of the RNA polymerase B′ subunit gene (rpoB′) in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21:2340–2351. https://doi.org/10.1093/molbev/msh248
doi: 10.1093/molbev/msh248
pubmed: 15356285
Xin H-W, Itoh T, Zhou P-J, Suzuki K-I, Nakase T (2001) Natronobacterium nitratireducens sp. nov., a aloalkaliphilic archaeon isolated from a soda lake in China. Int J Syst Evol Microbiol 51:1825–1829. https://doi.org/10.1099/00207713-51-5-1825
doi: 10.1099/00207713-51-5-1825
pubmed: 11594615
Xin Y-J, Bao C-X, Li S-Y, Hu X-Y, Zhu L, Wei W, Hou J, Cui H-L (2022) Genome-based taxonomy of genera Halomicrobium and Halosiccatus, and description of Halomicrobium salinisoli sp. nov. Syst Appl Microbiol 45:126308. https://doi.org/10.1016/j.syapm.2022.126308
doi: 10.1016/j.syapm.2022.126308
pubmed: 35290863
Xu X-W, Wu M, Zhou P-J, Liu S-J (2005) Halobiforma lacisalsi sp. nov., isolated from a salt lake in China. Int J Syst Evol Microbiol 55:1949–1952. https://doi.org/10.1099/ijs.0.63742-0
doi: 10.1099/ijs.0.63742-0
pubmed: 16166693
Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
doi: 10.1007/s10482-017-0844-4
pubmed: 28204908