A Novel Species of the Genus Thermanaerothrix Isolated from a Kamchatka Hot Spring Possesses Hydrolytic Capabilities.
Journal
Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448
Informations de publication
Date de publication:
01 Aug 2024
01 Aug 2024
Historique:
received:
09
01
2024
accepted:
20
07
2024
medline:
2
8
2024
pubmed:
2
8
2024
entrez:
1
8
2024
Statut:
epublish
Résumé
Hot springs are inhabited by specific microbial communities which are reservoirs of novel taxa. In this work strain 4228-RoL
Identifiants
pubmed: 39090416
doi: 10.1007/s00284-024-03815-5
pii: 10.1007/s00284-024-03815-5
doi:
Substances chimiques
Fatty Acids
0
RNA, Ribosomal, 16S
0
Polysaccharides
0
DNA, Bacterial
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
293Subventions
Organisme : Ministry of Science and Higher Education of the Russian Federation
ID : agreement no. 075-15-2021-1396
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
da Silva RR, Pedezzi R, Souto TB (2017) Exploring the bioprospecting and biotechnological potential of white-rot and anaerobic Neocallimastigomycota fungi: peptidases, esterases, and lignocellulolytic enzymes. Appl Microbiol Biotechnol 101:3089–3101. https://doi.org/10.1007/s00253-017-8225-5
doi: 10.1007/s00253-017-8225-5
pubmed: 28314873
Donadio S, Monciardini P, Alduina R et al (2002) Microbial technologies for the discovery of novel bioactive metabolites. J Biotechnol 99:187–198. https://doi.org/10.1016/s0168-1656(02)00209-2
doi: 10.1016/s0168-1656(02)00209-2
pubmed: 12385708
Challinor VL, Bode HB (2015) Bioactive natural products from novel microbial sources. Ann N Y Acad Sci 1354:82–97. https://doi.org/10.1111/nyas.12954
doi: 10.1111/nyas.12954
pubmed: 26509922
DeCastro ME, Rodríguez-Belmonte E, González-Siso MI (2016) Metagenomics of thermophiles with a focus on discovery of novel thermozymes. Front Microbiol 7:1521. https://doi.org/10.3389/fmicb.2016.01521
doi: 10.3389/fmicb.2016.01521
pubmed: 27729905
pmcid: 5037290
Bruins ME, Janssen AE, Boom RM (2001) Thermozymes and their applications: a review of recent literature and patents. Appl Biochem Biotechnol 90:155–186. https://doi.org/10.1385/abab:90:2:155
doi: 10.1385/abab:90:2:155
pubmed: 11297390
Patel AK, Singhania RR, Sim SJ, Pandey A (2019) Thermostable cellulases: current status and perspectives. Bioresour Technol 279:385–392. https://doi.org/10.1016/j.biortech.2019.01.049
doi: 10.1016/j.biortech.2019.01.049
pubmed: 30685132
Sharp CE, Brady AL, Sharp GH et al (2014) Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments. ISME J 8:1166–1174. https://doi.org/10.1038/ismej.2013.237
doi: 10.1038/ismej.2013.237
pubmed: 24430481
pmcid: 4030231
Kublanov IV, Perevalova AA, Slobodkina GB et al (2009) Biodiversity of thermophiiic prokaryotes with hydrolytic activities in hot springs of uzon caldera, kamchatka (Russia). Appl Environ Microbiol 75:286–291. https://doi.org/10.1128/AEM.00607-08
doi: 10.1128/AEM.00607-08
pubmed: 18978089
Suleiman M, Klippel B, Busch P et al (2019) Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates. Extremophiles 23:277–281. https://doi.org/10.1007/s00792-019-01079-7
doi: 10.1007/s00792-019-01079-7
pubmed: 30741334
Kochetkova TV, Toshchakov SV, Zayulina KS et al (2020) Hot in cold: Microbial life in the hottest springs in permafrost. Microorganisms 8:1308. https://doi.org/10.3390/microorganisms8091308
doi: 10.3390/microorganisms8091308
pubmed: 32867302
pmcid: 7565842
Kadnikov VV, Mardanov AV, Beletsky AV et al (2021) Thermophilic chloroflexi dominate in the microbial community associated with coal-fire gas vents in the Kuznetsk coal basin. Russia Microorg 9:948. https://doi.org/10.3390/microorganisms9050948
doi: 10.3390/microorganisms9050948
Toshchakov SV, Izotova AO, Vinogradova EN et al (2021) Culture-independent survey of thermophilic microbial communities of the north caucasus. Biology 10(12):1352. https://doi.org/10.3390/biology10121352
doi: 10.3390/biology10121352
pubmed: 34943267
pmcid: 8698779
Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV (2022) Diversity of thermophilic prokaryotes Inhabiting russian natural hot springs. Microbiology 91:1–27. https://doi.org/10.1134/S0026261722010064
doi: 10.1134/S0026261722010064
Menzel P, Gudbergsdóttir SR, Rike AG et al (2015) Comparative Metagenomics of eight geographically remote terrestrial hot springs. Microb Ecol 70:411–424. https://doi.org/10.1007/s00248-015-0576-9
doi: 10.1007/s00248-015-0576-9
pubmed: 25712554
Chernyh NA, Mardanov AV, Gumerov VM et al (2015) Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka. Extremophiles 19:1157–1171. https://doi.org/10.1007/s00792-015-0787-5
doi: 10.1007/s00792-015-0787-5
pubmed: 26349929
Keppen OI, Tourova TP, Kuznetsov BB et al (2000) Proposal of Oscillochloridaceae fam. nov. on the basis of a phylogenetic analysis of the filamentous anoxygenic phototrophic bacteria, and emended description of Oscillochloris and Oscillochloris trichoides in comparison with further new isolates. Int J Syst Evol Microbiol 50:1529–1537. https://doi.org/10.1099/00207713-50-4-1529
doi: 10.1099/00207713-50-4-1529
pubmed: 10939660
Yamada T, Sekiguchi Y, Hanada S et al (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56:1331–1340. https://doi.org/10.1099/ijs.0.64169-0
doi: 10.1099/ijs.0.64169-0
pubmed: 16738111
Wu D, Raymond J, Wu M et al (2009) Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4:e4207. https://doi.org/10.1371/journal.pone.0004207
doi: 10.1371/journal.pone.0004207
pubmed: 19148287
pmcid: 2615216
Löffler FE, Yan J, Ritalahti KM et al (2013) Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63:625–635. https://doi.org/10.1099/ijs.0.034926-0
doi: 10.1099/ijs.0.034926-0
pubmed: 22544797
Kochetkova TV, Zayulina KS, Zhigarkov VS et al (2020) Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14. Int J Syst Evol Microbiol 70:1192–1202. https://doi.org/10.1099/ijsem.0.003902
doi: 10.1099/ijsem.0.003902
pubmed: 31769750
Grégoire P, Fardeau ML, Joseph M et al (2011) Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum “Chloroflexi”, isolated from a deep hot aquifer in the Aquitaine Basin. Syst Appl Microbiol 34:494–497. https://doi.org/10.1016/j.syapm.2011.02.004
doi: 10.1016/j.syapm.2011.02.004
pubmed: 21621938
Zavarzina DG, Kochetkova TV, Chistyakova NI et al (2020) Siderite-based anaerobic iron cycle driven by autotrophic thermophilic microbial consortium. Sci Rep 10(1):21661. https://doi.org/10.1038/s41598-020-78605-7
doi: 10.1038/s41598-020-78605-7
pubmed: 33303863
pmcid: 7729950
Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA et al (2013) Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae. Int J Syst Evol Microbiol 63:86–92. https://doi.org/10.1099/ijs.0.041012-0
doi: 10.1099/ijs.0.041012-0
pubmed: 22328612
Podosokorskaya OA, Kochetkova TV, Novikov AA et al (2020) Tenuifilum thalassicum gen nov, sp nov, a novel moderate thermophilic anaerobic bacterium from a Kunashir Island shallow hot spring representing a new family Tenuifilaceae fam nov in the class Bacteroidia. Syst Appl Microbiol 43:126126. https://doi.org/10.1016/j.syapm.2020.126126
doi: 10.1016/j.syapm.2020.126126
pubmed: 32847792
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, pp 607–654
Slobodkina GB, Merkel AY, Novikov AA et al (2020) Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano. Extremophiles 24:177–185. https://doi.org/10.1007/s00792-019-01145-0
doi: 10.1007/s00792-019-01145-0
pubmed: 31705207
Wick RR, Judd LM, Holt KE (2019) Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 20:129. https://doi.org/10.1186/s13059-019-1727-y
doi: 10.1186/s13059-019-1727-y
pubmed: 31234903
pmcid: 6591954
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
doi: 10.1089/cmb.2012.0021
pubmed: 22506599
pmcid: 3342519
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. https://doi.org/10.1371/journal.pcbi.1005595
doi: 10.1371/journal.pcbi.1005595
pubmed: 28594827
pmcid: 5481147
Parks DH, Imelfort M, Skennerton CT et al (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25(7):1043–1055. https://doi.org/10.1101/gr.186072.114
doi: 10.1101/gr.186072.114
pubmed: 25977477
pmcid: 4484387
Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
doi: 10.1093/nar/gkw569
pubmed: 27342282
pmcid: 5001611
Zhang H, Yohe T, Huang L et al (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46:W95–W101. https://doi.org/10.1093/nar/gky418
doi: 10.1093/nar/gky418
pubmed: 29771380
pmcid: 6031026
Boutet E, Lieberherr D, Tognolli M et al (2016) UniProtKB/swiss-prot, the manually annotated section of the UniProt knowledgebase: how to use the entry view. Methods Mol Biol 1374:23–54. https://doi.org/10.1007/978-1-4939-3167-5_2
doi: 10.1007/978-1-4939-3167-5_2
pubmed: 26519399
Teufel F, Almagro Armenteros JJ, Johansen AR et al (2022) SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 40:1023–1025
doi: 10.1038/s41587-021-01156-3
pubmed: 34980915
pmcid: 9287161
Bendtsen JD, Jensen LJ, Blom N et al (2004) Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel 17:349–356. https://doi.org/10.1038/s41587-021-01156-3
doi: 10.1038/s41587-021-01156-3
pubmed: 15115854
Hallgren J, Tsirigos KD, Damgaard Pedersen M et al (2022) DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv. https://doi.org/10.1101/2022.04.08.487609
doi: 10.1101/2022.04.08.487609
Pritchard L, Glover RH, Humphris S et al (2016) Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 8:12–24
doi: 10.1039/C5AY02550H
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2022) 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
pubmed: 34634793
Zayulina KS, Prokofeva MI, Elcheninov AG et al (2020) Arenimonas fontis sp. nov., a bacterium isolated from Chukotka hot spring, Arctic region. Russia Int J Syst Evol Microbiol 70:2726–2731. https://doi.org/10.1099/ijsem.0.004099
doi: 10.1099/ijsem.0.004099
pubmed: 32176605
Parks DH, Chuvochina M, Waite DW et al (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. https://doi.org/10.1038/nbt.4229
doi: 10.1038/nbt.4229
pubmed: 30148503
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH (2022) GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38:5315–5316. https://doi.org/10.1093/bioinformatics/btac672
doi: 10.1093/bioinformatics/btac672
pubmed: 36218463
pmcid: 9710552
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348
doi: 10.1093/bioinformatics/btp348
pubmed: 19505945
pmcid: 2712344
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313. https://doi.org/10.1093/bioinformatics/btu033
doi: 10.1093/bioinformatics/btu033
pubmed: 24451623
pmcid: 3998144
Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428. https://doi.org/10.1021/ac60147a030
doi: 10.1021/ac60147a030
Kim M, Oh H, Park S, 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
Wayne LG, Brenner DJ, Colwell RR et al (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464. https://doi.org/10.1099/00207713-37-4-463
doi: 10.1099/00207713-37-4-463
Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264. https://doi.org/10.1128/JB.187.18.6258-6264.2005
doi: 10.1128/JB.187.18.6258-6264.2005
pubmed: 16159757
pmcid: 1236649
Lu Y, Zhang Y-HP, Lynd LR (2006) Enzyme-microbe synergy during cellulose hydrolysis by Clostridium thermocellum. Proc Natl Acad Sci U S A 103:16165–16169
doi: 10.1073/pnas.0605381103
pubmed: 17060624
pmcid: 1637554
Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:590–596. https://doi.org/10.1073/pnas.0605381103
doi: 10.1073/pnas.0605381103
Pace LA, Hemp J, Ward LM, Fischer WW (2015) Draft genome of Thermanaerothrix daxensis GNS-1, a thermophilic facultative anaerobe from the Chloroflexi Class Anaerolineae. Genome Announc 3:e01354-e1415. https://doi.org/10.1128/genomeA.01354-15
doi: 10.1128/genomeA.01354-15
pubmed: 26586891
pmcid: 4653793