Abstract
A novel mesophilic bacterial strain, designated S502T, was isolated from a deep-sea hydrothermal vent at Suiyo Seamount, Japan. Cells were Gram-positive, asporogenous, motile, and curved rods, measuring 1.6–5.6 µm in length. The strain was an obligate anaerobe that grew fermentatively on complex substrates such as yeast extract and Bacto peptone. Elemental sulfur stimulated the growth of the strain, and was reduced to hydrogen sulfide. The strain grew within a temperature range of 10–23 °C (optimum at 20 °C), pH range of 4.8–8.3 (optimum at 7.4), and a NaCl concentration range of 1.0–4.0% (w/v) (optimum at 3.0%, w/v). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the class Clostridia, with Fusibacter paucivorans strain SEBR 4211T (91.1% sequence identity) being its closest relative. The total size of the genome of the strain was 3.12 Mbp, and a G + C content was 28.2 mol%. The highest values for average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) value of strain S502T with relatives were 67.5% (with Marinisporobacter balticus strain 59.4MT), 51.5% (with M. balticus strain 59.4MT), and 40.9% (with Alkaliphilus serpentinus strain LacTT), respectively. Based on a combination of phylogenetic, genomic, and phenotypic characteristics, we propose strain S502T to represent a novel genus and species, Helicovermis profundi gen. nov., sp. nov., with the type strain S502T (= DSM 112048T = JCM 39167T).
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Data availability
The 16S rRNA gene sequence and the complete genome sequence of strain S502T have been deposited under the GenBank/EMBL/DDBJ accession numbers LC775851and AP028654, respectively. The raw sequencing data have been deposited in the DDBJ Sequence Read Archive (DRA) under accession numbers DRR514774 (Illumina NovaSeq 6000) and DRR514775 (PacBio Sequel).
References
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. https://doi.org/10.1093/nar/25.17.3389
Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D (2020) A genus definition for Bacteria and Archaea based on a standard genome relatedness index. Mbio 11:e02475-e12419. https://doi.org/10.1128/mBio.02475-19
Baross JA (1995) Isolation, growth and maintenance of hyperthermophiles. In: Robb FT, Place RA (eds) Archaea: a laboratory manual: Thermophiles. Cold Spring Harbor Laboratory, New York, pp 15–23
Ben Hania W, Fraj B, Postec A, Fadhlaoui K, Hamdi M, Ollivier B, Fardeau ML (2012) Fusibacter tunisiensis sp. nov., isolated from an anaerobic reactor used to treat olive-mill wastewater. Int J Syst Evol Microbiol 62:1365–1368. https://doi.org/10.1099/ijs.0.034603-0
Benoit SL, Maier RJ, Sawers RG, Greening C (2020) Molecular hydrogen metabolism: a widespread trait of pathogenic bacteria and protists. Microbiol Mol Biol Rev 84:e00092-e119. https://doi.org/10.1128/MMBR.00092-19
Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451-454. https://doi.org/10.1093/nar/gki487
Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH (2008) Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment. Proc Natl Acad Sci U S A 105:10583–10588. https://doi.org/10.1073/pnas.0709942105
Brisbarre N, Fardeau ML, Cueff V et al (2003) Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney. Int J Syst Evol Microbiol 53:1043–1049. https://doi.org/10.1099/ijs.0.02471-0
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. https://doi.org/10.1038/nmeth.3176
Cao X, Liu X, Dong X (2003) Alkaliphilus crotonatoxidans sp. nov., a strictly anaerobic, crotonate-dismutating bacterium isolated from a methanogenic environment. Int J Syst Evol Microbiol 53:971–975. https://doi.org/10.1099/ijs.0.02373-0
Chan M, Himes RH, Akagi JM (1971) Fatty acid composition of thermophilic, mesophilic, and psychrophilic clostridia. J Bacteriol 106:876–881. https://doi.org/10.1128/jb.106.3.876-881.1971
Fadhlaoui K, Ben Hania W, Postec A, Fauque G, Hamdi M, Ollivier B, Fardeau ML (2015) Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring. Int J Syst Evol Microbiol 65:3501–3506. https://doi.org/10.1099/ijsem.0.000445
Galperin MY, Yutin N, Wolf YI, Vera Alvarez R, Koonin EV (2022) Conservation and evolution of the sporulation gene set in diverse members of the Firmicutes. J Bacteriol 204:e0007922. https://doi.org/10.1128/jb.00079-22
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
Green E, Minton N, Heeg D (2017) Making Clostridia great again. Indust. Biotech 13:52–56. https://doi.org/10.1089/ind.2017.29075.egr
Hashimoto Y, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S (2021) Desulfomarina profundi gen nov., sp. Nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005083
Hashimoto Y, Shimamura S, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S (2022) Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen nov., sp. Nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent. Front Microbiol 13:1042116. https://doi.org/10.3389/fmicb.2022.1042116
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066. https://doi.org/10.1093/nar/gkf436
Kawagucci S, Chiba H, Ishibashi J et al (2011) Hydrothermal fluid geochemistry at the Iheya North field in the mid-Okinawa Trough: implication for origin of methane in subseafloor fluid circulation systems. Geochem J 45:109–124. https://doi.org/10.2343/geochemj.1.0105
Kim J, Na SI, Kim D, Chun J (2021) UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59:609–615. https://doi.org/10.1007/s12275-021-1231-4
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic Acid Techniques in Bacterial Systematics. Wiley, New York, pp 115–175
Lauro FM, Bertoloni G, Obraztsova A, Kato C, Tebo BM, Bartlett DH (2004) Pressure effects on Clostridium strains isolated from a cold deep-sea environment. Extremophiles 8:169–173. https://doi.org/10.1007/s00792-003-0367-y
Li G, Zeng X, Liu X, Zhang X, Shao Z (2016) Wukongibacter baidiensis gen. nov., sp. nov., an anaerobic bacterium isolated from hydrothermal sulfides, and proposal for the reclassification of the closely related Clostridium halophilum and Clostridium caminithermale within Maledivibacter gen. nov. and Paramaledivibacter gen. nov., respectively. Int J Syst Evol Microbiol 66:4355–4361. https://doi.org/10.1099/ijsem.0.001355
Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S (2020) One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 113:659–671. https://doi.org/10.1111/mmi.14469
Meier-Kolthoff JP, Klenk HP, Goker M (2014) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356. https://doi.org/10.1099/ijs.0.056994-0
Meijer WG, Nienhuis-Kuiper ME, Hansen TA (1999) Fermentative bacteria from estuarine mud: phylogenetic position of Acidaminobacter hydrogenoformans and description of a new type of gram-negative, propionigenic bacterium as Propionibacter pelophilus gen. nov., sp. nov. Int J Syst Bacteriol 49:1039–1044. https://doi.org/10.1099/00207713-49-3-1039
Minnikin D, O’Donnell A, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Miyazaki U, Tame A, Miyazaki J et al (2023) Haliovirga abyssi gen nov., sp. Nov., a mesophilic fermentative bacterium isolated from the Iheya North hydrothermal field, and proposal of Haliovirgaceae fam nov. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.006014
Nagata R, Takaki Y, Tame A et al (2017) Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough. Syst Appl Microbiol 40:352–356. https://doi.org/10.1016/j.syapm.2017.06.002
Nakagawa S, Takai K, Inagaki F et al (2005a) Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol Ecol 54:141–155. https://doi.org/10.1016/j.femsec.2005.03.007
Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y (2005b) Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the epsilon-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 55:925–933. https://doi.org/10.1099/ijs.0.63480-0
Nakagawa S, Saito H, Tame A et al (2017) Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon. Sci Rep 7:8764. https://doi.org/10.1038/s41598-017-09355-2
Oren A, Garrity GM (2021) Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005056
Porter K, Feig Y (1980) The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25:943–948. https://doi.org/10.4319/lo.1980.25.5.0943
Qiu D, Zeng X, Zeng L, Li G, Shao Z (2021) Fusibacter ferrireducens sp. Nov., an anaerobic, Fe(III)- and sulphur-reducing bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 71:371. https://doi.org/10.1099/ijsem.0.004952
Ravot G, Magot M, Fardeau ML, Patel BK, Thomas P, Garcia JL, Ollivier B (1999) Fusibacter paucivorans gen. nov., sp. nov., an anaerobic, thiosulfate-reducing bacterium from an oil-producing well. Int J Syst Bacteriol 49:1141–1147. https://doi.org/10.1099/00207713-49-3-1141
Reed AD, Theriot CM (2021) Contribution of inhibitory metabolites and competition for nutrients to colonization resistance against Clostridioides difficile by commensal Clostridium. Microorganisms 9:371. https://doi.org/10.3390/microorganisms9020371
Richter M, Rossello-Mora R, Oliver Glockner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe Magazine 9:111–118. https://doi.org/10.1128/microbe.9.111.1
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Schut GJ, Boyd ES, Peters JW, Adams MW (2013) The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev 37:182–203. https://doi.org/10.1111/j.1574-6976.2012.00346.x
Slobodkina GB, Kolganova TV, Tourova TP, Kostrikina NA, Jeanthon C, Bonch-Osmolovskaya EA, Slobodkin AI (2008) Clostridium tepidiprofundi sp. nov., a moderately thermophilic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 58:852–855. https://doi.org/10.1099/ijs.0.65485-0
Smii L, Ben Hania W, Cayol JL, Joseph M, Hamdi M, Ollivier B, Fardeau ML (2015) Fusibacter bizertensis sp. nov., isolated from a corroded kerosene storage tank. Int J Syst Evol Microbiol 65:117–121. https://doi.org/10.1099/ijs.0.066183-0
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
Stetter KO, König H, Stackebrandt E (1983) Pyrodictium gen. nov., a new genus of submarine disc-shaped sulphur reducing archaebacteria growing optimally at 105°C. System Appl Microbiol 4:535–551. https://doi.org/10.1016/s0723-2020(83)80011-3
Suzuki D, Ueki A, Amaishi A, Ueki K (2007) Desulfobulbus japonicus sp. nov., a novel Gram-negative propionate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. Int J Syst Evol Microbiol 57:849–855. https://doi.org/10.1099/ijs.0.64855-0
Takai K, Moser D, Onstott T, Spoelstra N, Pfiffner S, Dohnalkova A, Fredrickson J (2001) Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine. Int J Syst Evol Microbiol 51:1245–1256. https://doi.org/10.1099/00207713-51-4-1245
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Urios L, Cueff V, Pignet P, Barbier G (2004) Tepidibacter formicigenes sp. nov., a novel spore-forming bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol 54:439–443. https://doi.org/10.1099/ijs.0.02836-0
Vandieken V, Niemann H, Engelen B, Cypionka H (2017) Marinisporobacter balticus gen. nov., sp. nov., Desulfosporosinus nitroreducens sp. nov. and Desulfosporosinus fructosivorans sp. nov., new spore-forming bacteria isolated from subsurface sediments of the Baltic Sea. Int J Syst Evol Microbiol 67:1887–1893. https://doi.org/10.1099/ijsem.0.001883
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
Wyss C, Dewhirst FE, Paster BJ, Thurnheer T, Luginbuhl A (2005) Guggenheimella bovis gen. nov., sp. nov., isolated from lesions of bovine dermatitis digitalis. Int J Syst Evol Microbiol 55:667–671. https://doi.org/10.1099/ijs.0.63116-0
Yang M, Derbyshire MK, Yamashita RA, Marchler-Bauer A (2020) NCBI’s conserved domain database and tools for protein domain analysis. Curr Protoc Bioinformatics 69:e90. https://doi.org/10.1002/cpbi.90
Yarza P, Yilmaz P, Pruesse E et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645. https://doi.org/10.1038/nrmicro3330
Zhang J, Zhang Y, Liu R, Cai R, Liu F, Sun C (2021) Iocasia fonsfrigidae NS-1 gen nov., sp. Nov., a novel deep-sea bacterium possessing diverse carbohydrate metabolic pathways. Front Microbiol 12:725159. https://doi.org/10.3389/fmicb.2021.725159
Acknowledgements
We express our sincere appreciation to the crews of R/V Yokosuka and the operation teams of DSV Shinkai 6500 for their invaluable support in facilitating the collection of samples
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This work was partially supported by JSPS KAKENHI Grant Numbers JP20H03322, JP22KJ1983, and JP22J22463.
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U.M. conducted the experiment, analyzed data, and drafted the manuscript; D.M. helped perform the experiment; Y.H. was responsible for sample preparation; A.T. managed electron microscopy; S.S. aided in editing the manuscript; J.M. and K.T. oversaw the sampling cruise; S.N. conceptualized the study, supervised the project, and finalized the manuscript writing.
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Miyazaki, U., Mizutani, D., Hashimoto, Y. et al. Helicovermis profundi gen. nov., sp. nov., a novel mesophilic, asporogenous bacterium within the Clostridia isolated from a deep-sea hydrothermal vent chimney. Antonie van Leeuwenhoek 117, 24 (2024). https://doi.org/10.1007/s10482-023-01919-9
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DOI: https://doi.org/10.1007/s10482-023-01919-9