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Volume 74, Issue 1

sp. nov., isolated from deep-sea sediment of the Mariana Trench No Access

Abstract

A Gram-stain-negative, aerobic, rod-shaped, non-flagellated, non-gliding bacterial strain, designated MT50, was isolated from a deep-sea sediment sample collected from the Mariana Trench. Optimal growth of strain MT50 was observed at 25 °C, pH 7.0–7.5 and in the presence of 3–5 % (w/v) NaCl. The strain was positive for oxidase and catalase. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain MT50 is affiliated with the genus , showing the highest sequence similarity (98.5 %) to the type strain of . The digital DNA–DNA hybridization and average nucleotide identity values between strain MT50 and four closely related type strains of known species (14.1–54.8 % and 72.7–86.8 %, respectively) were all below the threshold values to discriminate bacterial species, indicating that strain MT50 is affiliated with a novel species within the genus. The genomic G+C content deduced from the genome of strain MT50 was 36.2 mol%. The major fatty acids of strain MT50 were iso-C, iso-C 3-OH and anteiso-C. The predominant respiratory quinone of the strain was MK-6. The polar lipids of strain MT50 included phosphatidylethanolamine and two unidentified lipids. Based on the polyphasic data presented in this study, strain MT50 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is MT50 (=MCCC 1K07833=KCTC 92380).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): deep-sea sediment , Mesonia profundi sp. nov. and polyphasic taxonomy
Funding
This study was supported by the:
  • the National Science Foundation of Shandong Province (Award ZR2021QD071)
    • Principle Award Recipient: NotApplicable
  • the Taishan Scholars Program of Shandong Province, China (Award tsqn202306092)
    • Principle Award Recipient: NotApplicable
  • the Taishan Scholar Foundation of Shandong Province, China (Award tspd20181203)
    • Principle Award Recipient: NotApplicable
  • Major Scientific and Technological Innovation Project (MSTIP) of Shandong Province (Award 2019JZZY010817)
    • Principle Award Recipient: NotApplicable
  • the Fundamental Research Funds for the Central Universities (Award 202141006)
    • Principle Award Recipient: NotApplicable
  • the Fundamental Research Funds for the Central Universities (Award 202041011)
    • Principle Award Recipient: NotApplicable
  • the Fundamental Research Funds for the Central Universities (Award 202172002)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 42076151)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 31961133016)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 42106142)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 42076229)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 42276102)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 92251303)
    • Principle Award Recipient: NotApplicable
  • National Science Foundation of China (Award 42176156)
    • Principle Award Recipient: Hui-huiFu
  • National Key Research and Development Program of China (Award 2021YFA0909600)
    • Principle Award Recipient: NotApplicable
  • National Key Research and Development Program of China (Award 2022YFC2807500)
    • Principle Award Recipient: Hui-huiFu
© 2024 The Authors
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References

  1. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
     [Google Scholar]
  2. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  3. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M et al. Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm. Int J Syst Evol Microbiol 2003; 53:1967–1971 [View Article] [PubMed]
     [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  5. Choi A, Baek K, Lee H, Cho JC. Mesonia aquimarina sp. nov., a marine bacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2015; 65:135–140 [View Article] [PubMed]
     [Google Scholar]
  6. Zhou Y, Gao X, Xu J, Li G, Ma R et al. Mesonia hitae sp. nov., isolated from the seawater of the South Atlantic Ocean. Int J Syst Evol Microbiol 2021; 71:004911 [View Article] [PubMed]
     [Google Scholar]
  7. Sung HR, Joh K, Shin KS. Mesonia maritimus sp. nov., isolated from seawater of the South Sea of Korea. Int J Syst Evol Microbiol 2017; 67:4285–4286 [View Article] [PubMed]
     [Google Scholar]
  8. Nedashkovskaya OI, Kim SB, Zhukova NV, Kwak J, Mikhailov VV et al. Mesonia mobilis sp. nov., isolated from seawater, and emended description of the genus Mesonia. Int J Syst Evol Microbiol 2006; 56:2433–2436 [View Article]
     [Google Scholar]
  9. Lucena T, Sanz-Sáez I, Arahal DR, Acinas SG, Sánchez O et al. Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters. Int J Syst Evol Microbiol 2020; 70:4329–4338 [View Article] [PubMed]
     [Google Scholar]
  10. Kolberg J, Busse H-J, Wilke T, Schubert P, Kämpfer P et al. Mesonia hippocampi sp. nov., isolated from the brood pouch of a diseased Barbour’s seahorse (Hippocampus barbouri). Int J Syst Evol Microbiol 2015; 65:2241–2247 [View Article] [PubMed]
     [Google Scholar]
  11. Lee SY, Lee MH, Yoon JH. Mesonia ostreae sp. nov., isolated from seawater of an oyster farm, and emended description of the genus Mesonia. Int J Syst Evol Microbiol 2012; 62:1804–1808 [View Article]
     [Google Scholar]
  12. Kang HS, Lee SD. Mesonia phycicola sp. nov., isolated from seaweed, and emended description of the genus Mesonia. Int J Syst Evol Microbiol 2010; 60:591–594 [View Article] [PubMed]
     [Google Scholar]
  13. Wang FQ, Xie ZH, Zhao JX, Chen GJ, Du ZJ. Mesonia sediminis sp. nov., isolated from a sea cucumber culture pond. Antonie van Leeuwenhoek 2015; 108:1205–1212 [View Article] [PubMed]
     [Google Scholar]
  14. Rao H, Huan R, Chen Y, Xiao X, Li W et al. Characteristics and application of a novel cold-adapted and salt-tolerant protease EK4-1 produced by an arctic bacterium Mesonia algae K4-1. Int J Mol Sci 2023; 24:7985 [View Article] [PubMed]
     [Google Scholar]
  15. Huan R, Huang J, Liu D, Wang M, Liu C et al. Genome sequencing of Mesonia algae K4-1 reveals its adaptation to the Arctic ocean. Front Microbiol 2019; 10:2812 [View Article] [PubMed]
     [Google Scholar]
  16. Jeong S, Vollprecht R, Cho K, Leiknes T, Vigneswaran S et al. Advanced organic and biological analysis of dual media filtration used as a pretreatment in a full-scale seawater desalination plant. Desalination 2016; 385:83–92 [View Article]
     [Google Scholar]
  17. Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG et al. Ecology of marine bacteroidetes: a comparative genomics approach. ISME J 2013; 7:1026–1037 [View Article] [PubMed]
     [Google Scholar]
  18. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  19. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  26. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  28. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  30. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  31. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  32. Zhang X-Y, Zhang Y-J, Chen X-L, Qin Q-L, Zhao D-L et al. Myroides profundi sp. nov., isolated from deep-sea sediment of the southern Okinawa Trough. FEMS Microbiol Lett 2008; 287:108–112 [View Article] [PubMed]
     [Google Scholar]
  33. Qin Q-L, Wang Z-B, Su H-N, Chen X-L, Miao J et al. Oxidation of trimethylamine to trimethylamine N-oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage. Sci Adv 2021; 7:eabf9941 [View Article] [PubMed]
     [Google Scholar]
  34. Ziegler C, Bremer E, Krämer R. The BCCT family of carriers: from physiology to crystal structure. Mol Microbiol 2010; 78:13–34 [View Article] [PubMed]
     [Google Scholar]
  35. Murray RGE, Doetsch RN, Robinow CF. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 21–41
     [Google Scholar]
  36. Clarke PH. Hydrogen sulphide production by bacteria. J Gen Microbiol 1953; 8:397–407 [View Article] [PubMed]
     [Google Scholar]
  37. Smibert RM, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  38. Ventosa A, Márquez MC, Garabito MJ, Arahal DR. Moderately halophilic gram-positive bacterial diversity in hypersaline environments. Extremophiles 1998; 2:297–304 [View Article] [PubMed]
     [Google Scholar]
  39. Shieh WY, Lin YT, Jean WD. Pseudovibrio denitrificans gen. nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification. Int J Syst Evol Microbiol 2004; 54:2307–2312 [View Article] [PubMed]
     [Google Scholar]
  40. Sasser M. MIDI Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 2001
     [Google Scholar]
  41. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  42. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4‐diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
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Mesonia profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench
Int J Syst Evol Microbiol 74, 006211 (2024); https://doi.org/10.1099/ijsem.0.006211
/content/journal/ijsem/10.1099/ijsem.0.006211
/content/journal/ijsem/10.1099/ijsem.0.006211
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