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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 4

sp. nov., isolated from sediment of the Challenger Deep of Mariana Trench, and reclassification of as comb. nov. No Access

Abstract

A rod-shaped, white-pigmented, non-motile, Gram-stain-negative bacterium, designated RHL897, was isolated from sediments collected at the Mariana Trench Challenger Deep (10,816 m). Strain RHL897 was strictly aerobic and grew at 4–37 °C, pH 6.0–10.0 and in the presence of 0–11.0 % (w/v) NaCl. Its genomic DNA G+C content was 41.2%. Metabolic analysis revealed mechanisms for salt tolerance, abundant metal ion transport proteins and stronger resistance to heavy metals such as arsenic and mercury compared to the closest reference strains, likely linked to adaptation to the hadal sediment environment. The predominant menaquinone was MK-7, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified glycolipid. The main fatty acids were iso-C, summed feature 3 (C  and/or C  ) and iso-C 3OH. Strain RHL897 exhibited the highest 16S rRNA gene sequence similarity to the type strain of (97.9%) and (96.1%). Phylogenetic trees constructed based on 16S rRNA gene sequences and a 549 core gene set indicated that strain RHL897 was closely related to and , with all three species clustering within a distinct clade. Combined with the analyses of average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization, strain RHL897 represented a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RHL897 (=MCCC 1K09221=KCTC 102276). Furthermore, the revised phylogeny with the inclusion of RHL897 suggested that should be reclassified under the genus and renamed .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Albibacterium indicum , Albibacterium profundi , Challenger Deep sediment , heavy metal resistance and salt tolerance
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41976101)
    • Principle Award Recipient: JiwenLiu
  • Shandong Provincial Natural Science Foundation (Award ZR2024JQ006)
    • Principle Award Recipient: JiwenLiu
  • Shandong Provincial Natural Science Foundation (Award ZR2022YQ38)
    • Principle Award Recipient: JiwenLiu
  • Scientific and Technological Innovation Project of Laoshan Laboratory (Award LSKJ202203206)
    • Principle Award Recipient: JiwenLiu
© 2025 The Authors
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2025-04-23
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References

  1. Jamieson AJ, Fujii T, Mayor DJ, Solan M, Priede IG. Hadal trenches: the ecology of the deepest places on earth. Trends Ecol Evol 2010; 25:190–197 [View Article]
     [Google Scholar]
  2. Nunoura T, Takaki Y, Hirai M, Shimamura S, Makabe A et al. Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth. Proc Natl Acad Sci USA 2015; 112:1230–1236 [View Article] [PubMed]
     [Google Scholar]
  3. Zhao X, Liu J, Zhou S, Zheng Y, Wu Y et al. Diversity of culturable heterotrophic bacteria from the mariana trench and their ability to degrade macromolecules. Mar Life Sci Technol 2020; 2:181–193 [View Article]
     [Google Scholar]
  4. Zhu X-Y, Li Y, Xue C-X, Lidbury IDEA, Todd JD et al. Deep-sea bacteroidetes from the mariana trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems. Microbiome 2023; 11:175 [View Article] [PubMed]
     [Google Scholar]
  5. Dang Y-R, Cha Q-Q, Liu S-S, Wang S-Y, Li P-Y et al. Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench. Microbiome 2024; 12:77 [View Article] [PubMed]
     [Google Scholar]
  6. Jing H, Xiao X, Zhang Y, Li Z, Jian H et al. Composition and ecological roles of the core microbiome along the abyssal-hadal transition zone sediments of the Mariana Trench. Microbiol Spectr 2022; 10:e0198821 [View Article] [PubMed]
     [Google Scholar]
  7. Liu Y, Chen S, Xie Z, Zhang L, Wang J et al. Influence of extremely high pressure and oxygen on hydrocarbon-enriched microbial communities in sediments from the challenger deep, mariana trench. Microorganisms 2023; 11:630 [View Article] [PubMed]
     [Google Scholar]
  8. Liu J, Ren Q, Zhang Y, Li Y, Tian X et al. Alcanivorax profundi sp. nov., isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2019; 69:371–376 [View Article]
     [Google Scholar]
  9. Li Y, Sun X-M, Li J, Song X-Y, Qin Q-L et al. Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:5747–5752 [View Article]
     [Google Scholar]
  10. Wei Y, Mao H, Xu Y, Zou W, Fang J et al. Pseudomonas abyssi sp. nov., isolated from the abyssopelagic water of the Mariana Trench. Int J Syst Evol Microbiol 2018; 68:2462–2467 [View Article] [PubMed]
     [Google Scholar]
  11. Yang S, Li X, Xiao X, Zhuang G, Zhang Y. Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:3809–3815 [View Article] [PubMed]
     [Google Scholar]
  12. Ahmad W, Zheng Y, Li Y, Sun W, Hu Y et al. Marinobacter salinexigens sp. nov., a marine bacterium isolated from hadal seawater of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:3794–3800 [View Article] [PubMed]
     [Google Scholar]
  13. Zhang Y, Gao Y, Pei J, Cao J, Xie Z et al. Muricauda hadalis sp. nov., a novel piezophile isolated from hadopelagic water of the Mariana Trench and reclassification of Muricauda antarctica as a later heterotypic synonym of Muricauda teanensis. Int J Syst Evol Microbiol 2020; 70:4315–4320 [View Article]
     [Google Scholar]
  14. Zhou H-Z, Zhang J, Sun Q-L. Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis. Int J Syst Evol Microbiol 2021; 71:004910 [View Article] [PubMed]
     [Google Scholar]
  15. Zhang W-J, Zhang C, Zhou S, Li X-G, Mangenot S et al. Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the challenger deep, Mariana Trench. Microb Genom 2021; 7:000591 [View Article] [PubMed]
     [Google Scholar]
  16. Li S, Li C, Pei J, Liu R, Fang J et al. Tepidibacillus marianensis sp. nov., a novel heterotrophic iron-reducing bacterium isolated from Mariana Trench sediment. Int J Syst Evol Microbiol 2024; 74:006438 [View Article] [PubMed]
     [Google Scholar]
  17. Wei T-T, He S, Quan Z-X. Thalassolituus alkanivorans sp. nov., a hydrocarbon-utilizing bacterium isolated from the Mariana Trench. Int J Syst Evol Microbiol 2022; 72:005404 [View Article] [PubMed]
     [Google Scholar]
  18. Tamburini C, Boutrif M, Garel M, Colwell RR, Deming JW. Prokaryotic responses to hydrostatic pressure in the ocean--a review. Environ Microbiol 2013; 15:1262–1274 [View Article] [PubMed]
     [Google Scholar]
  19. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
     [Google Scholar]
  20. Zhang D-C, Schinner F, Margesin R. Pedobacter bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2592–2595 [View Article]
     [Google Scholar]
  21. He X-Y, Li N, Chen X-L, Zhang Y-Z, Zhang X-Y et al. Pedobacter indicus sp. nov., isolated from deep-sea sediment. Antonie Van Leeuwenhoek 2020; 113:357–364 [View Article] [PubMed]
     [Google Scholar]
  22. Acinas SG, Rodrı́guez-Valera F, Pedrós-Alió C. Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol Ecol 1997; 24:27–40 [View Article]
     [Google Scholar]
  23. Zhang Z, Yu C, Wang X, Yu S, Zhang X-H. Arcobacter pacificus sp. nov., isolated from seawater of the South Pacific Gyre. Int J Syst Evol Microbiol 2016; 66:542–547 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  26. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  29. Mount DW. Maximum parsimony method for phylogenetic prediction. CSH Protoc 2008; 2008:db [View Article] [PubMed]
     [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  31. Vernette C, Lecubin J, Sánchez P, Sunagawa S, Delmont TO et al. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res 2022; 50:W516–W526 [View Article] [PubMed]
     [Google Scholar]
  32. Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H-J et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 2019; 179:1068–1083 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  35. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  36. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
     [Google Scholar]
  37. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
     [Google Scholar]
  38. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  39. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  40. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article] [PubMed]
     [Google Scholar]
  41. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008; 36:D480–D484 [View Article] [PubMed]
     [Google Scholar]
  42. Kanehisa M, Furumichi M, Sato Y, Kawashima M, Ishiguro-Watanabe M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res 2023; 51:D587–D592 [View Article] [PubMed]
     [Google Scholar]
  43. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  44. Graham ED, Heidelberg JF, Tully BJ. Potential for primary productivity in a globally-distributed bacterial phototroph. ISME J 2018; 12:1861–1866 [View Article] [PubMed]
     [Google Scholar]
  45. Doetsch RN. Determinative methods of light microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. eds Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 21–33
     [Google Scholar]
  46. Hong W, Wang X, Yuan Y, Liu R, Zhao W et al. Photobacterium obscurum sp. nov., a marine bacterium isolated from the coast of Qingdao. Int J Syst Evol Microbiol 2023; 73:006096 [View Article] [PubMed]
     [Google Scholar]
  47. Yu C, Yu S, Zhang Z, Li Z, Zhang X-H. Oceanobacillus pacificus sp. nov., isolated from a deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:1278–1283 [View Article] [PubMed]
     [Google Scholar]
  48. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In Technical Note vol 101 MIDI Inc: Newark, DE; 1990
     [Google Scholar]
  49. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  50. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
     [Google Scholar]
  51. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207 [View Article]
     [Google Scholar]
  52. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article] [PubMed]
     [Google Scholar]
  53. Liu J, Li D-W, He X, Liu R, Cheng H et al. A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation. Mar Life Sci Technol 2024; 6:168–181 [View Article]
     [Google Scholar]
  54. Liu R, He X, Ren G, Li D-W, Zhao M et al. Niche partitioning and intraspecific variation of Thaumarchaeota in deep ocean sediments. Environ Microbiol 2025; 27:e70018 [View Article] [PubMed]
     [Google Scholar]
  55. Ventosa A, Nieto JJ, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev 1998; 62:504–544 [View Article] [PubMed]
     [Google Scholar]
  56. Okabe S, Kamizono A, Zhang L, Kawasaki S, Kobayashi K et al. Salinity tolerance and osmoadaptation strategies in four genera of anammox bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua. Environ Sci Technol 2024; 58:5357–5371 [View Article]
     [Google Scholar]
  57. Wang D, Hosteen O, Fierke CA. ZntR-mediated transcription of zntA responds to nanomolar intracellular free zinc. J Inorg Biochem 2012; 111:173–181 [View Article] [PubMed]
     [Google Scholar]
  58. Fan Y, Zhou Z, Liu F, Qian L, Yu X et al. The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes. Water Res 2024; 262:122113 [View Article] [PubMed]
     [Google Scholar]
  59. Baumann KBL, Mazzoli A, Salazar G, Ruscheweyh H-J, Müller B et al. Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments. ISME Commun 2024; 4:ycae110 [View Article] [PubMed]
     [Google Scholar]
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Albibacterium profundi sp. nov., isolated from sediment of the Challenger Deep of Mariana Trench, and reclassification of Pedobacter indicus as Albibacterium indicum comb. nov.
Int J Syst Evol Microbiol 75, 006754 (2025); https://doi.org/10.1099/ijsem.0.006754
/content/journal/ijsem/10.1099/ijsem.0.006754
/content/journal/ijsem/10.1099/ijsem.0.006754
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