1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment Free

Abstract

An alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7 were 0.4–0.6 µm wide and 1.0–8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7 could grow at 10–37 °C (optimum, 25–28 °C), at pH 6.0–8.0 (optimum, pH 7.0) and in the presence of 0.5–6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7 belonged to the genus of the family . It showed the highest similarity to JCM 19152 (96.8 %), followed by KCTC 42253 (96.1%). The values of average nucleotide identity and DNA–DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7 with JCM 19152 and KCTC 42253, respectively. The major respiratory quinone of strain BM_7 was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C, anteiso-C, C ω6, iso-C 3-OH, C 6 C 3-OH and C. The genome size of strain BM_7 is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7 was considered to represent a novel species of the genus , and the name sp. nov. is proposed. The type strain is BM_7 (=MCCC 1A15882=KCTC 72696).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): lignin degradation , mangrove sediment , Mangrovibacterium lignilyticum and taxonomy
Funding
This study was supported by the:
  • Xiamen Ocean Economic Innovation and Development Demonstration Project (Award 16PZP001SF16)
    • Principle Award Recipient: Zongze Shao
  • COMRA program (Award No. DY135-B2-01)
    • Principle Award Recipient: Zongze Shao
  • National Infrastructure of Microbial Resources of China (Award NMRC-2020-9)
    • Principle Award Recipient: Zongze Shao
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004305
2020-06-29
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4502.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004305&mimeType=html&fmt=ahah

References

  1. Chen Q, Zhao Q, Li J, Jian S, Ren H. Mangrove succession enriches the sediment microbial community in South China. Sci Rep 2016; 6:27468 [View Article][PubMed]
     [Google Scholar]
  2. Leung JYS. Habitat heterogeneity affects ecological functions of macrobenthic communities in a mangrove: implication for the impact of restoration and afforestation. Glob Ecol Conserv 2015; 4:423–433 [View Article]
     [Google Scholar]
  3. Mohd-Azlan J, Noske R, Lawes M. The role of habitat heterogeneity in structuring mangrove bird assemblages. Diversity 2015; 7:118–136 [View Article]
     [Google Scholar]
  4. Kristensen E, Bouillon S, Dittmar T, Marchand C. Organic carbon dynamics in mangrove ecosystems: a review. Aquat Bot 2008; 89:201–219 [View Article]
     [Google Scholar]
  5. Bashan Y, Holguin G. Azospirillum – plant relationships: environmental and physiological advances (1990–1996). Can J Microbiol 1997; 43:103–121 [View Article]
     [Google Scholar]
  6. Huang X-F, Liu YJ, Dong J-D, Qu L-Y, Zhang Y-Y et al. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov. Int J Syst Evol Microbiol 2014; 64:875–881 [View Article][PubMed]
     [Google Scholar]
  7. Wu W-J, Zhou Y-X, Liu Y, Chen G-J, Du Z-J. Mangrovibacterium marinum sp. nov., isolated from a coastal sediment. Antonie Van Leeuwenhoek 2015; 107:1583–1589 [View Article][PubMed]
     [Google Scholar]
  8. Holmes DE, Nevin KP, Woodard TL, Peacock AD, Lovley DR. Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell. Int J Syst Evol Microbiol 2007; 57:701–707 [View Article][PubMed]
     [Google Scholar]
  9. Irgens RL. Meniscus, a new genus of aerotolerant, Gas-Vacuolated bacteria. Int J Syst Bacteriol 1977; 27:38–43 [View Article]
     [Google Scholar]
  10. Iino T, Mori K, Itoh T, Kudo T, Suzuki K-I et al. Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:3660–3667 [View Article][PubMed]
     [Google Scholar]
  11. Qu L, Zhu F, Hong X, Gao W, Chen J et al. Sunxiuqinia elliptica gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment in a sea cucumber farm. Int J Syst Evol Microbiol 2011; 61:2885–2889 [View Article][PubMed]
     [Google Scholar]
  12. Du Z-J, Wang Y, Dunlap C, Rooney AP, Chen G-J. Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 2014; 64:1690–1696 [View Article][PubMed]
     [Google Scholar]
  13. Wu W-J, Liu Q-Q, Chen G-J, Du Z-J. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 2015; 65:2260–2264 [View Article][PubMed]
     [Google Scholar]
  14. Liu Q-Q, Li X-L, Rooney AP, Du Z-J, Chen G-J. Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae . Int J Syst Evol Microbiol 2014; 64:3473–3477 [View Article][PubMed]
     [Google Scholar]
  15. Zhou L-Y, Yu Z-L, Xu W, Mu D-S, Du Z-J. Maribellus luteus gen. nov., sp. nov., a marine bacterium in the family Prolixibacteraceae isolated from coastal seawater. Int J Syst Evol Microbiol 2019; 69:2388–2394 [View Article][PubMed]
     [Google Scholar]
  16. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that AIDS in distinguishing gram-positive from gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448 [View Article][PubMed]
     [Google Scholar]
  17. Huang Z, Dong C, Shao Z. Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. Int J Syst Evol Microbiol 2016; 66:3050–3056 [View Article][PubMed]
     [Google Scholar]
  18. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990; 28:1942–1946 [View Article][PubMed]
     [Google Scholar]
  19. Chun J, Lee J-H, Jung Y, Kim M, Kim S et al. Eztaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  20. McGinnis S, Madden TL. Blast: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32:W20–W25 [View Article][PubMed]
     [Google Scholar]
  21. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
     [Google Scholar]
  24. 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]
  25. Yoon S-H, Ha S-M, 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]
  26. 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]
  27. Kates M, Work TS, Work E. Techniques of lipidology: isolation, analysis and identification of lipids. North-Holland Amsterdam 1972; 350:
     [Google Scholar]
  28. Lara MA, Rodríguez-Malaver AJ, Rojas OJ, Holmquist O, González AM et al. Black liquor lignin biodegradation by Trametes elegans . Int Biodeterior Biodegrad 2003; 52:167–173 [View Article]
     [Google Scholar]
  29. Billings AF, Fortney JL, Hazen TC, Simmons B, Davenport KW et al. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov. Stand Genomic Sci 2015; 10:106 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004305
Loading
Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment
Int J Syst Evol Microbiol 70, 4502 (2020); https://doi.org/10.1099/ijsem.0.004305
/content/journal/ijsem/10.1099/ijsem.0.004305
/content/journal/ijsem/10.1099/ijsem.0.004305
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error