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Current Microbiology

, Volume 76, Issue 2, pp 231–236 | Cite as

Complete Genome Sequence of Saccharospirillum mangrovi HK-33T Sheds Light on the Ecological Role of a Bacterium in Mangrove Sediment Environment

  • Weiyan Zhang
  • Xuezhen Zhou
  • Ye Yuan
  • Biyin Liu
  • Slava S. EpsteinEmail author
  • Shan HeEmail author
Article
  • 73 Downloads

Abstract

We present the genome sequence of Saccharospirillum mangrovi HK-33T, isolated from a mangrove sediment sample in Haikou, China. The complete genome of S. mangrovi HK-33T consisted of a single-circular chromosome with the size of 3,686,911 bp as well as an average G + C content of 57.37%, and contained 3,383 protein-coding genes, 4 operons of 16S-23S-5S rRNA genes, and 52 tRNA genes. Genomic annotation indicated that the genome of S. mangrovi HK-33T had many genes related to oligosaccharide and polysaccharide degradation and utilization of polyhydroxyalkanoate. For nitrogen cycle, genes encoding nitrate and nitrite reductase, glutamate dehydrogenase, glutamate synthase, and glutamine synthetase could be found. For phosphorus cycle, genes related to polyphosphate kinases (ppk1 and ppk2), the high-affinity phosphate-specific transport (Pst) system, and the low-affinity inorganic phosphate transporter (pitA) were predicted. For sulfur cycle, cysteine synthase and type III acyl coenzyme A transferase (dddD) coding genes were searched out. This study provides evidence about carbon, nitrogen, phosphorus, and sulfur metabolic patterns of S. mangrovi HK-33T and broadens our understandings about ecological roles of this bacterium in the mangrove sediment environment.

Notes

Acknowledgements

This work was supported by the Natural Science Foundation of Zhejiang Province of China (LQ18C010001, LH19H300001), the Natural Science Foundation of China (41776168), the Natural Science Foundation of Ningbo City (2018A610303), Ningbo Public Service Platform for High-Value Utilization of Marine Biological Resources (NBHY-2017-P2), Ningbo Sci. & Tech. Projects for Common Wealth (2017C10016), the 111 project (D16013), the Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Development Fund, the K.C. Wong Magna Fund in Ningbo University.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

284_2018_1600_MOESM1_ESM.doc (50 kb)
Supplementary material 1 (DOC 49 KB)

References

  1. 1.
    Nedwell DB, Blackburn TH, Wiebe WJ (1994) Dynamic nature of turnover of organic carbon, nitrogen and sulphur in the sediments of a Jamaican mangrove forest. Mar Ecol Prog Ser 110:203–212CrossRefGoogle Scholar
  2. 2.
    Nehru P, Balasubramanian P (2018) Mangrove species diversity and composition in the successional habitats of Nicobar Islands, India: a post-tsunami and subsidence scenario. For Ecol Manag 427:70–77CrossRefGoogle Scholar
  3. 3.
    Sreelekshmi S, Preethy CM, Varghese R, Joseph P, Asha CV, Nandan SB, Radhakrishnan CK (2018) Diversity, stand structure, and zonation pattern of mangroves in southwest coast of India. J Asia-Pac Biodivers.  https://doi.org/10.1016/j.japb.2018.08.001 Google Scholar
  4. 4.
    Bhattacharya M, Kar A, Chini DS, Malick RC, Patra BC, Das BK (2018) Multi-cluster analysis of crabs and ichthyofaunal diversity in relation to habitat distribution at tropical mangrove ecosystem of the Indian Sundarbans. Reg Stud Mar Sci 24:203–211CrossRefGoogle Scholar
  5. 5.
    Ngo-Massou VM, Din N, Kenn M, Dongmo AB (2018) Brachyuran crab diversity and abundance patterns in the mangroves of Cameroon. Reg Stud Mar Sci 24:324–335CrossRefGoogle Scholar
  6. 6.
    Rajamani T, Suryanarayanan TS, Murali TS, Thirunavukkarasu N (2018) Distribution and diversity of foliar endophytic fungi in the mangroves of Andaman Islands, India. Fungal Ecol 36:109–116CrossRefGoogle Scholar
  7. 7.
    Bouchez A, Pascault N, Chardon C, Bouvy M, Cecchi P, Lambs L, Herteman M, Fromard F, Got P, Leboulanger C (2013) Mangrove microbial diversity and the impact of trophic contamination. Mar Pollut Bull 66:39–46CrossRefGoogle Scholar
  8. 8.
    Zhang XY, Hu BX, Ren HJ, Zhang J (2018) Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences. Sci Total Environ 633:518–528CrossRefGoogle Scholar
  9. 9.
    Deborde J, Marchand C, Molnar N, Patrona LD, Meziane T (2015) Concentrations and fractionation of carbon, iron, sulfur, nitrogen and phosphorus in mangrove sediments along an intertidal gradient (semi-arid climate, New Caledonia). J Mar Sci Eng 3:52–72CrossRefGoogle Scholar
  10. 10.
    Labrenz M, Lawson PA, Tindall BJ, Collins MD, Hirsch P (2003) Saccharospirillum impatiens gen. nov., sp. nov., a novel γ-Proteobacterium isolated from hypersaline Ekho Lake (East Antarctica). Int J Syst Evol Microbiol 53:653–660CrossRefGoogle Scholar
  11. 11.
    Chen YG, Cui XL, Li QY, Wang YX, Tang SK (2009) Saccharospirillum salsuginis sp. nov., a gammaproteobacterium from a subterranean brine. Int J Syst Evol Microbiol 59:1382–1386CrossRefGoogle Scholar
  12. 12.
    Choi A, Oh HM, Cho JC (2011) Saccharospirillum aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Saccharospirillum. Int J Syst Evol Microbiol 61:487–492CrossRefGoogle Scholar
  13. 13.
    Fidalgo C, Rocha J, Proença DN, Morais PV, Alves A (2017) Saccharospirillum correiae sp. nov., an endophytic bacterium isolated from the halophyte Halimione portulacoides. Int J Syst Evol Microbiol 67:2026–2030CrossRefGoogle Scholar
  14. 14.
    Zhang WY, Yuan Y, Su DQ, Ding LJ, Yan XJ, Wu M, Epstein SS, He S (2018) Saccharospirillum mangrovi sp. nov., a bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 68(9):2813–2818CrossRefGoogle Scholar
  15. 15.
    Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G (2008) Consensus generation and variant detection by Celera Assembler. Bioinformatics 24:1035–1040CrossRefGoogle Scholar
  16. 16.
    Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J (2013) SOAPindel: efficient identification of indels from short paired reads. Genome Res 23:195–200CrossRefGoogle Scholar
  17. 17.
    Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214CrossRefGoogle Scholar
  18. 18.
    Lowe TM, Chan PP (2016) tRNAscan-SE On-line: search and contextual analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57CrossRefGoogle Scholar
  19. 19.
    Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108CrossRefGoogle Scholar
  20. 20.
    Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41CrossRefGoogle Scholar
  21. 21.
    Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9CrossRefGoogle Scholar
  22. 22.
    Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280CrossRefGoogle Scholar
  23. 23.
    Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785–786CrossRefGoogle Scholar
  24. 24.
    Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35(web server issue):W52–W57CrossRefGoogle Scholar
  25. 25.
    Stothard P, Wishart DS (2004) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539CrossRefGoogle Scholar
  26. 26.
    Zhang H, Yohe T, Huang L, Entwistle S, Wu PZ, Yang ZL, Busk PK, Xu Y, Yin YB (2018) dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 46:W95–W101CrossRefGoogle Scholar
  27. 27.
    Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495CrossRefGoogle Scholar
  28. 28.
    Lu JN, Tappel RC, Nomura CT (2009) Mini-review: biosynthesis of poly (hydroxyalkanoates). Polym Rev 49:226–248CrossRefGoogle Scholar
  29. 29.
    Satinsky BM, Crump BC, Smith CB, Sharma S, Zielinski BL. Doherty M, Meng J, Sun S, Medeiros PM, Paul JH, Coles VJ, Yager PL, Moran MA (2014) Microspatial gene expression patterns in the Amazon River Plume. Proc Natl Acad Sci USA 111(30):11085–11090CrossRefGoogle Scholar
  30. 30.
    Kim SJ, Do KT, Park SJ (2018) Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat. Mar Genomics 37:43–45CrossRefGoogle Scholar
  31. 31.
    Branco dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P (2017) Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. Appl Environ Microbiol 83:e01528–e01517CrossRefGoogle Scholar
  32. 32.
    Zhong C, Fu J, Jiang T, Zhang C, Cao G (2018) Polyphosphate metabolic gene expression analyses reveal mechanisms of phosphorus accumulation and release in Microlunatus phosphovorus strain JN459. FEMS Microbiol Lett 365(6)Google Scholar
  33. 33.
    Alcolombri U, Laurino P, Lara-Astiaso P, Vardi A, Tawfik DS (2014) DddD is a CoA-transferase/lyase producing dimethyl sulfide in the marine environment. Biochemistry 53(34):5473–5475CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical SciencesNingbo UniversityNingboPeople’s Republic of China
  2. 2.Department of BiologyNortheastern UniversityBostonUSA

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