Skip to main content

Advertisement

SpringerLink
Log in

Complete Genome Sequence of Qipengyuania sediminis CGMCC 1.12928T, Shed Light on Its Role in Matter-Cycle and Cold Adaption Mechanism of the Genus Qipengyuania

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Qipengyuania sediminis CGMCC 1.12928T, a family member of Erythrobacteraceae, the class of Alphaproteobacteria, was isolated from a borehole sediment sample collected from Qiangtang Basin in Qinghai-Tibetan Plateau, the largest permafrost in China. Understanding bacterial molecular feature may shed light on the ecological strategy in the extreme environment. Here we describe the complete genome sequence and annotation of strain CGMCC 1.12928T, including the complete genome sequence and annotation. The genome of strain CGMCC 1.12928T consist of a single-circular chromosome, comprises 2,416,000 bp with an average G + C content of 66.7 mol%, and contains 2414 genes; including 2367 CDSs, 44 tRNA genes, as well as one operon of 16S-23S-5S rRNA genes. Genomic properties indicated that strain CGMCC 1.12928T has a relatively smaller genome size and higher G + C content within the family Erythrobacteraceae. In addition, genomic analysis revealed its genome contains multiple function genes responsible for nitrogen, sulfur and phosphorus cycles and explained the cold adaption mechanism. Thus, this strain plays an active role in the biogeochemical cycle in cold niche. The whole-genome of this isolate will widen our understanding of the ecological role of the genus Qipengyuania in permafrost.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Feng XM, Mo YX, Han L, Nogi Y, Zhu YH, Lv J (2015) Qipengyuania sediminis gen. nov., sp nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evolut Microbiol 65:3658–3665

    Article  CAS  Google Scholar 

  2. Zhao L, Li YN, Xu SX, Zhou HK, Gu S, Yu GR, Zhao XQ (2006) Diurnal, seasonal and annual variation in net ecosystem CO2 exchange of an alpine shrubland on Qinghai-Tibetan plateau. Globa Change Biol 12(10):1940–1953

    Article  Google Scholar 

  3. Kato T, Tang YH, Gu S, Cui XY, Hirota M, Du MY, Li YN, Zhao ZQ, Oikawa T (2004) Carbon dioxide exchange between the atmosphere and an alpine meadow ecosystem on the Qinghai-Tibetan Plateau. Chin Agric For Meteorol 124(1–2):121–134

    Article  Google Scholar 

  4. Lin WF, Yu ZS, Chen X, Liu RY, Zhang HX (2013) Molecular characterization of natural biofilms from household taps with different materials: PVC, stainless steel, and cast iron in drinking water distribution system. Appl Microbiol Biot 97(18):8393–8401

    Article  CAS  Google Scholar 

  5. Li E, Hamm CM, Gulati AS, Sartor RB, Chen HY, Wu X, Zhang TY, Rohlf FJ, Zhu W, Gu C, Robertson CE, Pace NR, Boedeker EC, Harpaz N, Yuan J, Weinstock GM, Sodergren E, Frank DN (2012) Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS ONE 7(6):e26284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nunez EV, Valenzuela-Encinas C, Alcantara-Hernandez RJ, Navarro-Noya YE, Luna-Guido M, Marsch R, Dendooven L (2012) Modifications of bacterial populations in anthracene contaminated soil. Appl Soil Ecol 61:113–126

    Article  Google Scholar 

  7. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19(6):1117–1123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. 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):3100–3108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44(W1):W54–W57

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. 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 FF, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42(D1):D206–D214

    Article  CAS  PubMed  Google Scholar 

  11. 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 Bioinformatics 4:41

    Article  PubMed  PubMed Central  Google Scholar 

  12. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 40: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785–786

    Article  CAS  PubMed  Google Scholar 

  13. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580

    Article  CAS  PubMed  Google Scholar 

  14. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57

    Article  PubMed  PubMed Central  Google Scholar 

  16. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21(4):537–539

    Article  CAS  PubMed  Google Scholar 

  17. Kanamori T, Kanou N, Atomi H, Imanaka T (2004) Enzymatic characterization of a prokaryotic urea carboxylase. J Bacteriol 186(9):2532–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Liu Q, Wu YH, Cheng H, Xu L, Wang CS, Xu XW (2017) Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434. Stand Genom Sci 12:32

    Article  CAS  Google Scholar 

  19. O’May GA, Jacobsen SM, Longwell M, Stoodley P, Mobley HL, Shirtliff ME (2009) The high-affinity phosphate transporter Pst in Proteus mirabilis HI4320 and its importance in biofilm formation. Microbiology 155(5):1523–1535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhong CQ, Fu JF, Jiang TY, Zhang CM, Cao GX (2018) Polyphosphate metabolic gene expression analyses reveal mechanisms of phosphorus accumulation and release in Microlunatus phosphovorus strain JN459. FEMS Microbiol Lett 365(6):fny034

    Article  CAS  Google Scholar 

  21. Moran MA, Belas R, Schell MA, Gonzalez JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A (2007) Ecological genomics of marine Roseobacters. Appl Environ Microbiol 73(14):4559–4569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Satinsky BM, Crump BC, Smith CB, Sharma S, Zielinski BL, Doherty M, Meng J, Sun SL, 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):11085–11090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Luo HW, Benner R, Long RA, Hu JJ (2009) Subcellular localization of marine bacterial alkaline phosphatases. Proc Natl Acad Sci USA 106(50):21219–21223

    Article  PubMed  PubMed Central  Google Scholar 

  24. Pontinen A, Markkula A, Lindstrom M, Korkeala H (2015) Two-component-system histidine kinases involved in growth of Listeria monocytogenes EGD-e at low temperatures. Appl Environ Microbiol 81(12):3994–4004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kumar R, Acharya V, Singh D, Kumar S (2018) Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. Stand Genomic Sci 13:11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Qin QL, Xie BB, Yu Y, Shu YL, Rong JC, Zhang YJ, Zhao DL, Chen XL, Zhang XY, Chen B, Zhou BC, Zhang YZ (2014) Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation. Environ Microbiol 16(6):1642–1653

    Article  CAS  PubMed  Google Scholar 

  27. Kumar R, Singh D, Swarnkar MK, Singh AK, Kumar S (2016) Complete genome sequence of Arthrobacter alpinus ERGS4:06, a yellow pigmented bacterium tolerant to cold and radiations isolated from Sikkim Himalaya. J Biotechnol 220:86–87

    Article  CAS  PubMed  Google Scholar 

  28. Hossain MM, Nakamoto H (2002) HtpG plays a role in cold acclimation in cyanobacteria. Curr Microbiol 44(4):291–296

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (DY135-B2-10), the Scientific Research Fund of the Second Institute of Oceanography, MNR (JT1702), and the National Natural Science Foundation of China (41876182 & 41806204).

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou, 310012, People’s Republic of China

    Yan Gao, Yue-Hong Wu, Lin Xu, Hong Cheng, Chun-Sheng Wang & Xue-Wei Xu

  2. Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People’s Republic of China

    Yan Gao, Yue-Hong Wu, Lin Xu, Hong Cheng, Chun-Sheng Wang & Xue-Wei Xu

  3. China Ocean Mineral Resources Research and Development Association, Beijing, 100000, People’s Republic of China

    Yan Gao

  4. College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China

    Lin Xu

Authors
  1. Yan Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yue-Hong Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lin Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hong Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chun-Sheng Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xue-Wei Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xue-Wei Xu.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 16 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gao, Y., Wu, YH., Xu, L. et al. Complete Genome Sequence of Qipengyuania sediminis CGMCC 1.12928T, Shed Light on Its Role in Matter-Cycle and Cold Adaption Mechanism of the Genus Qipengyuania. Curr Microbiol 76, 988–994 (2019). https://doi.org/10.1007/s00284-019-01712-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-019-01712-w

Search

Navigation