Skip to main content
SpringerLink
Log in

Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field

  • Notes and Short Communications
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph.

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
Fig. 2

Similar content being viewed by others

References

  1. Bachelet D, Neue H-U (1993) Methane emissions from wetland rice areas of Asia. Chemosphere 26:219–237

    Article  CAS  Google Scholar 

  2. Conrad R (2009) The global methane cycle: recent advances in understanding the microbial processes involved. Environ Microbiol Rep 1:285–292

    Article  CAS  PubMed  Google Scholar 

  3. Hanson RS, Hanson TE (1996) Methanotrophic bacteria. Microbiol Mol Biol Rev 60:439–471

    CAS  Google Scholar 

  4. Islam T, Jensen S, Reigstad LJ, Larsen Ø, Birkeland N-K (2008) Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci U S A 105:300–304

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MSM, Camp HJMOd (2007) Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450:874–878

    Article  CAS  PubMed  Google Scholar 

  6. Dianou D, Ueno C, Ogiso T, Kimura M, Asakawa S (2012) Diversity of cultivable methane-oxidizing bacteria in microsites of a rice paddy field: investigation by cultivation method and fluorescence in situ hybridization (FISH). Microbes Environ 27:278–287

    Article  PubMed  PubMed Central  Google Scholar 

  7. Ferrando L, Tarlera S (2009) Activity and diversity of methanotrophs in the soil-water interface and rhizospheric soil from a flooded temperate rice field. J Appl Microbiol 106:306–316

    Article  CAS  PubMed  Google Scholar 

  8. Geymonat E, Ferrando L, Tarlera SE (2011) Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 61:2568–2572

    Article  PubMed  Google Scholar 

  9. Ogiso T, Ueno C, Dianou D, Huy TV, Katayama A, Kimura M, Asakawa S (2012) Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field. Int J Syst Evol Microbiol 62:1832–1837

    Article  CAS  PubMed  Google Scholar 

  10. Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology Proceedings of the German Conference on Bioinformatics (GCB), vol. 99, Hanover, pp. 45–56.

  11. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  Google Scholar 

  12. 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:D206–214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Camp HJMO, Jetten MSM, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnayaa MG (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc 3:1–3

    Article  Google Scholar 

  14. Kalyuzhnaya MG, Korotkova N, Crowther G, Marx CJ, Lidstrom ME, Chistoserdova L (2005) Analysis of gene islands involved in methanopterin-linked C1 transfer reactions reveals new functions and provides evolutionary insights. J Bacteriol 187:4607–4614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Vuilleumier S, Khmelenina VN, Bringel F, Reshetnikov AS, Lajus A, Mangenot S, Rouy Z, Op den Camp HJ, Jetten MS, Dispirito AA, Dunfield P, Klotz MG, Semrau JD, Stein LY, Barbe V, Medigue C, Trotsenko YA, Kalyuzhnaya MG (2012) Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. J Bacteriol 194:551–552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Boden R, Cunliffe M, Scanlan J, Moussard H, Kits KD, Klotz MG, Jetten MS, Vuilleumier S, Han J, Peters L, Mikhailova N, Teshima H, Tapia R, Kyrpides N, Ivanova N, Pagani I, Cheng JF, Goodwin L, Han C, Hauser L, Land ML, Lapidus A, Lucas S, Pitluck S, Woyke T, Stein L, Murrell JC (2011) Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09. J Bacteriol 193:7001–7002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Aizenman E, Engelberg-Kulkat H, Glaser G (1996) An Escherichia coli chromosomal "addiction module" regulated by 3′,5′-bispyrophosphate: a model for programmed bacterial cell death and differentiation. Proc Natl Acad Sci USA 93:6059–6063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Katsuhiko K, Hanaoka F, Burley S (2003) Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition. Mol Cell 11:875–884

    Article  Google Scholar 

  19. Roslev P, King GM (1995) Aerobic and anaerobic starvation metabolism in methanotrophic bacteria. Appl Environ Microbiol 61:1563–1570

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

This work was supported by Department of Biotechnology under the DBT BioCARe programme (BT/BioCARe/06/840/2012) sanctioned to M. C. R and fellowship sanctioned to P. S. P. is acknowledged. CSIR research fellowship to Preeti Arora and Soham Pore is sincerely acknowledged.

Nucleotide sequence accession number

The draft genome sequence of Methylococcaceae bacterium strain Sn10-6 is deposited in the GenBank database under the accession number LAJX00000000.1 and the bioproject is registered as PRJNA278928.

Author information

Authors and Affiliations

  1. MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India

    Monali C. Rahalkar, Pranitha S. Pandit, Prashant K. Dhakephalkar, Soham Pore, Preeti Arora & Neelam Kapse

Authors
  1. Monali C. Rahalkar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pranitha S. Pandit
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prashant K. Dhakephalkar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Soham Pore
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Preeti Arora
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Neelam Kapse
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Monali C. Rahalkar.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Rahalkar, M.C., Pandit, P.S., Dhakephalkar, P.K. et al. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field. Microb Ecol 71, 519–523 (2016). https://doi.org/10.1007/s00248-015-0699-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-015-0699-z

Keywords

Search

Navigation