1887
  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 67, Issue 11
  5. Article

f Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai

PDF
1.60 MB
HTML
75.60 Kb
  • Authors: Katharina Frindte1​ ,  Sarah A. Maarastawi1​ ,  André Lipski2​ ,  Joachim Hamacher3​ , Claudia Knief1​
    • VIEW AFFILIATIONS
    • 1​ 1​Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany 2​ 2​Food Microbiology and Hygiene, Institute of Nutritional and Food Sciences, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany 3​ 3​Plant Diseases and Crop Protection, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 9, 53115 Bonn, Germany
  • *Correspondence: Claudia Knief [email protected]
  • First Published Online: 06 October 2017, International Journal of Systematic and Evolutionary Microbiology 67: 4507-4514, doi: 10.1099/ijsem.0.002319
  • Subject: New taxa - Proteobacteria
  • Received:
  • Accepted:
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai, Page 1 of 1

| /docserver/preview/fulltext/ijsem/67/11/4507_ijsem002319-1.gif

  • Three gammaproteobacterial methanotrophic strains (73a, 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73a contains high quantities of C16 : 1ω5c. 16S rRNA gene sequence analyses showed that strains 114 and 175 are most closely related to Methylomagnum ishizawai (≥99.6 % sequence identity). Strain 73a is representing a new genus within the family Methylococcaceae , most closely related to Methylococcus capsulatus (94.3 % sequence identity). Phylogenetic analysis of the PmoA sequence indicates that strain 73a represents rice paddy cluster I (RPCI), which has almost exclusively been detected in rice ecosystems. The G+C content of strain 73a is 61.0 mol%, while strains 114 and 175 have a G+C content of 63.3 mol%. Strain 73a (=LMG 29185, =VKM B-2986) represents the type strain of a novel species and genus, for which the name Methyloterricola oryzae gen. nov., sp. nov. is proposed and a description is provided. Strains 175 (=LMG 28717, VKM B-2989) and 114 are members of the species Methylomagnum ishizawai . This genus was so far only represented by one isolate, so an amended description of the species is given.

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and pmoA gene sequences of strain 114 are KY129802 and KY129803, respectively. Draft genome sequence data of strains 73a and 175 are available under the accession numbers JYNS00000000.1 and FXAM00000000.1.

  • One supplementary figure is available with the online Supplementary Material.

© 2017 IUMS | Published by the Microbiology Society

  • 1. Knief C. Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front Microbiol 2015; 6: 1346 [CrossRef] [PubMed]
    [Google Scholar]
  • 2. Conrad R. Microbial ecology of methanogens and methanotrophs. Adv Agron 2007; 96: 1– 63 [Crossref]
    [Google Scholar]
  • 3. Frenzel P. Plant-associated methane oxidation in rice fields and wetlands. Adv Microb Ecol 2000; 16: 85– 114
    [Google Scholar]
  • 4. Krüger M, Frenzel P, Conrad R. Microbial processes influencing methane emission from rice fields. Glob Chang Biol 2001; 7: 49– 63 [CrossRef]
    [Google Scholar]
  • 5. Yoshida N, Iguchi H, Yurimoto H, Murakami A, Sakai Y. Aquatic plant surface as a niche for methanotrophs. Front Microbiol 2014; 5: 30 [CrossRef] [PubMed]
    [Google Scholar]
  • 6. Lüke C, Krause S, Cavigiolo S, Greppi D, Lupotto E et al. Biogeography of wetland rice methanotrophs. Environ Microbiol 2010; 12: 862– 872 [CrossRef] [PubMed]
    [Google Scholar]
  • 7. Heyer J, Galchenko VF, Dunfield PF. Molecular phylogeny of type II methane-oxidizing bacteria isolated from various environments. Microbiology 2002; 148: 2831– 2846 [CrossRef] [PubMed]
    [Google Scholar]
  • 8. Ogiso T, Ueno C, Dianou D, Huy TV, Katayama A et al. Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field. Int J Syst Evol Microbiol 2012; 62: 1832– 1837 [CrossRef] [PubMed]
    [Google Scholar]
  • 9. Geymonat E, Ferrando L, Tarlera SE. Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 2011; 61: 2568– 2572 [CrossRef] [PubMed]
    [Google Scholar]
  • 10. Khalifa A, Lee CG, Ogiso T, Ueno C, Dianou D et al. Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere. Int J Syst Evol Microbiol 2015; 65: 3527– 3534 [CrossRef] [PubMed]
    [Google Scholar]
  • 11. Pandit PS, Rahalkar MC, Dhakephalkar PK, Ranade DR, Pore S et al. Deciphering community structure of methanotrophs dwelling in rice rhizospheres of an Indian rice field using cultivation and cultivation-independent approaches. Microb Ecol 2016; 71: 634– 644 [CrossRef] [PubMed]
    [Google Scholar]
  • 12. Whittenbury R, Phillips KC, Wilkinson JF. Enrichment, isolation and some properties of methane-utilizing bacteria. J Gen Microbiol 1970; 61: 205– 218 [CrossRef] [PubMed]
    [Google Scholar]
  • 13. Knief C, Lipski A, Dunfield PF. Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 2003; 69: 6703– 6714 [CrossRef] [PubMed]
    [Google Scholar]
  • 14. Knief C, Frances L, Vorholt JA. Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb Ecol 2010; 60: 440– 452 [CrossRef] [PubMed]
    [Google Scholar]
  • 15. Cain AJ. The use of nile blue in the examination of lipoids. Q J Microsc Sci 1947; 88: 383– 392
    [Google Scholar]
  • 16. Günther S, Trutnau M, Kleinsteuber S, Hause G, Bley T et al. Dynamics of polyphosphate-accumulating bacteria in wastewater treatment plant microbial communities detected via DAPI (4',6'-diamidino-2-phenylindole) and tetracycline labeling. Appl Environ Microbiol 2009; 75: 2111– 2121 [CrossRef] [PubMed]
    [Google Scholar]
  • 17. Karnovsky MJ. A formaldehyde-glutaraldehyde fixative of high osmolality for use in electron microscopy. J Cell Biol 1965; 27: A1-149A
    [Google Scholar]
  • 18. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44: 992– 993 [PubMed]
    [Google Scholar]
  • 19. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4: 770– 773 [CrossRef] [PubMed]
    [Google Scholar]
  • 20. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef] [PubMed]
    [Google Scholar]
  • 21. Frindte K, Kalyuzhnaya MG, Bringel F, Dunfield PF, Jetten MSM et al. Draft genome sequences of two gammaproteobacterial methanotrophs isolated from rice ecosystems. Genome Announc 2017; 5: e00526-17 [CrossRef] [PubMed]
    [Google Scholar]
  • 22. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28: 1823– 1829 [CrossRef] [PubMed]
    [Google Scholar]
  • 23. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kiado; 1990; pp. 199– 204
    [Google Scholar]
  • 24. Wiertz R, Schulz SC, Müller U, Kämpfer P, Lipski A. Corynebacterium frankenforstense sp. nov. and Corynebacterium lactis sp. nov., isolated from raw cow milk. Int J Syst Evol Microbiol 2013; 63: 4495– 4501 [CrossRef] [PubMed]
    [Google Scholar]
  • 25. Choi DW, Kunz RC, Boyd ES, Semrau JD, Antholine WE et al. The membrane-associated methane monooxygenase (pMMO) and pMMO-NADH:quinone oxidoreductase complex from Methylococcus capsulatus Bath. J Bacteriol 2003; 185: 5755– 5764 [CrossRef] [PubMed]
    [Google Scholar]
  • 26. Hanson RS, Hanson TE. Methanotrophic bacteria. Microbiol Rev 1996; 60: 439– 471 [PubMed]
    [Google Scholar]
  • 27. Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 2008; 63: 183– 229 [CrossRef] [PubMed]
    [Google Scholar]
  • 28. Danilova OV, Suzina NE, van de Kamp J, Svenning MM, Bodrossy L et al. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. Isme J 2016; 10: 2734– 2743 [CrossRef] [PubMed]
    [Google Scholar]
  • 29. Bowman JP, Skerratt JH, Nichols PD, Sly LI. Phospholipid fatty acid and lipopolysaccharide fatty acid signature lipids in methane-utilizing bacteria. FEMS Microbiol Lett 1991; 85: 15– 22 [CrossRef]
    [Google Scholar]
  • 30. Jia Z, Kikuchi H, Watanabe T, Asakawa S, Kimura M. Molecular identification of methane oxidizing bacteria in a Japanese rice field soil. Biol Fertil Soils 2007; 44: 121– 130 [CrossRef]
    [Google Scholar]
  • 31. Shrestha M, Abraham WR, Shrestha PM, Noll M, Conrad R. Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids. Environ Microbiol 2008; 10: 400– 412 [CrossRef] [PubMed]
    [Google Scholar]
  • 32. Hoefman S, van der Ha D, Iguchi H, Yurimoto H, Sakai Y et al. Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 2014; 64: 2100– 2107 [CrossRef] [PubMed]
    [Google Scholar]
  • 33. Bowman JP, Sly LI, Nichols PD, Hayward AC. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 1993; 43: 735– 753 [CrossRef]
    [Google Scholar]
  • 34. Bodrossy L, Holmes EM, Holmes AJ, Kovács KL, Murrell JC. Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch Microbiol 1997; 168: 493– 503 [CrossRef] [PubMed]
    [Google Scholar]
http://sgm.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002319
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002319
2017-10-06
2019-03-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4507.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002319&mimeType=html&fmt=ahah

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error