Cross-feeding of methane carbon among bacteria on rice roots revealed by DNA-stable isotope probing

Environmental Microbiology Reports

Volumn 1, Issue 5, 2009, Pages 355-361

  Qiu, Qiongfen ^a,b   Conrad, Ralf ^b   Lu, Yahai ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); METHYLOCOCCACEAE; METHYLOCYSTACEAE; METHYLOPHILALES; PROTEOBACTERIA; SPHINGOMONADALES;

EID: 77953026721     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2009.00045.x     Document Type: Article

References (28)

1. Ando, T., Yoshida, S., and Nishiyama, I. (1983) Nature of oxidizing power of rice roots. Plant Soil 72: 57-71.
2. Armstrong, W. (1971) Radial oxygen losses from intact rice roots as affected by distance from the apex, respiration and waterlogging. Physiol Plantarum 25: 192-197.
3. Bodelier, P.L.E., and Laanbroek, H.J. (2004) Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiol Ecol 47: 265-277.
4. Bodelier, P.L.E., Roslev, P., Henckel, T., and Frenzel, P. (2000) Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots. Nature 403: 421-424.
5. Bosse, U., and Frenzel, P. (1997) Activity and distribution of methane-oxidizing bacteria in flooded rice soil microcosms and in rice plants (Oryza sativa). Appl Environ Microbiol 63: 1199-1207.
6. Brayton, K.A., Kappmeyer, L.S., Herndon, D.R., Dark, M.J., Tibbals, D.L., Palmer, G.H., et al. (2005) Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. Proc Natl Acad Sci USA 102: 844-849.
7. Cebron, A., Bodrossy, L., Stralis-Pavese, N., Singer, A.C., Thompson, I.P., Prosser, J.I., and Murrell, J.C. (2007) Nutrient amendments in soil DNA stable isotope probing experiments reduce the observed methanotroph diversity. Appl Environ Microbiol 73: 798-807.
8. 4 oxidation-the activity of bacteria, their distribution and the microenvironment. Soil Biol Biochem 30: 1903-1916.
9. 13C-labelled methane. Biogeochemistry 64: 355-372.
10. Haichar, F.Z., Marol, C., Berge, O., Rangel-Castro, J.I., Prosser, J.I., Balesdent, J., et al. (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221-1230.
11. Hanson, R.S., and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol Rev 60: 439-471.
12. Henckel, T., Friedrich, M., and Conrad, R. (1999) Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl Environ Microbiol 65: 1980-1990.
13. 4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ Microbiol 2: 666-679.
14. Ikenaga, M., Asakawa, S., Muraoka, Y., and Kimura, M. (2003) Bacterial communities associated with nodal roots of rice plants along with the growth stages: estimation by PCR-DGGE and sequence analyses. Soil Sci Plant Nutr 49: 591-602.
15. Inagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., et al. (2004) Characterization of C-1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70: 7445-7455.
16. Lu, Y., Lueders, T., Friedrich, M.W., and Conrad, R. (2005) Detecting active methanogenic populations on rice roots using stable isotope probing. Environ Microbiol 7: 326-336.
17. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
18. Lueders, T., Wagner, B., Claus, P., and Friedrich, M.W. (2004) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil. Environ Microbiol 6: 60-72.
19. Macalady, J.L., McMillan, A.M.S., Dickens, A.F., Tyler, S.C., and Scow, K.M. (2002) Population dynamics of type I and II methanotrophic bacteria in rice soils. Environ Microbiol 4: 148-157.
20. Minami, K., and Neue, H.U. (1994) Rice paddies as a methane source. Climatic Change 27: 13-26.
21. Murase, J., and Frenzel, P. (2007) A methane-driven microbial food web in a wetland rice soil. Environ Microbiol 4: 3025-3034.
22. Murase, J., and Frenzel, P. (2008) Selective grazing of methanotrophs by protozoa in a rice field soil. FEMS Microbiol Ecol 65: 408-414.
23. Noll, M., Frenzel, P., and Conrad, R. (2008) Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing. FEMS Microbiol Ecol 65: 125-132.
24. Op den Camp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R., Hynes, A., Schouten, S., et al. (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep. (in press) doi:10. 1111/j.1758-2229.2009.00022.x.
25. Qiu, Q., Noll, M., Abraham, W.R., Lu, Y., and Conrad, R. (2008) Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ. ISME J 2: 602-614.
26. Shrestha, M., Abraham, W.R., Shrestha, P.M., Noll, M., and Conrad, R. (2008) 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 10: 400-412.
27. Wassmann, R., Papen, H., and Rennenberg, H. (1993) Methane emission from rice paddies and possible mitigation strategies. Chemosphere 26: 201-217.
28. Wu, L., Ma, K., and Lu, Y. (2009) Rice roots select for type I methanotrophs in the rice field soil. Syst Appl Microbiol. doi:10.1016/j.syapm.2009.05.001.