Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

FEMS Microbiology Ecology

Volumn 48, Issue 2, 2004, Pages 179-186

  Lu, Yahai ^a,c   Murase, Jun ^a   Watanabe, Akira ^a   Sugimoto, Atsuko ^b   Kimura, Makoto ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

Microbial community; Phospholipid fatty acids; Plant photosynthesis; Rice soil; Stable isotope labeling

Indexed keywords

CARBON; CARBON DIOXIDE; FATTY ACID;

CARBON CYCLE; CARBON FLUX; COMMUNITY DYNAMICS; MICROBIAL COMMUNITY; PHOTOSYNTHESIS; RICE; SOIL MICROORGANISM; WETLAND;

ARTICLE; BIOMASS; CARBON CYCLING; CARBON FIXATION; CONTROLLED STUDY; DECOMPOSITION; MICROBIAL ACTIVITY; MICROFLORA; MOLECULAR DYNAMICS; NONHUMAN; PHOTOSYNTHESIS; PHOTOTROPHIC BACTERIUM; PLANT GROWTH; PRIORITY JOURNAL; RHIZOSPHERE; RICE; SEASONAL VARIATION; SOIL; SOIL MICROFLORA; WETLAND;

BACTERIA; BIOMASS; CARBON; CARBON DIOXIDE; CARBON RADIOISOTOPES; ORYZA SATIVA; PHOSPHOLIPIDS; SOIL MICROBIOLOGY; STAINING AND LABELING; WETLANDS;

MICROBIOTA;

EID: 2142771702     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2004.01.004     Document Type: Article

References (41)

1. Lynch J.M., Whipps J.M. Substrate flow in the rhizosphere. Plant Soil. 129:1990;1-10
2. Hungate B.A., Holland E.A., Jackson R.B., Chapin F.S., Mooney H.A., Field C.B. The fate of carbon in grasslands under carbon dioxide enrichment. Nature. 388:1997;576-579
3. Hogberg P., Nordgren A., Buchmann N., Taylor A.F.S., Ekblad A., Hogberg M.N., Nyberg G., Ottosson-Lofvenius M., Read D.J. Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature. 411:2001;789-792
4. Kuzyakov Y. Separating microbial respiration of exudates from root respiration in non-sterile soils: a comparison of four methods. Soil Biol. Biochem. 34:2002;1621-1631
5. Dannenberg S., Conrad R. Effect of rice plants on methane production and rhizospheric metabolism in paddy soil. Biogeochemistry. 45:1999;53-71
6. Megonigal J.P., Whalen S.C., Tissue D.T., Bovard B.D., Albert D.B., Allen A.S. A plant-soil-atmosphere microcosm for tracing radiocarbon from photosynthesis through methanogenesis. Soil Sci. Soc. Am. J. 63:1999;665-671
7. 4 emitted to the atmosphere from paddy fields. J. Geophy. Res. 101:1996;21091-21097
8. 4 emissions from rice paddy fields. Proc. Natl. Acad. Sci. USA. 99:2002;12021-12024
9. Lu Y., Watanabe A., Kimura M. Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol. Fertil. Soils. 36:2002;136-142
10. 14C pulse chase. Biol. Fertil. Soils. 19:1995;280-286
11. 14C pulse-labeling of field-growth spring wheat: an evaluation of its use in rhizosphere carbon budget estimations. Soil Biol. Biochem. 26:1994;161-170
12. van Veen J.A., Merckx R., van de Geijn S.C. Plant and soil related controls of the low of carbon from roots through the soil microbial biomass. Plant Soil. 115:1989;179-188
13. Grosskopf R., Janssen P.E., Liesack W. Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms. Appl. Environ. Microbiol. 64:1998;4983-4989
14. Muraoka Y., Hamakawa E., Toyota K., Kimura M. Observation of microbial colonization on the surface of rice roots along with their development and degradation. Soil Sci. Plant Nutr. 46:2000;491-502
15. Yang C.H., Crowley D.E. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 66:2000;345-351
16. Kowalchuk G.A., Buma D.S., de Boer W., Klinkhamer P.G.L., van Veen J.A. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Anton. Leeuw. Int. J.G. 81:2002;509-520
17. Montealegre C.M., vanKessel C., Russelle M.P., Sadowsky M.J. Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide. Plant Soil. 243:2002;197-207
18. Söderberg K.H., Olsson P.A., Bååth E. Structure and activity of the bacterial community in the rhizosphere of different plant species and the effect of arbuscular mycorrhizal colonization. FEMS Microbiol. Ecol. 40:2002;223-231
19. Steer J., Harris J.A. Shifts in the microbial community in rhizosphere and non-rhizosphere soils during the growth of Agrostis stolonifera. Soil Biol. Biochem. 32:2000;869-878
20. Boschker H.T.S., de Brouwer J.F.C., Cappenberg T.E. The contribution of macrophyte derived organic matter to microbial biomass in salt marsh sediments: stable carbon-isotope analysis of microbial biomarkers. Limnol. Oceanogr. 44:1999;309-319
21. Boschker H.T.S., Wielemaker A., Schaub B.E.M., Holmer M. Limited coupling of macrophyte production and bacterial carbon cycling in the sediments of Zostera spp. meadows. Mar. Ecol. Prog. Ser. 203:2000;181-189
22. Butler J.L., Williams M.A., Bottomley P.J., Myrold D.D. Microbial community dynamics associated with rhizosphere carbon flow. Appl. Environ. Microbiol. 69:2003;6793-6800
23. Lu, Y., Watanabe, A., Kimura, M. (2004) Contribution of plant photosynthates to dissolved organic carbon in a flooded rice soil. Biogeochemistry, in press
24. Lu, Y., Watanabe, A., Kimura, M. (2002). Input and distribution of photosynthesized carbon in a flooded rice soil. Glob. Biogeochem. Cycles 16, article 1085
25. Magid J., Gorissen A., Giller K.E. In search of the elusive active fraction of soil organic matter: three size-density fractionation methods for tracing the fate of homogeneously 14C-labeled plant material. Soil Biol. Biochem. 28:1996;89-99
26. White D.C., Davis W.M., Nickles J.S., Kind J.D., Bobbie R.J. Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia. 40:1979;51-62
27. Okabe A., Toyota K., Kimura M. Seasonal variations of phospholipid fatty acid composition in the floodwater of a Japanese paddy field under a long-term fertilizer trial. Soil Sci. Plant Nutr. 46:2000;177-188
28. Rieley G. Derivation of organic compounds prior to gas chromatographic-combustion-isotope ratio spectrometric analysis: identification of isotope fractionation processes. Analyst. 119:1994;915-919
29. Boschker H.T.S., Middelburg J.J. Stable isotope and biomarkers in microbial ecology. FEMS Microbiol. Ecol. 40:2002;85-95
30. Gray N.D., Head I.M. Linking genetic identity and function in communities of uncultured bacteria. Environ. Microbiol. 3:2001;481-492
31. Bai Q., Gattinger A., Zelles L. Characterization of microbial consortia in paddy rice soil by phospholipid analysis. Microbiol. Ecol. 39:2000;273-281
32. Minoda T., Kimura M. Contribution of photosynthesized carbon to the methane emitted from paddy fields. Geophys. Res. Lett. 21:1994;2007-2010
33. Lovell C.R., Bagwell C.E., Czako M., Marton L., Piceno Y.M., Ringelberg D.B. Stability of a rhizosphere microbial community exposed to natural and manipulated environmental variability. FEMS Microbiol. Ecol. 38:2001;69-76
34. Radajewski S., Ineson P., Parekh N., Murrell J.C. Stable-isotope probing as a tool in microbial ecology. Nature. 403:2000;646-649
35. Chin K.J., Hahn D., Hengstmann U., Liesack W., Janssen P.H. Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl. Environ. Microbiol. 65:1999;5042-5049
36. Hengstmann U., Chin K.J., Janssen P.H., Liesack W. Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil. Appl. Environ. Microbiol. 65:1999;5050-5058
37. Lüdemann H., Arth I., Liesack W. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Appl. Environ. Microbiol. 66:2000;754-762
38. Weber S., Stubner S., Conrad R. Bacterial populations colonizing and degrading rice straw in anoxic paddy soil. Appl. Environ. Microbiol. 67:2001;1318-1327
39. O'Leary W.M., Wilkinson S.G. Gram-positive bacteria. Ratledge C., Wilkinson S.G. Microbial Lipids. 1988;117-185 Academic Press, London
40. Wilkinson S.G. Gram-negative bacteria. Ratledge C., Wilkinson S.G. Microbial Lipids. vol. 1:1988;299-489 Academic Press, London
41. Reichardt W., Mascarina G., Padre B., Doll J. Microbial communities of continuously cropped, irrigated rice fields. Appl. Environ. Microbiol. 63:1997;233-238