Microbiota responsible for the decomposition of rice straw in a submerged paddy soil estimated from phospholipid fatty acid composition

References

• Amann , R.I. , Ludwig , W. and Schleifer , K.-H. 1995 . Phylogenetic identification and in situ detection of individual microbial cells without cultivation . Microbiol. Rev. , 59 : 143 – 169 .
   PubMedGoogle Scholar
• Aoki, S. 1996: http://aoki2.si.gunma-u.ac.jp/BlackBox/BlackBox.html
   Google Scholar
• Arao , T. , Okano , S. and Kanamori , T. 1998 . Analysis of the phospholipid fatty acids of upland light colored Andosol and the relationship among the size of biomass based on phospholipid fatty acid analysis, microscopical counts and chloroform fumigation-incubation . Jpn. J. Soil Sci. Plant Nutr. , 69 : 38 – 46 . (in Japanese with English summary)
   Google Scholar
• Bai , Q. , Gattinger , A. and Zelles , L. 2000 . Characterization of microbial consortia in paddy rice soil by phospholipid analysis . Microb. Ecol. , 39 : 273 – 281 .
   PubMed Web of Science ®Google Scholar
• Bligh , E.G. and Dyer , W.J. 1959 . A rapid method of total lipid extraction and purification . Can. J. BioChem. Physiol. , 37 : 911 – 917 .
   PubMedGoogle Scholar
• Barga , P. , Nilsson , M. and Tunlid , A. 1994 . Bacterial communities in peat in relation to botanical composition as revealed by phospholipid fatty acid analysis . Soil Biol. Biochem. , 26 : 841 – 848 .
   Web of Science ®Google Scholar
• Bossio , D.A. and Scow , K.M. 1998 . Impacts of carbon and flooding on soil microbial communities: Phospholipid fatty acid profiles and substrate utilization patterns . Microb. Ecol. , 35 : 265 – 278 .
   PubMed Web of Science ®Google Scholar
• Frostegård , A. , Petersen , S.D. , Bååth , E. and Nielsen , T.H. 1997 . Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses . Appl. Environ. Microbiol. , 63 : 2224 – 2231 .
   PubMed Web of Science ®Google Scholar
• Frostegård , A. , Tunlid , A. and Bååth , E. 1993 . Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals . Appl. Environ. Microbiol. , 59 : 3605 – 3617 .
   PubMed Web of Science ®Google Scholar
• Frostegård , A. , Tunlid , A. and Bååth , E. 1996 . Changes in microbial community structure during long-term incubation in two soils experimentally contaminated with metals . Soil Biol. Biochem. , 28 : 55 – 63 .
   Web of Science ®Google Scholar
• Guckert , J.B. , Antworth , C.P. , Nichols , P.D. and White , D.C. 1985 . Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments . FEMS Microbiol. Ecol. , 31 : 147 – 158 .
   Web of Science ®Google Scholar
• Guckert , J.B. , Hood , M.A. and White , D.C. 1986 . Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: Increases in the trans/cis ratio and proportion of cyclopropyl fatty acids . Appl. Environ. Microbiol. , 52 : 794 – 801 .
   PubMed Web of Science ®Google Scholar
• Haack , S.K. , Garchow , H. , Odelson , D.A. , Forney , L.J. and Klug , M.J. 1994 . Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities . Appl. Environ. Microbiol. , 60 : 2483 – 2493 .
   PubMed Web of Science ®Google Scholar
• Kimura , M. , Tanaka , N. , Wada , H. and Takai , Y. 1980 . Quantitative estimation of decomposition process of plant debris in the paddy field (Part I) . lpn. l. Soil Sci Plant Nutr. , 51 : 169 – 174 . (in Japanese)
   Google Scholar
• Kimura , M. and Tun , C.C. 1999 . Microscopic observation of the decomposition process ofleaf sheath of rice straw and colonizing microorganisms during the cultivation period of paddy rice . Soil Sci. Plant Nutr. , 45 : 427 – 437 .
   Web of Science ®Google Scholar
• Klamer , M. and Bååth , E. 1998 . Microbial community dynamics during composting of straw material studied using phospholipid fatty acid analysis . FEMS Microbiol. Ecol. , 27 : 9 – 20 .
   Web of Science ®Google Scholar
• Kroppenstedt , R.M. 1992 . “ The genus Nocardiopsis ” . In The Procaryotes , Edited by: Balows , A. , Triiper , H.G. , Dworkin , M. , Harder , W. and Schleifer , K.H. Vol. 2 , 1139 – 1156 . Berlin : Springer .
   Google Scholar
• Okabe , A. , Oike , H. , Toyota , K. and Kimura , M. 2000a . 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 : 177 – 188 .
   Web of Science ®Google Scholar
• Okabe , A. , Toyota , K. and Kimura , M. 2000b . Comparison of phospholipid fatty acid composition in floodwater and plow layer soil during the rice cultivation period in a Japanese paddy field . Soil Sci. Plant Nutr. , 46 : 893 – 904 .
   Web of Science ®Google Scholar
• Ratledge , C. and Wilkinson , S.G. 1988 . Microbial Lipids , Vol. 1 , 23 – 29 . London : Academic Press . 117-457, 699-794
   Google Scholar
• Reichardt , W. , Mascarina , G. , Padre , B. and Doll , L. 1997 . Microbial communities of continuously cropped, irrigated rice fields . Appl. Environ. Microbiol. , 63 : 233 – 238 .
   PubMed Web of Science ®Google Scholar
• Sass , R.L. , Fisher , F.M. , Harcombe , P.A. and Turner , F.T. 1991 . Mitigation of methane emissions from rice fields: Possible adverse effects of incorporated rice straw . Global Biogeochem. Cycles , 4 : 47 – 68 .
   Web of Science ®Google Scholar
• Shiga , H. , Ohyama , N. , Maeda , K. and Suzuki , M. 1985 . An evaluation of different organic materials based on their decomposition patterns in paddy soils . Bull. Natl. Agric. Res. Cent. , 5 : 1 – 19 . (in Japanese with English summary)
   Google Scholar
• Tun , C.C. and Kimura , M. 2000 . Microscopic observation of the decomposition process of leaf blade of rice straw and colonizing microorganisms in a Japanese paddy field soil during the cultivation period of paddy rice . Soil Sci. Plant Nutr. , 46 : 127 – 137 .
   Web of Science ®Google Scholar
• Watanabe , A. , Takeda , T. and Kimura , M. 1999 . Evaluation of origins of CH4 carbon emitted from rice paddies . J. Geophys. Res. , 104D : 23623 – 23629 .
   Web of Science ®Google Scholar
• Watanabe , A. , Yoshida , M. and Kimura , M. 1998 . Contribution ofrice straw carbon to CH4 emission from rice paddies using 13C-enriched rice straw . J. Geophys. Res. , 103D : 8237 – 8242 .
   Web of Science ®Google Scholar
• White , D.C. , Davis , W.M. , Nickels , J.S. , Kind , J.D. and Bobbie , R.J. 1979 . Determination of the sedimentary microbial biomass by extractable lipid phosphate . Oecologia , 40 : 51 – 62 .
   PubMed Web of Science ®Google Scholar
• Yoneyama , T. and Yoshida , T. 1977a . Decomposition of rice residue in tropical soils. I. Nitrogen uptake by rice plants from straw incorporated, fertilizer (ammonium sulfate) and soil . Soil Sci. Plant Nutr. , 23 : 33 – 40 .
   Google Scholar
• Yoneyama , T. and Yoshida , T. 1977b . Decomposition of rice residue in tropical soils. II. Immobilization of soil and fertilizer nitrogen by intact rice residue in soil . Soil Sci Plant Nutr. , 23 : 41 – 48 .
   Google Scholar
• Yoneyama , T. and Yoshida , T. 1977c . Decomposition of rice residue in tropical soils. III. Nitrogen mineralization of rice residue during its decomposition in soil . Soil Sci. Plant Nutr. , 23 : 175 – 183 .
   Google Scholar
• Zelles , L. 1999 . Fatty acid patterns of phospholipids and Iipopolysaccharides in the characterization of microbial communities in soil: a review . Biol. Ferti!. Soils , 29 : 111 – 129 .
   Web of Science ®Google Scholar