Succession and phylogenetic profile of methanogenic archaeal communities during the composting process of rice straw estimated by PCR-DGGE analysis

References

• Achenbach , L and Woese , C . 1995 . “ 16S and 23S rRNA-like primers ” . In Archaea: A Laboratory Manual , Edited by: Robb , FT . 521 – 523 . New York : Cold Spring Harbor Laboratory Press .
   Google Scholar
• Asakawa , S , Akagawa-Matsushita , M , Koga , Y and Hayano , K . 1998 . Communities of methanogenic bacteria in paddy field soils with long-term application of organic matter . Soil Biol. Biochem. , 30 : 299 – 303 .
   Web of Science ®Google Scholar
• Cahyani , VR , Matsuya , K , Asakawa , S and Kimura , M . 2003 . Succession and phylogenetic composition of bacterial communities responsible for the composting process of rice straw estimated by PCR-DGGE analysis . Soil Sci. Plant Nutr. , 49 : 619 – 630 .
   Web of Science ®Google Scholar
• Cahyani , VR , Matsuya , K , Asakawa , S and Kimura , M . Succession and phylogenetic profile of eukaryotic communities in the composting process of rice straw estimated by PCRDGGE analysis . Biol. Fertil. Soils , (in press)
   Web of Science ®Google Scholar
• Cahyani , YR , Watanabe , A , Matsuya , K , Asakawa , S and Kimura , M . 2002 . Succession of microbiota estimated by phospholipid fatty acid analysis and changes in organic constituents during the composting process of lice straw . Soil Sci. Plant Nutr. , 48 : 735 – 743 .
   Web of Science ®Google Scholar
• Chin , KJ , Lukow , T , Stubner , S and Conrad , R . 1999 . Structure and function of the methanogenic archaeal community in stable cellulose-degrading enrichment cultures at two different temperatures (15 and 30°C) . FEMS Microbial. Ecol. , 30 : 313 – 326 .
   PubMed Web of Science ®Google Scholar
• Corton , TM , Bajita , JB , Grospe , FS , Pamplona , RR , Asis , CA,Wassmann R , Lantin , RS and Buendia , LV . 2000 . Methane emission from irrigated and intensively managed rice fields in central Luzon (Philippines) . Nutr. Cycl. Agroecasyst. , 58 : 37 – 53 .
   Web of Science ®Google Scholar
• Derikx , PJL , de , Jong GAH , Op , den Camp HJM , van , der Drift C , van Griensven , LJLD and Vogels , GD . 1989 . Isolation and charactelization of thermophilic methanogenic bacteria from mushroom compost . FEMS Microbiol. Ecol. , 62 : 251 – 258 .
   Web of Science ®Google Scholar
• Derikx , PJL , Op , den Camp HJM , Bosch , WPGM , Vogels , GD , Gerrits , JPG and van Griensven , LJLD . 1988 . Production of methane during preparation of mushroom compost . Meded. Fac. Landbouwwet. Rijksuniv. Gent , 53 : 1727 – 1732 .
   Google Scholar
• Egert , M , Wagner , B , Lemke , T , Bmne , A and Friedrich , MW . 2003 . Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnada ephippiata (Coleoptera: Scarabaeidae) . Appl. Environ. Microbiol. , 69 : 6659 – 6668 .
   PubMed Web of Science ®Google Scholar
• Eleazer , WE , Odie , WS , Wang , YS and Barlaz , MA . 1997 . Biodegradability of municipal solid waste components in laboratory-scale landfills . Environ. Sci. Technol. , 31 : 911 – 917 .
   Web of Science ®Google Scholar
• Finstein , MS and Mon-is , ML . 1975 . “ Microbiology of municipal solid waste composting ” . In Advances in Applied Microbiology , Edited by: Perlman , D . Vol. 19 , 113 – 153 . New York : Academic Press Inc. .
   Google Scholar
• Großkopf , R , Stubner , S and Liesack , W . 1998 . Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms . Appl. Environ. Microbiol. , 64 : 4983 – 4989 .
   PubMed Web of Science ®Google Scholar
• Hellmann , B , Zelles , L , Palojarvi , A and Bai , Q . 1997 . Emission of climate-relevant trace gases and succession of microbial communities during open-windrow composting . Appl. Environ. Microbiol. , 63 : 1011 – 1018 .
   PubMed Web of Science ®Google Scholar
• Lopez-Real , JM and Baptista , M . 1996 . A preliminary comparative study of three manure composting systems and their influence on process parameters and methane emissions . Compost Sci. Util. , 4 : 71 – 82 .
   Web of Science ®Google Scholar
• Lueders , T and Friedlich , M . 2000 . Archaeal population dynamics during sequential reduction processes in rice field soil . Appl. Environ. Microbiol. , 66 : 2732 – 2742 .
   PubMed Web of Science ®Google Scholar
• Miura , Y . 2000 . Studies on the current status of methane emission from Japanese rice fields and the rational management of rice straw for mitigating methane emission, Ph.D thesis , Japan : Nagoya University .
   Google Scholar
• Muyzer , G , Brikhoff , T , Nubel , U , Santegoeds , C , Chafer , H and Wawer , C . 1998 . Denaturing gradient gel electrophoresis (DGGE) in microbial ecology . Mol. Microb. Ecol. Manual , 3.4.4 : 1 – 27 .
   Google Scholar
• Øvreåls , L , Forney , L , Daae , FL and Torsvik , V . 1997 . Distribution of bacterioplankton in meromictic lake Srelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA . Appl. Environ. Microbiol. , 63 : 3367 – 3373 .
   PubMed Web of Science ®Google Scholar
• Ramakrishnan , B , Lueders , T , Dunfield , PF , Conrad , R and Friedrich , MW . 2001 . Archaeal community structures in rice soils from different geographical regions before and after initiation of methane production . FEMS Microbial. Ecol. , 37 : 175 – 186 .
   Web of Science ®Google Scholar
• Rivard , CJ and Smith , PH . 1982 . Isolation and characterization of a thennophilic marine methanogenic bacterium, Methanogenium thermophilicum sp. nov . Int. J. Syst. Bacteriol. , 32 : 430 – 436 .
   Google Scholar
• Sommer , SG and Moller , HB . 2000 . Emission of greenhouse gases during composting of deep litter from pig production effect of straw content . J. Agric. Sci. , 134 : 327 – 335 .
   Web of Science ®Google Scholar
• Wasserfallen , A , Nailing , J , Pfister , P , Reeve , J and Conway , de Macario E . 2000 . Phylogenetic analysis of 18 thennophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermabacter thermoautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov . Int. J. Syst. Evol. Microbiol. , 50 : 43 – 53 .
   PubMed Web of Science ®Google Scholar
• Watanabe , T , Asakawa , S , Nakamura , A , Nagaoka , K and Kimura , M . 2004 . DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil . FEMS Microbial. Lett. , 232 : 153 – 163 .
   PubMed Web of Science ®Google Scholar
• Yagi , K and Minami , K . 1990 . Effect of organic matter application on methane emission from some Japanese paddy fields . Soil Sci. Plant Nutr. , 36 : 599 – 610 .
   Web of Science ®Google Scholar
• Zeman , C , Depken , D and Rich , M . 2002 . Literature review: Research on how the composting process impacts greenhouse gas emissions and global warming . Compost Sci. Util. , 10 : 72 – 86 .
   Web of Science ®Google Scholar