Novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosms

摘要: Because excised, washed roots of rice (Oryza sativa) immediately produce CH4 when they are incubated under anoxic conditions (P. Frenzel and U. Bosse, FEMS Microbiol. Ecol. 21:25–36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on plants. Archaeal small-subunit rRNA-encoding genes were amplified directly from total root DNA by PCR then cloned. Thirty-two archaeal (ARR) gene clones randomly selected, primary structures ca. 750 nucleotide sequence positions compared. Only 10 environmental sequences affiliated with known methanogens; 5 Methanosarcina spp., Methanobacterium spp. The remaining 22 ARR formed four distinct lineages (rice clusters I through IV) which not closely related any cultured member Archaea. Rice II clades within phylogenetic radiation orders “Methanosarcinales” Methanomicrobiales. cluster was novel, obtained bog peat in northern England. III occurred same branch as Thermoplasma acidophilum marine group but only distantly these taxa. IV deep-branching crenarchaeotal assemblage that clone pGrfC26, an recovered temperate marsh environment. use domain-specific oligonucleotide probe fluorescent situ hybridization analysis revealed viable members Archaea surfaces roots. In addition, describe novel euryarchaeotal main line descent, designated V, detected paddy soil. These results indicate there is astonishing richness diversity surrounding