Structure and diversity of Gram-negative sulfate-reducing bacteria on riceroots

Specific PCR assays were used to amplify the 16S rRNA genes of the Desulfob acteriaceae and the Desulfovibrionaceae from extracted environmental DNA fr om rice roots. 16S rDNA-based community patterns of the Desulfobacteriaceae were generated via terminal restriction fragment length polymorphism analy sis from rice roots and compared with bulk soil. The molecular fingerprints showed no significant difference between rice roots and bulk soil. but cha nges during the vegetation period. 16S rDNA clone libraries and sequencing showed that the predominant terminal restriction fragments represented dist inct phylogenetic groups. The 16S rDNA clone sequences of the Desulfobacter iaceae fell in the phylogenetic radiation of Desulfonema and Desulfosarcina or grouped within the Desulfohabdus-Syntrophobacter assemblage. Three of t he latter sequences were closely affiliated with the MPN isolate EZ-2C2 fro m rice roots. All Desulfovibrionaceae 16S rDNA clone sequences, with one ex ception. were affiliated with the MPN isolate FI-7b from rice roots. The cl ustering of the clone sequences and the close phylogenetic affiliation with isolates from MPN enrichments from the same habitat in two cases indicated that these sequence clusters may represent predominant Gram-negative sulfa te reducers on rice roots. Quantification of the bacterial abundances was a ccomplished by rRNA dot blot hybridization. In total the Gram-negative sulf ate reducers accounted for approximately 2-3% of the total rRNA content. Th e relative rRNA abundance of the Desulfobacteriaceae was, at 1.4%, higher t han that of the Desulfovibrionaceae crf (0.5%). (C) 2001 Federation of Euro pean Microbiological Societies. Published by Elsevier Science B.V. All righ ts reserved.