Phylogeny of numerically abundant culturable anaerobic bacteria associated with degradation of rice plant residue in Japanese paddy field soil

Abstract

Culturable anaerobic bacterial populations on rice plant residue (straw and stubble with roots) in paddy field soil were found on the order of 10(9) CFU (colony-forming units) (g dry weight of plant residue)(-1), and the percentages of spores were usually less than 1% of the total anaerobes. Anaerobic bacteria were isolated from each sample by picking up colonies on the roll tube agar used for the enumeration. The phylogenetic analysis of 47 isolates based on 16S rRNA gene sequences revealed that the composition of dominant culturable anaerobic bacteria on rice plant residue was rather simple. The most dominant group was closely related to the Cellulomonas species in the Actinobacteria phylum and accounted for more than 60% of the isolates for most of the samples. The second major group was also affiliated with the Actinobacteria phylum and tentatively named the 'propionate-producing Actinobacteria group' because the strains in the group commonly produced propionate. Strains in the third group, the 'Prevotella-like group', were Gram-negative, strictly anaerobic rods and placed in the Bacteroides phylum with 16S rRNA gene similarities of 86-92% to the closest relatives. Some other strains belonging to Betaproteobacteria and the clostridial group were also isolated. Most of the strains affiliated to the clostridial group were isolated from the heat-treated samples. Some phenotypic characteristics of representative strains of each group are also described.