Phylogenetic diversity of Fe(III)-reducing microorganisms in rice paddy soil: enrichment cultures with different short-chain fatty acids as electron donors

Microbial ferric iron reduction is an important biogeochemical process in nonsulfidogenic anoxic environments, yet the structure of microbial communities involved is poorly understood because of the lack of a functional gene marker. Here, with ferrihydrite as the iron source, we characterized the potential Fe(III)-reducing bacteria from the paddy soil in the presence of different short-chain fatty acids, formate, acetate, propionate, pyruvate, succinate, and citrate. Enrichment culture was used to characterize the potential Fe(III)-reducing bacteria in the present study. Clone library and terminal restriction fragment length polymorphism (T-RFLP) analyses of bacterial 16S rRNA gene sequence fragments were conducted to reveal the bacterial community structure. T-RFLP and cloning/sequence analysis showed that Firmicutes were the predominant phylotype in all the enrichment cultures (more than 81% of total peak height, more than 75% of all clones), whereas Geobacter spp. represented a small fraction of the bacterial community. Specifically, distinct bacterial families in the phylum Firmicutes were enriched depending on the short-chain fatty acid amended. Clostridium spp. were the predominant microorganisms in pyruvate treatment, while both Bacillus and Clostridium were enriched in formate, acetate, and propionate treatments. Sequences related to Veillonellaceae and Alkaliphilus were predominant in succinate and citrate treatment, respectively. The results indicated Fe(III)-reducing microorganisms in rice paddy soil are phylogenetically diverse. Besides the well-known Geobacter species, Firmicutes-related Fe(III)-reducing bacteria might also be an important group of Fe(III) reducers in paddy soil. To confirm the populations which play an important role in situ, further studies with culture-independent mRNA-based analysis are needed.