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

Abstract

Purpose 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. Materials and methods 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. Results and discussion 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 shortchain 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. Conclusions The results indicated Fe(III)-reducing microorganisms in rice paddy soil are phylogenetically diverse. Besides the well-known Geobacter species, Firmicutesrelated 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.

Geochemical Control on Uranium(IV) Mobility in a Mining-Impacted Wetland

“…represents 0.07%, 0.42%, and 0.92% of the microbial community at 0−5 cm and 20−25 cm at spot B and at 0−15 cm at spot C, respectively. Additionally, Clostridium spp., known to reduce Fe(III) through fermentation 26 or respiration, 27 is also found at 100−105 cm at spot B (0.61%). Moreover, iron-oxidizing bacteria from the Crenothrix genus 28 are identified in samples from spot B at 0−5 cm (1.4%) and at 20−25 cm (3.95%) and from spot C at 0−15 cm (0.33%) (Figure 4).…”

Biogas slurry application elevated arsenic accumulation in rice plant through increased arsenic release and methylation in paddy soil

“…As a class one carcinogen, arsenic in the soil can present a significant risk to humans through the food chain after its high uptake into rice plants. It has been estimated that rice is the major dietary source of As for populations with rice as the staple food (Meharg and Rahman 2003;Mondal and Polya 2008;Zhu et al 2008;Li et al 2011).…”

Geographic distance and amorphous iron affect the abundance and distribution of Geobacteraceae in paddy soils in China

“…It has been suggested that genomics data can be integrated into biogeochemical model to predict environmental changes modulated by diverse functional microbes (Reed et al 2014). The importance of microbe-mediated iron redox changes in controlling the biogeochemistry of elements in the environment, particularly in sediments and wetland, is well established (Melton et al 2014), Paddy soils are subjected to regular dry-wet cycles, and longterm paddy cultivation will lead to the accumulation of amorphous iron, which is a common terminal electron acceptor (Ding et al 2015;Li et al 2011). Therefore, understanding the diversity and distribution of Geobacteraceae, a major group of microbes involved in dissimilatory iron reducers in paddy soils, at large scale will be indispensible in predicting the biogeochemical cycling of contaminants and nutrients.…”