Physiological and Genomic Characterization of a Nitrate-Reducing Fe(II)-Oxidizing Bacterium Isolated from Paddy Soil

Abstract

Abstract In this study, a neutrophilic, heterotrophic bacterium (strain Paddy-2) that is capable of ferrous iron [Fe(II)] oxidation coupled with nitrate (NO3−) reduction (NRFO) under anoxic conditions was isolated from paddy soil. The molecular identification by 16S rRNA gene sequencing identified the strain as Cupriavidus metallidurans. Strain Paddy-2 reduced 97.7% of NO3−and oxidized 89.7% of Fe(II) over 6\u2009days with initial NaNO3 and FeCl2 concentrations of 9.37\u2009mM and 4.72\u2009mM, respectively. Acetate (5\u2009mM) was also supplied as a carbon source and an alternative electron donor. A poorly crystalline Fe(III) mineral was the main component observed after 15\u2009days of growth in culture, whereas lepidocrocite was detected in the X-ray diffraction spectrum after 3\u2009months of culture. The homologous genes in electron transfer during Fe(II) oxidation (cyc1, cymA, FoxY, FoxZ, and mtoD) were also identified in the genomes of strain Paddy-2 and other reported NRFO bacteria. These genes encoding c-Cyts may play a role in electron transfer during the process of NRFO. These results provide evidence for the potential of NO3− to affect Fe(II) oxidation and biomineralization in bacterium from anoxic paddy soil.