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

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 days with initial NaNO₃ and FeCl₂ concentrations of 9.37 mM and 4.72 mM, respectively. Acetate (5 mM) 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 days of growth in culture, whereas lepidocrocite was detected in the X-ray diffraction spectrum after 3 months 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.

Keywords:

• Cupriavidus metallidurans
• Fe(II) oxidation
• NO3-reduction
• biomineralization
• comparative genome analysis

Additional information

Funding

This work was supported by the National Science Foundation of China [41330857], Natural Science Foundation of Guangdong Province [2017A030313218], Guangdong Key Technologies R&D Program [2015B020207001] and Guangzhou Science and Technology Program [201604020039].