A novel organotrophic nitrate-reducing Fe(ii)-oxidizing bacterium isolated from paddy soil and draft genome sequencing indicate its metabolic versatility

Abstract

The extensive application of fertilizers for growing rice results in a large input of nitrogen into paddy soils. During rice growth, iron is exposed to periodic transition under different redox conditions. Nitrate (NO₃⁻) reduction coupled to Fe(II) oxidation (NRCFO) links the iron and nitrogen cycles. However, little is known about the biogeochemical mechanism and microorganisms involved in NRCFO in paddy soil. In the present study, we isolated an anaerobic, NO₃⁻-reducing Fe(II) oxidizer known as strain Paddy-1 from paddy soil. After 6 days of culture in 5 mM acetate, this strain reduced 97% of NO₃⁻ and oxidized 86% of Fe(II) from initial concentrations of 9.3 and 5.1 mM, respectively. A phylogenetic analysis of the 16S rRNA gene sequence placed strain Paddy-1 in a clade within the order Rhodocyclales. In accordance with other NRCFO species, Fe(III) oxides produced by strain Paddy-1 were in the form of amorphous Fe(III) oxides. The reported draft genome of strain Paddy-1 predicts the presence of genes involved in denitrification, outer membrane electron transport, and iron homeostasis as well as candidate Fe(II) oxidation genes. The physiological and genomic information on this strain provide a basis for investigating the mechanism of NRCFO in microorganisms from paddy soil.