Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov.

Abstract

In paddy soil, bacteria from the family <i>Geobacteraceae</i> have been shown to strongly contribute to the biogeochemical cycle. However, no <i>Geobacteraceae</i> species with validly published names have been isolated from paddy soil. In this study, we isolated and characterized four novel ferric reducing bacteria in the family <i>Geobacteraceae</i> from the paddy soils of three different fields in Japan. The four strains, S43^T, Red53^T, S62^T, and Red111^T, were Gram-stain negative, strictly anaerobic, chemoheterotrophic, and motile with peritrichous flagella. Phylogenetic studies based on 16S rRNA gene sequences, five concatenated housekeeping genes (<i>fusA</i>, <i>rpoB</i>, <i>recA</i>, <i>nifD</i>, and <i>gyrB</i>) and 92 concatenated core genes revealed that the four strains belong to the family <i>Geobacteraceae</i> and are most closely related to <i>Geobacter bemidjiensis</i> Bem^T (97.4-98.2%, 16S rRNA gene sequence similarities) and <i>Geobacter bremensis</i> Dfr1^T (97.1-98.0%). Genomic analysis with average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) calculations clearly distinguished the four isolated strains from other species of the family <i>Geobacteraceae</i> and indicated that strains S43^T, Red53^T, S62^T, and Red111^T represent independent species, with values below the thresholds for species delineation. Chemotaxonomic characteristics, including major fatty acid and whole cell protein profiles, showed differences among the isolates and their closest relatives, which were consistent with the results of DNA fingerprints and physiological characterization. Additionally, each of the four isolates shared a low 16S rRNA gene sequence similarity (92.4%) and average amino acid identity (AAI) with the type strain of the type species <i>Geobacter metallireducens</i>. Overall, strains S43^T, Red53^T, S62^T, and Red111^T represent four novel species, which we propose to classify in a novel genus of the family <i>Geobacteraceae</i>, and the names <i>Geomonas oryzae</i> gen. nov., sp. nov. (type strain S43^T), <i>Geomonas edaphica</i> sp. nov. (type strain Red53^T), <i>Geomonas ferrireducens</i> sp. nov. (type strain S62^T), and <i>Geomonas terrae</i> sp. nov. (type strain Red111^T) are proposed. Based on phylogenetic and genomic analyses, we also propose the reclassification of <i>Geobacter bremensis</i> as <i>Geomonas bremensis</i> comb. nov., <i>Geobacter pelophilus</i> as <i>Geomonas pelophila</i> comb. nov., and <i>Geobacter bemidjiensis</i> as <i>Geomonas bemidjiensis</i> comb. nov.