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Description of Three Novel Members in the Family <i>Geobacteraceae</i>, <i>Oryzomonas japonicum</i> gen. nov., sp. nov., <i>Oryzomonas sagensis</i> sp. nov., and <i>Oryzomonas ruber</i> sp. nov.
oleh: Zhenxing Xu, Yoko Masuda, Chie Hayakawa, Natsumi Ushijima, Keisuke Kawano, Yutaka Shiratori, Keishi Senoo, Hideomi Itoh
| Format: | Article |
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| Diterbitkan: | MDPI AG 2020-04-01 |
Deskripsi
Bacteria of the family <i>Geobacteraceae</i> are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96<sup>T</sup>, Red100<sup>T</sup>, and Red88<sup>T</sup>, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, <i>gyrB, rpoB, nifD, fusA,</i> and <i>recA</i>) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family <i>Geobacteraceae</i>. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96<sup>T</sup>, Red100<sup>T</sup>, and Red88<sup>T</sup> from other species in the family <i>Geobacteraceae</i>, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family <i>Geobacteraceae</i>. Hence, we concluded that strains Red96<sup>T</sup>, Red100<sup>T</sup>, and Red88<sup>T</sup> represented three novel species of a novel genus in the family <i>Geobacteraceae</i>, for which the names <i>Oryzomonas japonicum</i> gen. nov., sp. nov., <i>Oryzomonas sagensis</i> sp. nov., and <i>Oryzomonas ruber</i> sp. nov. are proposed, with type strains Red96<sup>T</sup> (= NBRC 114286<sup>T</sup> = MCCC 1K04376<sup>T</sup>), Red100<sup>T</sup> (= NBRC 114287<sup>T</sup> = MCCC 1K04377<sup>T</sup>), and Red88<sup>T</sup> (= MCCC 1K03694<sup>T</sup> = JCM 33033<sup>T</sup>), respectively.