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 Geobacteraceae have been shown to strongly contribute to the biogeochemical cycle. However, no Geobacteraceae 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 Geobacteraceae from the paddy soils of three different fields in Japan. The four strains, S43T, Red53T, S62T, and Red111T, were Gram-stain negative, strictly anaerobic, chemoheterotrophic, and motile with peritrichous flagella. Phylogenetic studies based on 16S rRNA gene sequences, five concatenated housekeeping genes (fusA, rpoB, recA, nifD, and gyrB) and 92 concatenated core genes revealed that the four strains belong to the family Geobacteraceae and are most closely related to Geobacter bemidjiensis BemT (97.4–98.2%, 16S rRNA gene sequence similarities) and Geobacter bremensis Dfr1T (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 Geobacteraceae and indicated that strains S43T, Red53T, S62T, and Red111T 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 Geobacter metallireducens. Overall, strains S43T, Red53T, S62T, and Red111T represent four novel species, which we propose to classify in a novel genus of the family Geobacteraceae, and the names Geomonas oryzae gen. nov., sp. nov. (type strain S43T), Geomonas edaphica sp. nov. (type strain Red53T), Geomonas ferrireducens sp. nov. (type strain S62T), and Geomonas terrae sp. nov. (type strain Red111T) are proposed. Based on phylogenetic and genomic analyses, we also propose the reclassification of Geobacter bremensis as Geomonas bremensis comb. nov., Geobacter pelophilus as Geomonas pelophila comb. nov., and Geobacter bemidjiensis as Geomonas bemidjiensis comb. nov.

Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov.

“…Although U. marinus IMCC12008 T made a robust cluster with strain KK4 T in the phylogenetic trees based on 16S rRNA genes, UBGCs and DarAB (Figs 1 and 2, S2), the AAI value between them was 72.5 % (), which was around the genus boundary provided by previous studies [28–31] and this study; type strains in the UMA cluster shared >73 % AAI values in each genus (73.7 % in Ulvibater ; 75.0–84.5 % in Aequorivita (Table S7). Similarity in 16S rRNA gene between strain KK4 T and U.…”

“…Moreover, AAI between strain KK4 T / U. marinus IMCC12008 T and other related strains were 61.9–68.2% and 61.5–67.4 % (), which are lower than the genus delineation threshold (70–76 %) recommended in previous studies [28–31]. These results indicated the novel genus status of strain KK4 T as well as U.…”

Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas

“…Therefore, to improve the accuracy of culture-independent analyses, it is important to expand the availability of cultured strains and the genomic information of Geobacteraceae species. As a result of our pilot screening for Geobacteracea strains, we successfully isolated seven derivative strains from paddy soils and pond sediment, and proposed the new genera Geomonas and Oryzomonas in the family Geobacteraceae [1, 7]. In this study, three strains, designated Red330 T , Red736 T and Red745 T , were newly isolated from forest and paddy soils in Japan, which formed reddish colonies and showed a high similarity of the 16S rRNA gene sequence to those of the type strains of Geomonas species.…”

“…The description is as per Xu et al . [1] with the following modification: the genomic DNA G+C content of the type strains is 60.0–62.6 mol%.…”

“…The type species of the genus Geomonas (G. oryzae S43 T ) was used in parallel as the reference strain for fatty acid determination. Respiratory quinones were prepared from cells that were culture under the same conditions as described previously [1] and identified using HPLC with the Acquity UPLC H-Class system (Waters). Genomic G+C content (mol%) of strains Red330 T , Red736 T and Red745 T were calculated based on genomic data using DFAST version 1.1.0 [18].…”