Abstract
Bacteria of the family Geobacteraceae 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 Red96T, Red100T, and Red88T, 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, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA–DNA hybridization, clearly differentiated the strains Red96T, Red100T, and Red88T from other species in the family Geobacteraceae, 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 Geobacteraceae. Hence, we concluded that strains Red96T, Red100T, and Red88T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96T (= NBRC 114286T = MCCC 1K04376T), Red100T (= NBRC 114287T = MCCC 1K04377T), and Red88T (= MCCC 1K03694T = JCM 33033T), respectively.
Highlights
The family Geobacteraceae, belonging to the order Desulfuromonadales, is described as consisting of the genera Geobacter, Geomonas, and a single species Pelobacter propionicus [1,2]
Taxonomic and phylogenetic analysis of the nearly complete 16S rRNA gene sequences and five concatenated housekeeping genes revealed that the three isolated strains were most similar to the species in the family Geobacteraceae, they shared lower 16S rRNA similarities with the two type species, G. metallireducens GS-15T and G. oryzae S43T
These three strains differed from the other two neighbors, Geobacter lovleyi SZT and Geobacter thiogenes K1T, because both of them were tested in this study that they cannot grow using R2A agar plates or broth with 5mM fumarate
Summary
The family Geobacteraceae, belonging to the order Desulfuromonadales, is described as consisting of the genera Geobacter, Geomonas, and a single species Pelobacter propionicus [1,2]. The type genus Geobacter, which was first described by Lovley et al [3] with Geobacter metalireducens as the type species, is the most major group, including 17 validated species at the time of writing (Available online: http://www.bacterio.net/geobacter.html). These species are mesophilic and obligate anaerobes, which were usually isolated from terrestrial environments such as forest soil, lotus field mud, freshwater sediments, and oil/metal-contaminated soils [4,5,6]. The ubiquitous distribution and metabolic properties of Geobacter species suggest their importance in the biogeochemical cycle of both inorganic and organic materials in the terrestrial and freshwater ecosystems
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