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Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.

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Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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School of Agriculture, Utsunomiya University, Tochigi 321-8505, Japan
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Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
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Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Hokkaido 005-8601, Japan
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Niigata Agricultural Research Institute, Niigata 940-0826, Japan
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Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Hokkaido 062-8517, Japan
*
Authors to whom correspondence should be addressed.
Present address: Division of Agriculture, Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.
Microorganisms 2020, 8(5), 634; https://doi.org/10.3390/microorganisms8050634
Received: 17 March 2020 / Revised: 24 April 2020 / Accepted: 25 April 2020 / Published: 27 April 2020
(This article belongs to the Section Systems Microbiology)
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. View Full-Text
Keywords: Oryzomonas japonicum sp. nov.; Oryzomonas sagensis sp. nov.; Oryzomonas ruber sp. nov.; Geobacteraceae; paddy soil; pond sediment; iron-reducing bacteria Oryzomonas japonicum sp. nov.; Oryzomonas sagensis sp. nov.; Oryzomonas ruber sp. nov.; Geobacteraceae; paddy soil; pond sediment; iron-reducing bacteria
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MDPI and ACS Style

Xu, Z.; Masuda, Y.; Hayakawa, C.; Ushijima, N.; Kawano, K.; Shiratori, Y.; Senoo, K.; Itoh, H. Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. Microorganisms 2020, 8, 634. https://doi.org/10.3390/microorganisms8050634

AMA Style

Xu Z, Masuda Y, Hayakawa C, Ushijima N, Kawano K, Shiratori Y, Senoo K, Itoh H. Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. Microorganisms. 2020; 8(5):634. https://doi.org/10.3390/microorganisms8050634

Chicago/Turabian Style

Xu, Zhenxing, Yoko Masuda, Chie Hayakawa, Natsumi Ushijima, Keisuke Kawano, Yutaka Shiratori, Keishi Senoo, and Hideomi Itoh. 2020. "Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov." Microorganisms 8, no. 5: 634. https://doi.org/10.3390/microorganisms8050634

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