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Thapa BS, Flynn TM, Jensvold ZD, Kemner KM, Sladek MF, O'Loughlin EJ, Marshall CW. Effects of soluble electron shuttles on microbial iron reduction and methanogenesis. Appl Environ Microbiol 2025; 91:e0222224. [PMID: 40277367 DOI: 10.1128/aem.02222-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 04/02/2025] [Indexed: 04/26/2025] Open
Abstract
In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.
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Affiliation(s)
- Bhim Sen Thapa
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, USA
| | - Zena D Jensvold
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, USA
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, USA
| | - Margaret F Sladek
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, USA
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Prokofeva MI, Elcheninov AG, Klyukina AA, Novikov AA, Kachmazov GS, Toshchakov SV, Frolov EN, Podosokorskaya OA. Anaeroselena agilis gen. nov., sp. nov., a Novel Sulfite- and Arsenate-Respiring Bacterium Within the Family Acetonemataceae Isolated from a Thermal Spring of North Ossetia. Curr Microbiol 2025; 82:71. [PMID: 39757269 DOI: 10.1007/s00284-024-04046-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 12/18/2024] [Indexed: 01/07/2025]
Abstract
A novel Gram-negative, motile, rod-shaped bacterium, designated 4137-clT, was isolated from a thermal spring of North Ossetia (Russian Federation). Strain 4137-clT grew at 30-50 °C (optimum 42 °C) with 0-3.5% NaCl (optimum 0-0.3%) and within pH range 4.0-8.7 (optimum pH 6.8-7.3). It was a strictly anaerobic microorganism capable of fermentation and respiration on organic acids and proteinaceous substrates. Sulfur, sulfite, polysulfide, and arsenate were used as electron acceptors. In addition to heterotrophic growth it grew autotrophically with H2/CO2. The major fatty acids were C16:1 ω8c and C16:0. The size of the genome and genomic DNA G+C content of strain 4137-clT were 4.5 Mb and 59.2%, respectively. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, strain 4137-clT represented a distinct lineage of the family Acetonemataceae within the class Negativicutes. As inferred from the morphology, physiology, chemotaxonomical and phylogenomic analyses, strain 4137-clT ought to be recognized as a novel genus for which the name Anaeroselena agilis gen. nov., sp. nov., we propose. The type strain is 4137-clT(=KCTC 25383T = VKM B-3575T).
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Affiliation(s)
- Maria I Prokofeva
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, Moscow, Russia, 117312
| | - Alexander G Elcheninov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, Moscow, Russia, 117312
| | - Alexandra A Klyukina
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, Moscow, Russia, 117312
| | - Andrei A Novikov
- Gubkin Russian State University of Oil and Gas, Leninsky Prospect 65/1, Moscow, Russia, 119991
| | - Gennady S Kachmazov
- Faculty of Chemistry, Biology and Biotechnology, North Ossetian State University Named After K.L.Khetagurov, Vatutina Str., 44-46, Vladikavkaz, Russia, 362025
| | - Stepan V Toshchakov
- National Research Centre "Kurchatov Institute", Akademika Kurchatova Sq., 1, Moscow, Russia, 123182
| | - Evgenii N Frolov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, Moscow, Russia, 117312
| | - Olga A Podosokorskaya
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, Moscow, Russia, 117312.
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Xu Z, Hattori S, Masuda Y, Toyoda S, Koba K, Yu P, Yoshida N, Du ZJ, Senoo K. Unprecedented N 2O production by nitrate-ammonifying Geobacteraceae with distinctive N 2O isotopocule signatures. mBio 2024; 15:e0254024. [PMID: 39475233 PMCID: PMC11633192 DOI: 10.1128/mbio.02540-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 10/03/2024] [Indexed: 12/12/2024] Open
Abstract
Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO2- to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3- and NO2- into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.
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Affiliation(s)
- Zhenxing Xu
- Marine College, Shandong University, Weihai, China
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shohei Hattori
- International Center for Isotope Effects Research (ICIER), Nanjing University, Nanjing, China
- Frontiers Science Center for Critical Earth Material Cycling, State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Sakae Toyoda
- School of Materials and Chemical Technology, Institute of Science Tokyo, Yokohama, Japan
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Pei Yu
- SDU-ANU Joint Science College, Shandong University, Weihai, China
| | - Naohiro Yoshida
- Earth-Life Science Institute, Institute of Science Tokyo, Tokyo, Japan
- National Institute of Information and Communications Technology, Tokyo, Japan
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, China
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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Ito K, Kuramata M, Tanikawa H, Suda A, Yamaguchi N, Ishikawa S. Diversity and transcription of genes involved in respiratory As(V) reduction and As(III) methylation in Japanese paddy soils. BMC Microbiol 2024; 24:396. [PMID: 39379826 PMCID: PMC11462812 DOI: 10.1186/s12866-024-03562-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Arsenic (As) metabolism by soil microorganisms has an impact on As geochemical cycling in paddy soils, which in turn affects As uptake in rice. However, little is known about the key microorganisms involved in this process in Japanese paddy soil. RESULTS Total RNA was extracted from Japanese paddy soils with different levels of dissolved As under flooded conditions, and the transcription of As metabolic genes (arrA, ttrA and arsM) was analyzed via a metatranscriptomic approach. The results showed that ttrA was the predominant respiratory arsenate reductase gene transcribed in these soils rather than arrA, suggesting that ttrA contributes to the reductive dissolution of As. The predominant taxa expressing ttrA differed among soils but were mostly associated with genera known for their iron- and/or sulfate-reduction activity. In addition, a wide variety of microorganisms expressed and upregulated arsM approximately 5.0- to 13.2-fold at 9 d compared with 3 d of incubation under flooded conditions in flasks. CONCLUSIONS Our results support the involvement of microbial activity in the geochemical cycling of As in Japanese paddy soils and suggest that ttrA may be one of the key genes involved in the formation of arsenite, an inorganic species taken up by rice.
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Affiliation(s)
- Koji Ito
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Aomi Suda
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
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Wang H, Song X, Xu Z, Du ZJ. Maribellus mangrovi sp. nov., an iron-reducing bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2024; 74. [PMID: 38995174 DOI: 10.1099/ijsem.0.006448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
A novel facultatively anaerobic and Gram-stain-negative bacterium, designated FJH33T, was isolated from mangrove sediment sampled in Zhangzhou, PR China. Cells of strain FJH33T were rod-shaped or slightly curved-shaped, with widths of 0.3-0.5 µm and lengths of 1.0-3.0 µm. Optimum growth of strain FJH33T occurred in the presence of 3 % NaCl (w/v), at 33 °C and at pH 7.0. Oxidase activity was negative, while catalase activity was positive. Its iron-reducing ability was determined. Based on 16S rRNA gene sequence similarity, strain FJH33T was most closely related to Maribellus luteus XSD2T (95.1 %), followed by Maribellus sediminis Y2-1-60T (95.0 %) and Maribellus maritimus 5E3T (94.9 %). Genome analysis of strains FJH33T and M. luteus XSD2T revealed low genome relatedness, with an average nucleotide identity value of 73.8% and a digital DNA-DNA hybridization value of 19.0%. Phylogenetic trees built from 16S rRNA genes and genome sequences showed that strain FJH33T represents a relatively independent phylogenetic lineage within the genus Maribellus. The major cellular fatty acids (≥10 %) were iso-C15 : 0 and C18 : 1 ω9c. The sole respiratory quinone was MK-7. The polar lipids consisted of phosphatidylethanolamine, diphosphatidylcholine, diphosphatidyglycerol and one unidentified lipid. The DNA G+C content was 41.4 mol%. Based on the integrated results of phylogenetic, physiological, biochemical and chemotaxonomic characterizations, we propose that strain FJH33T represents a novel species of the genus Maribellus, for which the name Maribellus mangrovi sp. nov. is proposed. The type strain is FJH33T (=KCTC 102210T=MCCC 1H01459T).
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Affiliation(s)
- Hongxuan Wang
- SDU-ANU Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Xiaoxuan Song
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
| | - Zhenxing Xu
- SDU-ANU Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Shandong University-Weihai Research Institute of Industrial Technology, Weihai, Shandong, 264209, PR China
| | - Zong-Jun Du
- SDU-ANU Joint Science College, Shandong University, Weihai, Shandong, 264209, PR China
- Marine College, Shandong University, Weihai, Shandong, 264209, PR China
- Shandong University-Weihai Research Institute of Industrial Technology, Weihai, Shandong, 264209, PR China
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Masuda Y, Mise K, Xu Z, Zhang Z, Shiratori Y, Senoo K, Itoh H. Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome. MICROBIOME 2024; 12:95. [PMID: 38790049 PMCID: PMC11127431 DOI: 10.1186/s40168-024-01812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 04/09/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome. RESULTS After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). CONCLUSION Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, 857 Nagakura-machi, Nagaoka, Niigata, 940-0826, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, 2-17-2-1 Tsukisamu-higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan.
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Masuda Y, Chihara M, Senoo K. Ferrihydrite Addition Activated Geobacteraceae, the Most Abundant Iron-reducing Diazotrophs, and Suppressed Methanogenesis by Heterogeneous Methanogens in Xylan-amended Paddy Soil Microcosms. Microbes Environ 2024; 39:n/a. [PMID: 39261060 PMCID: PMC11427309 DOI: 10.1264/jsme2.me24028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
Paddy fields are a major emission source of the greenhouse gas methane. In the present study, the addition of ferrihydrite to xylan-amended paddy soil microcosms suppressed methane emissions. PCR-based and metatranscriptomic ana-lyses revealed that the addition of ferrihydrite suppressed methanogenesis by heterogeneous methanogens and simultaneously activated Geobacteraceae, the most abundant iron-reducing diazotrophs. Geobacteraceae may preferentially metabolize xylan and/or xylan-derived carbon compounds that are utilized by methanogens. Geomonas terrae R111 utilized xylan as a growth substrate under liquid culture conditions. This may constitute a novel mechanism for the mitigation of methane emissions previously observed in ferric iron oxide-applied paddy field soils.
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Affiliation(s)
- Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
| | - Mitsutaka Chihara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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Liu GH, Yang S, Han S, Xie CJ, Liu X, Rensing C, Zhou SG. Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils. mBio 2023; 14:e0215023. [PMID: 37855611 PMCID: PMC10746287 DOI: 10.1128/mbio.02150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.
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Affiliation(s)
- Guo-Hong Liu
- Institute of Resources, Environment and Soil Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou City, Fujian Province, China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, Fujian Province, China
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Itoh H, Sugisawa Y, Mise K, Xu Z, Kuniyasu M, Ushijima N, Kawano K, Kobayashi E, Shiratori Y, Masuda Y, Senoo K. Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils. Int J Syst Evol Microbiol 2023; 73. [PMID: 37675765 DOI: 10.1099/ijsem.0.006073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T, W786T, Red222T, Red802T, Red803T, and Red804T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T, Red802T, Red803T, and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains. The former four strains shared 97.95-99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix, whereas the latter two strains 94.86-95.49% similarities. The average amino acid identity of strains W79T and W786T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79T, W786T, Red222T, Red803T, and Red804T) except for strain Red802T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota/Holophagae/Holophagales/Holophagaceae, comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yumi Sugisawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Kazumori Mise
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Present address: Marine College, Shandong University, Weihai, Shandong, PR China
| | - Miyu Kuniyasu
- Department of Biotechnology, Hokkaido High-technology College, Hokkaido 061-1396, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Keisuke Kawano
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
- Present address: Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Emiko Kobayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido 062-8517, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940-0826, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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10
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Bahulikar RA. Prevalence of Deltaproteobacterial sequences in nifH gene pools associated with the rhizosphere of native switchgrass from Tall Grass Prairie (Oklahoma, USA). 3 Biotech 2023; 13:210. [PMID: 37251732 PMCID: PMC10209375 DOI: 10.1007/s13205-023-03640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
The potential nitrogen-fixing bacterial diversity in the rhizospheric soil of the native switchgrass (Panicum virgatum L.) from Tall Grass Prairies of Northern Oklahoma was studied using a partial region of nitrogenase structural gene-nifH. Eleven clone libraries constructed from nifH amplicons gave 407 good-quality sequences. More than 70% of sequences showed similarity of nifH with uncultured bacteria (< 98%). The dominance of sequences affiliated with Deltaproteobacterial nifH was observed, followed by Betaproteobacterial nifH sequences. The nifH gene library was dominated by the genera Geobacter, Rhizobacter, Paenibacillus, and Azoarcus. Sequences affiliated with rhizobia, such as Bradyrhizobium, Methylocystis, Ensifer, etc., were also in the rhizosphere in small numbers. From Deltaproteobacteria, five genera, namely Geobacter, Pelobacter, Geomonas, Desulfovibrio, and Anaeromyxobacter, contributed to 48% of the total sequences suggesting the dominance of group Deltaproteobacteria in the rhizosphere of native switchgrass. Considering the percent similarity of the nifH sequences with cultivated bacteria, this study demonstrated the presence of novel bacterial species in switchgrass rhizospheric soil from Tall Grass Prairie.
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Affiliation(s)
- Rahul A. Bahulikar
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- Present Address: BAIF Development Research Foundation, Central Research Station, Urali Kanchan, Pune, 412 202 India
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11
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Rai A, Suresh G, Ria B, L V, Pk S, Ipsita S, Sasikala C, Venkata Ramana C. Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748586 DOI: 10.1099/ijsem.0.005672] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
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Affiliation(s)
- Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Vighnesh L
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sreya Pk
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sahu Ipsita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad-500 085, India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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12
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Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of
Anaeromyxobacter
species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of
Anaeromyxobacter
,
Anaeromyxobacter dehalogenans
2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in
A. dehalogenans
2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.
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13
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Nixon SL, Bonsall E, Cockell CS. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiol Rev 2022; 46:6645348. [PMID: 35849069 PMCID: PMC9629499 DOI: 10.1093/femsre/fuac033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microbial iron reduction is a widespread and ancient metabolism on Earth, and may plausibly support microbial life on Mars and beyond. Yet, the extreme limits of this metabolism are yet to be defined. To investigate this, we surveyed the recorded limits to microbial iron reduction in a wide range of characterized iron-reducing microorganisms (n = 141), with a focus on pH and temperature. We then calculated Gibbs free energy of common microbially mediated iron reduction reactions across the pH-temperature habitability space to identify thermodynamic limits. Comparing predicted and observed limits, we show that microbial iron reduction is generally reported at extremes of pH or temperature alone, but not when these extremes are combined (with the exception of a small number of acidophilic hyperthermophiles). These patterns leave thermodynamically favourable combinations of pH and temperature apparently unoccupied. The empty spaces could be explained by experimental bias, but they could also be explained by energetic and biochemical limits to iron reduction at combined extremes. Our data allow for a review of our current understanding of the limits to microbial iron reduction at extremes and provide a basis to test more general hypotheses about the extent to which biochemistry establishes the limits to life.
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Affiliation(s)
- Sophie L Nixon
- Corresponding author: Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
| | - Emily Bonsall
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, United Kingdom
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14
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Ma T, Xue H, Piao C, Liu C, Yang M, Bian D, Li Y. Reclassification of 11 Members of the Family Rhodobacteraceae at Genus and Species Levels and Proposal of Pseudogemmobacter hezensis sp. nov. Front Microbiol 2022; 13:849695. [PMID: 35495672 PMCID: PMC9044078 DOI: 10.3389/fmicb.2022.849695] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, motile bacterial strain, D13-10-4-6T, was isolated from the bark sample of Populus × euramericana. The strain could grow at 15-35°C, at pH 6-10 and in 0-4% (w/v) NaCl, and the strain tested positive for oxidase and catalase activities. The main polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main respiratory quinone was Q-10, and the predominant fatty acid was C18:1 ω7c. The phylogenetic analyses showed that the strain belonged to the genus Pseudogemmobacter of the family Rhodobacteraceae. The family Rhodobacteraceae is an ecologically diverse group that includes bacteria from aquatic to terrestrial ecosystems. As a consequence, the classification of the family Rhodobacteraceae is difficult, not least when the early taxonomy work relied heavily on 16S rRNA gene analysis. Recently, the taxonomic status of many members of the family has been revised based on the genome analysis; however, there are still some classification conflicts due to the lack of genome sequences and parallel publication time. In this study, phylogenetic trees based on 16S rRNA gene, gyrB gene, and 120 concatenated proteins, the average amino acid identity (AAI) and percentage of conserved proteins (POCP) have been used for the analysis of strain D13-10-4-6T and other members of 15 genera within the family to further clarify their taxonomic relationships. For the data of phylogeny, AAI, and POCP, the taxonomic proposals are (1) reclassification of Rhodobacter tardus as the type species of a novel genus, Stagnihabitans gen. nov., as Stagnihabitans tardus comb. nov.; (2) reclassification of Tabrizicola alkalilacus, Tabrizicola sediminis, Tabrizicola algicola into a novel genus, Pseudotabrizicola gen. nov., as Pseudotabrizicola alkalilacus comb. nov., Pseudotabrizicola sediminis comb. nov., Pseudotabrizicola algicola comb. nov.; (3) reclassification of Rhodobacter sediminicola into the genus Cereibacter as Cereibacter sediminicola comb. nov.; (4) reclassification of Rhodobacter flagellatus, Rhodobacter thermarum, and Xinfangfangia soli into the genus Tabrizicola as Tabrizicola flagellatus comb. nov., Tabrizicola thermarum comb. Nov., and Tabrizicola soli comb. nov.; (5) reclassification of Xinfangfangia humi into the genus Pseudogemmobacter as Pseudogemmobacter humicola comb. nov.; (6) classification of strain D13-10-4-6T as a novel species of the genus Pseudogemmobacter, for which the name P. hezensis sp. nov. is proposed, the type strain is D13-10-4-6T (= CFCC 12033T = KCTC 82215T).
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Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Chengyi Liu
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, China
| | - Danran Bian
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
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15
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Genome-based reclassification of the genus Meiothermus along with the proposal of a new genus Allomeiothermus gen. nov. Antonie van Leeuwenhoek 2022; 115:645-659. [PMID: 35348967 DOI: 10.1007/s10482-022-01723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/23/2022] [Indexed: 10/18/2022]
Abstract
Phylogenomic analyses were performed on the nine species of the genus Meiothermus and four species of the genus Calidithermus. Phylogenetic analysis, low values of genomic relatedness indices and functional diversity analysis indicated that Meiothermus silvanus should not be classified within the clades for Meiothermus and Calidithermus but instead be reclassified as a new genus, for which we propose the name Allomeiothermus gen. nov., with Allomeiothermus silvanus comb. nov. as type species. In addition, the species Meiothermus cateniformans Zhang et al. (Int J Syst Evol Microbial 60:840-844, 2010) should also be reclassified as a later heterotypic synonym of Meiothermus taiwanensis Chen et al. (Int J Syst Evol Microbiol 52:1647-1654, 2002) emend. Raposo et al. (2019). This reclassification is based on the high genomic relatedness indices (98.8% ANI; 90.2% dDDH; 99% AAI) that are above the threshold values necessary for defining a new species, as well as on the observation of overlapping functions on Principal Coordinate Analysis plot generated from Clusters of Orthologous Genes.
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16
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Yang S, Liu GH, Tang R, Han S, Xie CJ, Zhou SG. Description of two nitrogen-fixing bacteria, Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., isolated from paddy soils. Antonie Van Leeuwenhoek 2022; 115:435-444. [PMID: 35094155 DOI: 10.1007/s10482-021-01704-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022]
Abstract
Two strictly anaerobic nitrogen-fixing strains, designated RG17T and RG53T, were isolated from paddy soils in China. Strains RG17T and RG53T showed the highest 16S rRNA gene sequence similarities to the type strain Geomonas paludis (97.9-98.4%). Phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Geomonas. Growth of strain RG17T was observed at 20-42 °C, pH 5.5-8.5 and 0-0.3% (w/v) NaCl while strain RG53T growth was observed at 20-42 °C, pH 5.5-9.5 and 0-0.7% (w/v) NaCl. Strains RG17T and RG53T contained MK-8 as main menaquinone and C15:1 ω6c, iso-C15:0, and Summed Feature 3 as the major fatty acids. The genomic DNA G + C content of strains RG17T and RG53T were 61.6 and 60.7%, respectively. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cut-off value (dDDH 70% and ANI 95-96%) for prokaryotic species delineation. Both strains possessed nif genes nifHDK and nitrogenase activities. Based on the above results, the two strains represent two novel species of the genus Geomonas, for which the names Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., are proposed. The type strains are RG17T (= GDMCC 1.2687T = KTCC 25332T) and RG53T (= GDMCC 1.2630T = KCTC 25331T), respectively.
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Affiliation(s)
- Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.,Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou City, 350003, Fujian Province, People's Republic of China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou City, 350002, Fujian Province, People's Republic of China.
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17
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Liu GH, Yang S, Tang R, Xie CJ, Zhou SG. Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils. Front Microbiol 2022; 12:801462. [PMID: 35197944 PMCID: PMC8859169 DOI: 10.3389/fmicb.2021.801462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/14/2021] [Indexed: 12/05/2022] Open
Abstract
Five strictly anaerobic strains, designated RG2T, RG3, RG10T, RF4T, and RG29, were isolated from paddy soils in China. Strains RG2T, RF4T, RG10T, RG3, and RG29 grew at temperatures ranging 5–42°C and pH ranging 5.5–8.5. Strains RG2T, RF4T, RG3, and RG29 could tolerate NaCl up to 0–0.7% (w/v) while strain RG10T could tolerate NaCl up to 0–0.8% (w/v). The isolated strains showed the highest 16S rRNA gene sequence similarities to the type strains of Geomonas terrae Red111T and Geomonas paludis Red736T. In phylogenetic (based on 16S rRNA gene sequence) and phylogenomic trees, strains clustered with the members of the genus Geomonas. Menaquinone-8 was the predominant quinone present in all strains. The major fatty acid profiles of all strains were C15:1 ω6c, C16:0, iso-C15:0, and Summed Feature 3. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the isolated strains and the closely related Geomonas species were lower than the cutoff value (ANI 95–96% and dDDH 70%) for prokaryotic species delineation. Based on physiological, biochemical, and chemotaxonomic properties, strains RG2T, RG10T, and RF4T could easily be differentiated with the members of the genus Geomonas. Additionally, all the isolated strains possessed nifHDK clusters and catalytic compartments of nitrogenase. Based on the above results, the isolated five strains represent three novel species of the genus Geomonas, for which the names Geomonas oryzisoli sp. nov., Geomonas subterranea sp. nov., and Geomonas nitrogeniifigens sp. nov. are proposed. The type strains are RG10T (= GDMCC1.2537T = KCTC 26318T), RG2T (= GDMCC1.2536T = KCTC 25317T), and RF4T (= GDMCC 1.2547T = KCTC 25316T).
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Affiliation(s)
- Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Shang Yang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rong Tang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng-Jie Xie
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Shun-Gui Zhou,
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18
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Natronosporangium hydrolyticum gen. nov., sp. nov., a haloalkaliphilic polyhydrolytic actinobacterium from a soda solonchak soil in central asia. Syst Appl Microbiol 2022; 45:126307. [DOI: 10.1016/j.syapm.2022.126307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
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19
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Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H. Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol 2021; 12:737531. [PMID: 34659166 PMCID: PMC8516083 DOI: 10.3389/fmicb.2021.737531] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
Geobacterales is a recently proposed order comprising members who originally belonged to the well-known family Geobacteraceae, which is a key group in terrestrial ecosystems involved in biogeochemical cycles and has been widely investigated in bioelectrochemistry and bioenergy fields. Previous studies have illustrated the taxonomic structure of most members in this group based on genomic phylogeny; however, several members are still in a pendent or chaotic taxonomic status owing to the lack of genome sequences. To address this issue, we performed this taxonomic reassignment using currently available genome sequences, along with the description of two novel paddy soil-isolated strains, designated Red51T and Red69T, which are phylogenetically located within this order. Phylogenomic analysis based on 120 ubiquitous single-copy proteins robustly separated the species Geobacter luticola from other known genera and placed the genus Oryzomonas (fam. Geobacteraceae) into the family ‘Pseudopelobacteraceae’; thus, a novel genus Geomobilimonas is proposed, and the family ‘Pseudopelobacteraceae’ was emended. Moreover, genomic comparisons with similarity indexes, including average amino acid identity (AAI), percentage of conserved protein (POCP), and average nucleotide identity (ANI), showed proper thresholds as genera boundaries in this order with values of 70%, 65%, and 74% for AAI, POCP, and ANI, respectively. Based on this, the three species Geobacter argillaceus, Geobacter pelophilus, and Geobacter chapellei should be three novel genera, for which the names Geomobilibacter, Geoanaerobacter, and Pelotalea are proposed, respectively. In addition, the two novel isolated strains phylogenetically belonged to the genus Geomonas, family Geobacteraceae, and shared genomic similarity values higher than those of genera boundaries, but lower than those of species boundaries with each other and their neighbors. Taken together with phenotypic and chemotaxonomic characteristics similar to other Geomonas species, these two strains, Red51T and Red69T, represent two novel species in the genus Geomonas, for which the names Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. are proposed, respectively.
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Affiliation(s)
- Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Xueding Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido, Japan
| | | | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Hokkaido, Japan
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20
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Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol 2021; 20:5-19. [PMID: 34316046 DOI: 10.1038/s41579-021-00597-6] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 02/03/2023]
Abstract
Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.
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Affiliation(s)
- Derek R Lovley
- Electrobiomaterials Institute, Key Laboratory for Anisotropy and Texture of Materials (Ministry of Education), Northeastern University, Shenyang, China. .,Department of Microbiology, University of Massachusetts, Amherst, MA, USA. .,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA.,Department of Physical and Biological Sciences, Western New England University, Springfield, MA, USA
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21
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Zhang Z, Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, Itoh H. Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil. Syst Appl Microbiol 2021; 44:126233. [PMID: 34311149 DOI: 10.1016/j.syapm.2021.126233] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875T, Red259T, and Red421T were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO2, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Phylogenetic analysis based on the 16S rRNA gene and 92 concatenated core proteins sequences revealed that strains Red259T and Red421T clustered with the type strains of Geomonas species, whereas strain Red875T formed an independent lineage within the family Geobacteraceae. Genome comparison based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values clearly distinguished these three strains from other Geobacteraceae members, with lower values than the thresholds for species delineation. Moreover, strain Red875T also shared low average amino acid identity (AAI) and percentage of conserved proteins (POCP) values with the type species of the family Geobacteraceae. Based on these physiological, chemotaxonomic, and phylogenetic distinctions, we propose that strain Red875T (=NBRC 114290T = MCCC 1K04407T) represents a novel genus in the family Geobacteraceae, namely, Geomesophilobacter sediminis gen. nov., sp. nov., and strains Red259T (=NBRC 114288T = MCCC 1K05016T) and Red421T (=NBRC 114289T = MCCC 1K06216T) represent two novel independent species in the genus Geomonas, namely, Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., respectively.
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Affiliation(s)
- Zhengcheng Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
| | - Xueding Wang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Japan
| | | | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan
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22
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Guo Y, Aoyagi T, Hori T. Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. BMC Genomics 2021; 22:475. [PMID: 34171987 PMCID: PMC8235581 DOI: 10.1186/s12864-021-07809-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible application in bioremediation and bioelectrochemical engineering, some of phylogenetically close Desulfuromonas spp. strains have been isolated through enrichment with crystalline Fe (III) oxide and anode. The strains isolated using electron acceptors with distinct redox potentials may have different abilities, for instance, of extracellular electron transport, surface recognition and colonization. The objective of this study was to identify the different genomic signatures between the crystalline Fe (III) oxide-stimulated strain AOP6 and the anode-stimulated strains WTL and DDH964 by comparative genome analysis. RESULTS The AOP6 genome possessed the flagellar biosynthesis gene cluster, as well as diverse and abundant genes involved in chemotaxis sensory systems and c-type cytochromes capable of reduction of electron acceptors with low redox potentials. The WTL and DDH964 genomes lacked the flagellar biosynthesis cluster and exhibited a massive expansion of transposable gene elements that might mediate genome rearrangement, while they were deficient in some of the chemotaxis and cytochrome genes and included the genes for oxygen resistance. CONCLUSIONS Our results revealed the genomic signatures distinctive for the ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. These findings highlighted the different metabolic abilities, such as extracellular electron transfer and environmental stress resistance, of these phylogenetically close bacterial strains, casting light on genome evolution of the subsurface Fe (III) oxide reducers.
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Affiliation(s)
- Yong Guo
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
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23
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Devosia aurantiaca sp. nov., Isolated from Mountain Soil and Proposal of Albitalea gen. nov. to Replace the Illegitimate Prokaryotic Genus Name Geomonas Khan et al. 2020. Curr Microbiol 2021; 78:2548-2555. [PMID: 33963447 DOI: 10.1007/s00284-021-02515-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Strain H239T, a gram-negative, strictly aerobic, and oxidase-positive, and catalase-negative bacterium, was isolated from mountain soil in Gangwon-do of South Korea. Colonies were orange colored, and cells were motile rods with a single polar flagellum. Growth was observed between 25 and 30 °C (optimum, 30 °C), between pH 7.0 and pH 9.0 (optimum, pH 7.5), and in the presence of 0-1.5% (w/v) NaCl (optimum 0.5-1%). Ubiquinone-10 was detected as the sole respiratory quinone. The major fatty acids (>10%) of strain H239T were C18:1 ω7c, C18:0, and C16:0. The polar lipids detected from strain H239T consisted of two unidentified glycolipids, two unidentified phospholipids, and three unidentified polar lipids. The G+C content of strain H239T based on its genome sequence was 62.0 mol%. Comparative 16S rRNA gene sequence analysis indicated that strain H239T was most closely related to Devosia chinhatensis IPL18T (97.7%), Devosia submarina KMM 9415T (97.7%), and Devosia yakushimensis Yak96BT (97.3%). Phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain H239T formed a distinct phyletic lineage as a new species within the genus Devosia. Based on its physiological, chemotaxonomic, and molecular properties, strain H239T represents a novel species of the genus Devosia, for which the name Devosia aurantiaca sp. nov. is proposed. The type strain is H239T (=KACC 21662T=JCM 33930T). In addition, because the prokaryotic genus name Geomonas Khan et al. 2020 is a later homonym of Geomonas Xu et al. 2020, the name is illegitimate (Principle 6 in the International Code of Nomenclature of Prokaryotes). Therefore, we propose to replace the problematic prokaryotic names Geomonas and Geomonas soli with Albitalea with Albitalea terrae, respectively.
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24
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Pérez-Rodríguez I, Choi JK, Abuyen K, Tyler M, Ronkowski C, Romero E, Trujillo A, Tremblay J, Viney I, Savalia P, Amend JP. Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter. Int J Syst Evol Microbiol 2021; 71. [PMID: 33877046 DOI: 10.1099/ijsem.0.004739] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-20 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-25 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC 20015, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica K Choi
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla Abuyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Madeline Tyler
- Present address: College of Pharmacy, Oregon State University, Corvallis, OR 97330, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Cynthia Ronkowski
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Eric Romero
- Present address: Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Anthony Trujillo
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Jason Tremblay
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Isabella Viney
- Present address: Department of Microbiology, University of Arizona, Tucson, AZ 85721, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratixaben Savalia
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
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25
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Li J, Cheng JH, Teng ZJ, Sun ZZ, He XY, Wang P, Shi M, Song XY, Chen XL, Zhang YZ, Tian X, Zhang XY. Taxonomic and Enzymatic Characterization of Flocculibacter collagenilyticus gen. nov., sp. nov., a Novel Gammaproteobacterium With High Collagenase Production. Front Microbiol 2021; 12:621161. [PMID: 33786038 PMCID: PMC8005334 DOI: 10.3389/fmicb.2021.621161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Collagens from marine animals are an important component of marine organic nitrogen. Collagenase-producing bacteria and their collagenases play important roles in collagen degradation and organic nitrogen recycling in the ocean. However, only a few collagenase-producing marine bacteria have been so far discovered. Here, we reported the isolation and characterization of a collagenase-secreting bacterium, designated strain SM1988T, isolated from a green alga Codium fragile sample. Strain SM1988T is a Gram-negative, aerobic, oxidase-, and catalase-positive, unipolar flagellated, and rod-shaped bacterium capable of hydrolyzing casein, gelatin and collagens. Phylogenetic analysis revealed that strain SM1988T formed a distinct phylogenetic lineage along with known genera within the family Pseudoalteromonadaceae, with 16S rRNA gene sequence similarity being less than 93.3% to all known species in the family. Based on the phylogenetic, genomic, chemotaxonomic and phenotypic data, strain SM1988T was considered to represent a novel species in a novel genus in the family Pseudoalteromonadaceae, for which the name Flocculibacter collagenilyticus gen. nov., sp. nov. is proposed, with the type strain being SM1988T (= MCCC 1K04279T = KCTC 72761T). Strain SM1988T showed a high production of extracellular collagenases, which had high activity against both bovine collagen and codfish collagen. Biochemical tests combined with genome and secretome analyses indicated that the collagenases secreted by strain SM1988T are serine proteases from the MEROPS S8 family. These data suggest that strain SM1988T acts as an important player in marine collagen degradation and recycling and may have a promising potential in collagen resource utilization.
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Affiliation(s)
- Jian Li
- College of Life Science and Technology, Xinjiang University, Urumqi, China.,State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jun-Hui Cheng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Zhong-Zhi Sun
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xinmin Tian
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Institute of Marine Science and Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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26
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Sanford RA, Lloyd KG, Konstantinidis KT, Löffler FE. Microbial Taxonomy Run Amok. Trends Microbiol 2021; 29:394-404. [PMID: 33546975 DOI: 10.1016/j.tim.2020.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022]
Abstract
DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.
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Affiliation(s)
- Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA; Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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27
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Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, Senoo K. Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int J Syst Evol Microbiol 2020; 71. [PMID: 33295856 DOI: 10.1099/ijsem.0.004607] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae. Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas, were 96.3-98.5 %. The genome-related indexes, average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, among the three strains and G. oryzae S43T were 74.7-86.8 %, 21.2-33.3 % and 70.4-89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas, for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Zhenxing Xu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Chie Hayakawa
- School of Agriculture, Utsunomiya University, Tochigi 321-8505, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940-0826, Japan
| | - Keishi Senoo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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28
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Diazotrophic Anaeromyxobacter Isolates from Soils. Appl Environ Microbiol 2020; 86:AEM.00956-20. [PMID: 32532868 DOI: 10.1128/aem.00956-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/04/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium.IMPORTANCE Anaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.
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29
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Kawano K, Ushijima N, Kihara M, Itoh H. 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. Int J Syst Evol Microbiol 2020; 70:4119-4129. [DOI: 10.1099/ijsem.0.004254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A marine strain, designated KK4T, was isolated from the surface of a starfish, Patiria pectinifera, which was collected from seawater off the coast of Hokkaido, Japan. Strain KK4T is a Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium that forms yellow-pigmented colonies. A phylogenetic relationship analysis, based on 16S rRNA gene sequences, revealed that strain KK4T was closely related to
Ulvibacter marinus
IMCC12008T,
Ulvibacter antarcticus
IMCC3101T and
Ulvibacter litoralis
KMM 3912T, with similarities of 96.9, 95.8 and 95.6 %, respectively, but low sequence similarities (<94 %) among other genera in the family
Flavobacteriaceae
. Genomic similarities between strain KK4T and the three
Ulvibacter
type strains based on average nucleotide identity and digital DNA–DNA hybridization values were lower than the species delineation thresholds. Moreover, phylogenetic tree based on genome sequences showed that strain KK4T was clustered with
U. marinus
IMCC12008T and formed a branch independent from the cluster including type species of the genera
Ulvibacter
,
Marixanthomonas
,
Marinirhabdus
,
Aureitalea
and
Aequorivita
. Amino acid identity values between strain KK4T/
U. marinus
IMCC12008T and the neighbour type species/strains were 61.9–68.2% and 61.5–67.4 %, which were lower than the genus delineation threshold, implying the novel genus status of strain KK4T. Strain KK4T growth occurred at pH 6.0–9.0, 4–30 °C and in NaCl concentrations of 0.5–5.0 %, and optimally at pH 7.0, 25 °C and 3.0 %, respectively. Unlike
Ulvibacter
strains, strain KK4T could assimilate glucose, mannose, galactose and acetate. The major quinone and fatty acids were menaquinone-6 and iso-C15 : 0 (27.5 %), iso-C15 : 1 G (22.5 %) and iso-C17 : 0 3-OH (12.8 %), respectively. Based on genetic, phylogenetic and phenotypic properties, strain KK4T represents a novel species of the genus Patiriisocius, for which the name Patiriisocius marinistellae gen. nov., sp. nov. is proposed. The type strain is KK4T (=JCM 33344T=KCTC 72225T). In addition, based on the current data,
Ulvibacter marinus
should be reclassified as Patiriisocius marinus comb. nov.
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Affiliation(s)
- Keisuke Kawano
- Present address: Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo 060–8589, Japan
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minamisawa, Minami-ku, Sapporo, 005-8601, Japan
| | - Natsumi Ushijima
- Support Section for Education and Research, Graduate School of Dental Medicine, Hokkaido University, Hokkaido 060-8586, Japan
| | - Minoru Kihara
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minamisawa, Minami-ku, Sapporo, 005-8601, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
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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. Microorganisms 2020; 8:microorganisms8050634. [PMID: 32349406 PMCID: PMC7285026 DOI: 10.3390/microorganisms8050634] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 02/07/2023] Open
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.
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2020; 70:1-5. [DOI: 10.1099/ijsem.0.003881] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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