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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: 48] [Impact Index Per Article: 16.0] [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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Xie L, Yoshida N, Ishii S, Meng L. Isolation and Polyphasic Characterization of Desulfuromonas versatilis sp. Nov., an Electrogenic Bacteria Capable of Versatile Metabolism Isolated from a Graphene Oxide-Reducing Enrichment Culture. Microorganisms 2021; 9:1953. [PMID: 34576847 PMCID: PMC8465243 DOI: 10.3390/microorganisms9091953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/11/2023] Open
Abstract
In this study, a novel electrogenic bacterium denoted as strain NIT-T3 of the genus Desulfuromonas was isolated from a graphene-oxide-reducing enrichment culture that was originally obtained from a mixture of seawater and coastal sand. Strain NIT-T3 utilized hydrogen and various organic acids as electron donors and exhibited respiration using electrodes, ferric iron, nitrate, and elemental sulfur. The strain contained C16:1ω7c, C16:0, and C15:0 as major fatty acids and MK-8, 9, and 7 as the major respiratory quinones. Strain NIT-T3 contained four 16S rRNA genes and showed 95.7% similarity to Desulfuromonasmichiganensis BB1T, the closest relative. The genome was 4.7 Mbp in size and encoded 76 putative c-type cytochromes, which included 6 unique c-type cytochromes (<40% identity) compared to those in the database. Based on the physiological and genetic uniqueness, and wide metabolic capability, strain NIT-T3 is proposed as a type strain of 'Desulfuromonas versatilis' sp. nov.
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Affiliation(s)
- Li Xie
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Shun’ichi Ishii
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Kanagawa, Japan;
| | - Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
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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: 5.0] [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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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: 2.0] [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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Zhang K, Zhang Z, Hu Z, Zeng F, Chen C, Yang X, Li Y. Bacterial community composition and function succession under aerobic and anaerobic conditions impacts the biodegradation of 17β-estradiol and its environmental risk. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115155. [PMID: 32871481 DOI: 10.1016/j.envpol.2020.115155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
The widespread detection of 17β-estradiol (E2) in the environment has become an emerging concern worldwide due to its endocrine disrupting effects. This work focuses on the aerobic and anaerobic biodegradations of E2 in various sedimentary environments with different availabilities of electron acceptors, including O2, NO3-, Fe3+, SO42-, or HCO3-. The highest removal efficiency (98.9%) and shortest degradation half-life of E2 (t1/2 = 5.0 d) were achieved under aerobic condition, followed by nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions. We propose four different degradation pathways of E2 based on the metabolites identified under various redox conditions. Although most of E2 was effectively removed under aerobic condition, the potential environmental risk still needs to be considered due to the residual estrogenic activity induced by estrone (E1) formation. The endocrine-disrupting activities, as indicated by estradiol equivalent (EEQ) values, were related to E2 degradation rate and metabolite formation. We further analyzed the succession of bacterial community compositions and functions using Illumina HiSeq sequencing and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The findings herein evidenced that bacterial community compositions and metabolic functions associated with different redox conditions impact the biodegradation of E2 and its endocrine-disrupting activity. This knowledge will be useful in predicting the environmental fates of estrogenic hormones in various sedimentary environments and aid in establishing appropriate strategies for eliminating potential environmental risks.
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Affiliation(s)
- Kun Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China; College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Zheng Hu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Feifan Zeng
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Chengyu Chen
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China; Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin, 300191, China.
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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: 5.5] [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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Zhang K, Hu Z, Zeng F, Yang X, Wang J, Jing R, Zhang H, Li Y, Zhang Z. Biodegradation of petroleum hydrocarbons and changes in microbial community structure in sediment under nitrate-, ferric-, sulfate-reducing and methanogenic conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 249:109425. [PMID: 31446121 DOI: 10.1016/j.jenvman.2019.109425] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/16/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
In the present study, the biodegradation behaviors of petroleum hydrocarbons under various reducing conditions were investigated. n-Alkanes and polycyclic aromatic hydrocarbons (PAHs) were degraded with NO3-, Fe3+, SO42-, or HCO3- as terminal electron acceptors (TEAs), which link to four typical reducing conditions (i.e., nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions, respectively) in sediment. The fastest degradation rates were achieved under sulfate-reducing conditions with half-lives of 49.51 days for n-alkanes and 58.74 days for PAHs. For short-chain n-alkanes and low-molecular weight (LMW) PAHs, relatively higher removal efficiencies were achieved under nitrate- and ferric-reducing conditions. The degradation of long-chain n-alkanes and high-molecular weight (HMW) PAHs coupled to methanogenesis was the most favored as compared with other reducing conditions. Carboxylation was found to be the principle mechanism for regulating n-alkane degradation coupled to denitrification, while the activation of n-alkanes by the addition of fumarate was the principle mechanism for the n-alkane degradation under sulfate-reducing conditions. The anaerobic metabolism of n-alkanes may not proceed via fumarate addition or carboxylation under ferric-reducing and methanogenic conditions. Illumina HiSeq sequencing revealed dissimilar structures of the microbial communities under various reducing conditions. It is hypothesized that the utilization of different TEAs for n-alkane and PAH degradation resulted in distinct microbial community structures, which were highly correlated with the varied degradation behaviors of petroleum hydrocarbons in sediment. The current results may provide reference value on better understanding the biodegradation behaviors of n-alkanes and PAHs in association with the induced microbial communities in sedimentary environments under the four typical reducing conditions.
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Affiliation(s)
- Kun Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Zheng Hu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Feifan Zeng
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Jinjin Wang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Ran Jing
- Department of Civil and Environmental Engineering, University of Maryland at College Park, MD, 20742, USA
| | - Huanni Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China; Agro-Environmental Protection Institute, Ministry of Agriculture, Tianjin, 300191, China.
| | - Zhen Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China.
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Xu Z, Masuda Y, Itoh H, Ushijima N, Shiratori Y, Senoo K. Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov. Front Microbiol 2019; 10:2201. [PMID: 31608033 PMCID: PMC6773877 DOI: 10.3389/fmicb.2019.02201] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/09/2019] [Indexed: 11/13/2022] Open
Abstract
In paddy soil, bacteria from the family Geobacteraceae have been shown to strongly contribute to the biogeochemical cycle. However, no Geobacteraceae species with validly published names have been isolated from paddy soil. In this study, we isolated and characterized four novel ferric reducing bacteria in the family Geobacteraceae from the paddy soils of three different fields in Japan. The four strains, S43T, Red53T, S62T, and Red111T, were Gram-stain negative, strictly anaerobic, chemoheterotrophic, and motile with peritrichous flagella. Phylogenetic studies based on 16S rRNA gene sequences, five concatenated housekeeping genes (fusA, rpoB, recA, nifD, and gyrB) and 92 concatenated core genes revealed that the four strains belong to the family Geobacteraceae and are most closely related to Geobacter bemidjiensis BemT (97.4-98.2%, 16S rRNA gene sequence similarities) and Geobacter bremensis Dfr1T (97.1-98.0%). Genomic analysis with average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) calculations clearly distinguished the four isolated strains from other species of the family Geobacteraceae and indicated that strains S43T, Red53T, S62T, and Red111T represent independent species, with values below the thresholds for species delineation. Chemotaxonomic characteristics, including major fatty acid and whole cell protein profiles, showed differences among the isolates and their closest relatives, which were consistent with the results of DNA fingerprints and physiological characterization. Additionally, each of the four isolates shared a low 16S rRNA gene sequence similarity (92.4%) and average amino acid identity (AAI) with the type strain of the type species Geobacter metallireducens. Overall, strains S43T, Red53T, S62T, and Red111T represent four novel species, which we propose to classify in a novel genus of the family Geobacteraceae, and the names Geomonas oryzae gen. nov., sp. nov. (type strain S43T), Geomonas edaphica sp. nov. (type strain Red53T), Geomonas ferrireducens sp. nov. (type strain S62T), and Geomonas terrae sp. nov. (type strain Red111T) are proposed. Based on phylogenetic and genomic analyses, we also propose the reclassification of Geobacter bremensis as Geomonas bremensis comb. nov., Geobacter pelophilus as Geomonas pelophila comb. nov., and Geobacter bemidjiensis as Geomonas bemidjiensis comb. nov.
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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
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Sciences and Technology, Hokkaido, 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
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Abstract
The family Geobacteraceae, with its only valid genus Geobacter, comprises deltaproteobacteria ubiquitous in soil, sediments, and subsurface environments where metal reduction is an active process. Research for almost three decades has provided novel insights into environmental processes and biogeochemical reactions not previously known to be carried out by microorganisms. At the heart of the environmental roles played by Geobacter bacteria is their ability to integrate redox pathways and regulatory checkpoints that maximize growth efficiency with electron donors derived from the decomposition of organic matter while respiring metal oxides, particularly the often abundant oxides of ferric iron. This metabolic specialization is complemented by versatile metabolic reactions, respiratory chains, and sensory networks that allow specific members to adaptively respond to environmental cues to integrate organic and inorganic contaminants in their oxidative and reductive metabolism, respectively. Thus, Geobacteraceae are important members of the microbial communities that degrade hydrocarbon contaminants under iron-reducing conditions and that contribute, directly or indirectly, to the reduction of radionuclides, toxic metals, and oxidized species of nitrogen. Their ability to produce conductive pili as nanowires for discharging respiratory electrons to solid-phase electron acceptors and radionuclides, or for wiring cells in current-harvesting biofilms highlights the unique physiological traits that make these organisms attractive biological platforms for bioremediation, bioenergy, and bioelectronics application. Here we review some of the most notable physiological features described in Geobacter species since the first model representatives were recovered in pure culture. We provide a historical account of the environmental research that has set the foundation for numerous physiological studies and the laboratory tools that had provided novel insights into the role of Geobacter in the functioning of microbial communities from pristine and contaminated environments. We pay particular attention to latest research, both basic and applied, that has served to expand the field into new directions and to advance interdisciplinary knowledge. The electrifying physiology of Geobacter, it seems, is alive and well 30 years on.
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Leitner S, Berger H, Gorfer M, Reichenauer TG, Watzinger A. Isotopic effects of PCE induced by organohalide-respiring bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:24803-24815. [PMID: 28913587 DOI: 10.1007/s11356-017-0075-2] [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: 03/31/2017] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
Reductive dechlorination performed by organohalide-respiring bacteria (OHRB) enables the complete detoxification of certain emerging groundwater pollutants such as perchloroethene (PCE). Environmental samples from a contaminated site incubated in a lab-scale microcosm (MC) study enable documentation of such reductive dechlorination processes. As compound-specific isotope analysis is used to monitor PCE degradation processes, nucleic acid analysis-like 16S-rDNA analysis-can be used to determine the key OHRB that are present. This study applied both methods to laboratory MCs prepared from environmental samples to investigate OHRB-specific isotope enrichment at PCE dechlorination. This method linkage can enhance the understanding of isotope enrichment patterns of distinct OHRB, which further contribute to more accurate evaluation, characterisation and prospection of natural attenuation processes. Results identified three known OHRB genera (Dehalogenimonas, Desulfuromonas, Geobacter) in diverse abundance within MCs. One species of Dehalogenimonas was potentially involved in complete reductive dechlorination of PCE to ethene. Furthermore, the isotopic effects of PCE degradation were clustered and two isotope enrichment factors (ε) (- 11.6‰, - 1.7‰) were obtained. Notably, ε values were independent of degradation rates and kinetics, but did reflect the genera of the dechlorinating OHRB.
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Affiliation(s)
- Simon Leitner
- AIT Austrian Institute of Technology GmbH, Energy Department, Environmental Resources & Technologies, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Harald Berger
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Markus Gorfer
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Thomas G Reichenauer
- AIT Austrian Institute of Technology GmbH, Energy Department, Environmental Resources & Technologies, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria
| | - Andrea Watzinger
- AIT Austrian Institute of Technology GmbH, Energy Department, Environmental Resources & Technologies, Konrad-Lorenz-Str. 24, 3430, Tulln, Austria.
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Ueno A, Shimizu S, Hashimoto M, Adachi T, Matsushita T, Okuyama H, Yoshida K. Effects of Aerobic Growth on the Fatty Acid and Hydrocarbon Compositions of Geobacter bemidjiensis Bem T. J Oleo Sci 2017; 66:93-101. [PMID: 27928141 DOI: 10.5650/jos.ess16122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Geobacter spp., regarded as strict anaerobes, have been reported to grow under aerobic conditions. To elucidate the role of fatty acids in aerobiosis of Geobacter spp., we studied the effect of aerobiosis on fatty acid composition and turnover in G. bemidjiensis BemT. G. bemidjiensis BemT was grown under the following different culture conditions: anaerobic culture for 4 days (type 1) and type 1 culture followed by 2-day anaerobic (type 2) or aerobic culture (anaerobic-to-aerobic shift; type 3). The mean cell weight of the type 3 culture was approximately 2.5-fold greater than that of type 1 and 2 cultures. The fatty acid methyl ester and hydrocarbon fraction contained hexadecanoic (16:0), 9-cis-hexadecenoic [16:1(9c)], tetradecanoic (14:0), tetradecenoic [14:1(7c)] acids, hentriacontanonaene, and hopanoids, but not long-chain polyunsaturated fatty acids. The type 3 culture contained higher levels of 14:0 and 14:1(7c) and lower levels of 16:0 and 16:1(9c) compared with type 1 and 2 cultures. The weight ratio of extracted lipid per dry cell was lower in the type 3 culture than in the type 1 and 2 cultures. We concluded that anaerobically-grown G. bemidjiensis BemT followed by aerobiosis were enhanced in growth, fatty acid turnover, and de novo fatty acid synthesis.
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Affiliation(s)
- Akio Ueno
- Horonobe Research Institute for the Subsurface Environment (H-RISE), NOASTEC
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12
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van den Berg EM, Boleij M, Kuenen JG, Kleerebezem R, van Loosdrecht MCM. DNRA and Denitrification Coexist over a Broad Range of Acetate/N-NO 3- Ratios, in a Chemostat Enrichment Culture. Front Microbiol 2016; 7:1842. [PMID: 27933040 PMCID: PMC5121219 DOI: 10.3389/fmicb.2016.01842] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/02/2016] [Indexed: 11/13/2022] Open
Abstract
Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) compete for nitrate in natural and engineered environments. A known important factor in this microbial competition is the ratio of available electron donor and elector acceptor, here expressed as Ac/N ratio (acetate/nitrate-nitrogen). We studied the impact of the Ac/N ratio on the nitrate reduction pathways in chemostat enrichment cultures, grown on acetate mineral medium. Stepwise, conditions were changed from nitrate limitation to nitrate excess in the system by applying a variable Ac/N ratio in the feed. We observed a clear correlation between Ac/N ratio and DNRA activity and the DNRA population in our reactor. The DNRA bacteria dominated under nitrate limiting conditions in the reactor and were outcompeted by denitrifiers under limitation of acetate. Interestingly, in a broad range of Ac/N ratios a dual limitation of acetate and nitrate occurred with co-occurrence of DNRA bacteria and denitrifiers. To explain these observations, the system was described using a kinetic model. The model illustrates that the Ac/N effect and concomitant broad dual limitation range related to the difference in stoichiometry between both processes, as well as the differences in electron donor and acceptor affinities. Population analysis showed that the presumed DRNA-performing bacteria were the same under nitrate limitation and under dual limiting conditions, whereas the presumed denitrifying population changed under single and dual limitation conditions.
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Affiliation(s)
- Eveline M van den Berg
- Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology Delft, Netherlands
| | - Marissa Boleij
- Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology Delft, Netherlands
| | - J Gijs Kuenen
- Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology Delft, Netherlands
| | - Robbert Kleerebezem
- Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology Delft, Netherlands
| | - Mark C M van Loosdrecht
- Environmental Biotechnology Group, Department of Biotechnology, Delft University of Technology Delft, Netherlands
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13
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Hori T, Aoyagi T, Itoh H, Narihiro T, Oikawa A, Suzuki K, Ogata A, Friedrich MW, Conrad R, Kamagata Y. Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments. Front Microbiol 2015; 6:386. [PMID: 25999927 PMCID: PMC4419728 DOI: 10.3389/fmicb.2015.00386] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/15/2015] [Indexed: 11/13/2022] Open
Abstract
Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8-98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides.
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Affiliation(s)
- Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Hideomi Itoh
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Azusa Oikawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Sapporo, Japan
| | - Kiyofumi Suzuki
- Methane Hydrate Research & Development Division, Japan Oil, Gas and Metals National Corporation Chiba, Japan
| | - Atsushi Ogata
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry and MARUM, University of Bremen Bremen, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
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15
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Zhou S, Yang G, Lu Q, Wu M. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil. Int J Syst Evol Microbiol 2014; 64:3786-3791. [PMID: 25139417 DOI: 10.1099/ijs.0.066662-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)).
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Affiliation(s)
- Shungui Zhou
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Guiqin Yang
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Qin Lu
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Min Wu
- Guangdong Institute of Eco-environmental and Soil Sciences, Guangzhou 510650, PR China
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Bourdakos N, Marsili E, Mahadevan R. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell. Biotechnol Bioeng 2013; 111:709-18. [PMID: 24155100 DOI: 10.1002/bit.25137] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 10/11/2013] [Accepted: 10/13/2013] [Indexed: 02/03/2023]
Abstract
Wastewater-fed microbial fuel cells (MFCs) are a promising technology to treat low-organic carbon wastewater and recover part of the chemical energy in wastewater as electrical power. However, the interactions between electrochemically active and fermentative microorganisms cannot be easily studied in wastewater-fed MFCs because of their complex microbial communities. Defined co-culture MFCs provide a detailed understanding of such interactions. In this study, we characterize the extracellular metabolites in laboratory-scale membrane-less MFCs inoculated with Geobacter sulfurreducens and Escherichia coli co-culture and compare them with pure culture MFCs. G. sulfurreducens MFCs are sparged to maintain anaerobic conditions, while co-culture MFCs rely on E. coli for oxygen removal. G. sulfurreducens MFCs have a power output of 128 mW m(-2) , compared to 63 mW m(-2) from the co-culture MFCs. Analysis of metabolites shows that succinate production in co-culture MFCs decreases current production by G. sulfurreducens and that the removal of succinate is responsible for the increased current density in the late co-culture MFCs. Interestingly, pH adjustment is not required for co-culture MFCs but a base addition is necessary for E. coli MFCs and cultures in vials. Our results show that defined co-culture MFCs provide clear insights into metabolic interactions among bacteria while maintaining a low operational complexity.
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Affiliation(s)
- Nicholas Bourdakos
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St, Toronto, Ontario, M5S 3E5, Canada
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