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Park SY, Zhang Y, O'Loughlin EJ, Jo HY, Kwon JS, Kwon MJ. Temperature-dependent microbial reactions by indigenous microbes in bentonite under Fe(III)- and sulfate-reducing conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133318. [PMID: 38154187 DOI: 10.1016/j.jhazmat.2023.133318] [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: 09/09/2023] [Revised: 12/09/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
Bentonite is a promising buffer material for constructing spent nuclear fuel (SNF) repositories. However, indigenous microbes in bentonite can be introduced to the repository and subsequent sealing of the repository develops anoxic conditions over time which may stimulate fermentation and anaerobic respiration, possibly affecting bentonite structure and SNF repository stability. Moreover, the microbial activity in the bentonite can be impacted by the heat generated from radionuclides decay. Therefore, to investigate the temperature effect on microbial activities in bentonite, we created microcosms with WRK bentonil (a commercial bentonite) using lactate as the electron donor, and sulfate and/or ferrihydrite (Fe(III)) as electron acceptors with incubation at 18 ℃ and 50 ℃. Indigenous WRK microbes reduced sulfate and Fe(III) at both temperatures but with different rates and extents. Lactate was metabolized to acetate at both temperatures, but only to propionate at 18 ℃ during early-stage microbial fermentation. More Fe(III)-reduction at 18 ℃ but more sulfate-reduction at 50 ℃ was observed. Thermophilic and/or metabolically flexible microbes were involved in both fermentation and Fe(III)/sulfate reduction. Our findings illustrate the necessity of considering the influence of temperature on microbial activities when employing bentonite as an engineered buffer material in construction of SNF repository barriers.
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Affiliation(s)
- Su-Young Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | | | - Ho Young Jo
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jang-Soon Kwon
- Korea Atomic Energy Research Institute, Daejeon 34057, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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2
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Tang R, Yang S, Narsing Rao MP, Xie CJ, Han S, Yang QE, Rensing C, Liu GH, Yuan Y, Zhou SG. Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38323900 DOI: 10.1099/ijsem.0.006268] [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: 02/08/2024] Open
Abstract
Three microaerophilic bacterial strains, designated SG22T, SG63T and SG29T were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22T, SG63T and SG29T showed the highest 16S rRNA gene sequence similarities with the members of the genus Anaeromyxobacter. The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus Anaeromyxobacter. The main respiratory menaquinone of SG22T, SG63T and SG29T was MK-8 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 and C16 : 0. SG22T, SG29T and SG63T not only possessed iron reduction ability but also harboured genes (nifHDK) encoding nitrogenase. The genomic DNA G+C contents of SG22T, SG63T and SG29T ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22T, SG63T and SG29T and the closely related species of the genus Anaeromyxobacter were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22T, SG63T and SG29T represent three novel species within the genus Anaeromyxobacter, for which the names Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., are proposed. The type strains are SG22T (= GDMCC 1.3185T = JCM 35581T), SG63T (= GDMCC 1.2914T = JCM 35124T) and SG29T (= GDMCC 1.2911T = JCM 35123T).
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Affiliation(s)
- Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca 3460000, Chile
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qiu-E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, PR 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, Fujian 350002, PR China
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Zhang Y, O'Loughlin EJ, Park SY, Kwon MJ. Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166993. [PMID: 37717756 DOI: 10.1016/j.scitotenv.2023.166993] [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: 07/03/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.
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Affiliation(s)
- Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Su-Young Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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4
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Peco JD, Thouin H, Esbrí JM, Campos-Rodríguez HR, García-Noguero EM, Breeze D, Villena J, Gloaguen E, Higueras PL, Battaglia-Brunet F. Mobility of antimony in contrasting surface environments of a mine site: influence of redox conditions and microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:105808-105828. [PMID: 37721674 DOI: 10.1007/s11356-023-29734-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/02/2023] [Indexed: 09/19/2023]
Abstract
Microbial processes can influence the complex geochemical behaviour of the toxic metalloid antimony (Sb) in mining environments. The present study is aimed to evaluate the influence of microbial communities on the mobility of Sb from solid phases to water in different compartments and redox conditions of a mining site in southwest (SW) Spain. Samples of surface materials presenting high Sb concentrations, from two weathered mining waste dumps, and an aquatic sediment were incubated in slurries comparing oxic and anoxic conditions. The initial microbial communities of the three materials strongly differed. Incubations induced an increase of microbial biomass and an evolution of the microbial communities' structures and compositions, which diverged in different redox conditions. The presence of active bacteria always influenced the mobility of Sb, except in the neutral pH waste incubated in oxic conditions. The effect of active microbial activities in oxic conditions was dependent on the material: Sb oxic release was biologically amplified with the acidic waste, but attenuated with the sediment. Different bacterial genera involved in Sb, Fe and S oxidation or reduction were present and/or grew during incubation of each material. The results highlighted the wide diversity of microbial communities and metabolisms at the small geographic scale of a mining site and their strong implication in Sb mobility.
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Affiliation(s)
- Jesús Daniel Peco
- Instituto de Geología Aplicada, Escuela Universitaria Politécnica de Almadén, Universidad de Castilla-La Mancha, Plaza Manuel Meca, Ciudad Real, 13400, Almadén, Spain
- Escuela Técnica Superior de Ingenieros Agrónomos de Ciudad Real, Universidad de Castilla-La Mancha, Ronda de Calatrava 7, 13071, Ciudad Real, Spain
| | - Hugues Thouin
- BRGM, 3 Av. Claude Guillemin, 45060, Orléans, France
| | - José María Esbrí
- Departamento de Mineralogía y Petrología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Eva Maria García-Noguero
- Instituto de Geología Aplicada, Escuela Universitaria Politécnica de Almadén, Universidad de Castilla-La Mancha, Plaza Manuel Meca, Ciudad Real, 13400, Almadén, Spain
| | | | - Jaime Villena
- Escuela Técnica Superior de Ingenieros Agrónomos de Ciudad Real, Universidad de Castilla-La Mancha, Ronda de Calatrava 7, 13071, Ciudad Real, Spain
| | - Eric Gloaguen
- CNRS, BRGM, ISTO, UMR 7327, Université d'Orléans, 45071, Orléans, France
| | - Pablo Leon Higueras
- Instituto de Geología Aplicada, Escuela Universitaria Politécnica de Almadén, Universidad de Castilla-La Mancha, Plaza Manuel Meca, Ciudad Real, 13400, Almadén, Spain
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [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: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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6
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Vigderovich H, Eckert W, Elvert M, Gafni A, Rubin-Blum M, Bergman O, Sivan O. Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments. Front Microbiol 2023; 14:1206414. [PMID: 37577416 PMCID: PMC10415106 DOI: 10.3389/fmicb.2023.1206414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.
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Affiliation(s)
- Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Marcus Elvert
- MARUM—Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Almog Gafni
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Oded Bergman
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological Research, Migdal, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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7
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Shi C, Tong M, Cai Q, Li Z, Li P, Lu Y, Cao Z, Liu H, Zhao HP, Yuan S. Electrokinetic-Enhanced Bioremediation of Trichloroethylene-Contaminated Low-Permeability Soils: Mechanistic Insight from Spatio-Temporal Variations of Indigenous Microbial Community and Biodehalogenation Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5046-5055. [PMID: 36926893 DOI: 10.1021/acs.est.3c00278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electrokinetic-enhanced bioremediation (EK-Bio), particularly bioaugmentation with injection of biodehalogenation functional microbes such as Dehalococcoides, has been documented to be effective in treating a low-permeability subsurface matrix contaminated with chlorinated ethenes. However, the spatio-temporal variations of indigenous microbial community and biodehalogenation activity of the background matrix, a fundamental aspect for understanding EK-Bio, remain unclear. To fill this gap, we investigated the variation of trichloroethylene (TCE) biodehalogenation activity in response to indigenous microbial community succession in EK-Bio by both column and batch experiments. For a 195 day EK-Bio column (∼1 V/cm, electrolyte circulation, lactate addition), biodehalogenation activity occurred first near the cathode (<60 days) and then spread to the anode (>90 days), which was controlled by electron acceptor (i.e., Fe(III)) competition and microbe succession. Amplicon sequencing and metagenome analysis revealed that iron-reducing bacteria (Geobacter, Anaeromyxobacter, Geothrix) were enriched within initial 60 d and were gradually replaced by organohalide-respiring bacteria (versatile Geobacter and obligate Dehalobacter) afterward. Iron-reducing bacteria required an initial long time to consume the competitive electron acceptors so that an appropriate reductive condition could be developed for the enrichment of organohalide-respiring bacteria and the enhancement of TCE biodehalogenation activity.
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Affiliation(s)
- Chongwen Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Man Tong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Qizheng Cai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Zhengtao Li
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Yuxi Lu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Zixuan Cao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - Hui Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, No. 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan 430078, P. R. China
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Brito EMS, Guyoneaud R, Caretta CA, Joseph M, Goñi-Urriza M, Ollivier B, Hirschler-Réa A. Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches. Extremophiles 2023; 27:5. [PMID: 36800123 DOI: 10.1007/s00792-023-01291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.
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Affiliation(s)
- Elcia Margareth Souza Brito
- Environmental Engineering Department, Laboratory of Environmental Microbiology and Applied Molecular Biology, DI-CGT, Universidad de Guanajuato, CP 36000, Guanajuato (Gto.), Mexico
| | - Rémy Guyoneaud
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - César Augusto Caretta
- Astronomy Department, Universidad de Guanajuato, DCNE-CGT, CP 36023, Guanajuato (Gto.), Mexico.
| | - Manon Joseph
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Marisol Goñi-Urriza
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Bernard Ollivier
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Agnès Hirschler-Réa
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
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Li S, Li G, Huang X, Chen Y, Lv C, Bai L, Zhang K, He H, Dai J. Cultivar-specific response of rhizosphere bacterial community to uptake of cadmium and mineral elements in rice (Oryza sativa L.). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114403. [PMID: 36508785 DOI: 10.1016/j.ecoenv.2022.114403] [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: 07/12/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Toxic metal-contaminated farmland from Cadmium (Cd) can enhance the accumulation of Cd and impair the absorption of mineral elements in brown rice. Although several studies have been conducted on Cd exposure on rice, little has been reported on the relationship between Cd and mineral elements in brown rice and the regulatory mechanism of rhizosphere microorganisms during element uptake. Thus, a field study was undertaken to screen japonica rice cultivars with low Cd and high mineral elements levels, analyze the quantitative relationship between Cd and seven mineral elements, and investigate the cultivar-specific response of rice rhizosphere bacterial communities to differences in Cd and mineral uptake in japonica rice. Results showed that Huaidao-9 and Xudao-7 had low Cd absorption and high amounts of mineral nutrient elements (Fe, Zn, Mg, and Ca, LCHM group), whereas Zhongdao-1 and Xinkedao-31 showed opposite accumulation characteristics (HCLM group). Stepwise regression analysis showed that zinc, iron, and potassium are the key minerals that affect Cd accumulation in japonica rice and zinc was the most important factor, accounting for 68.99 %. The accumulation of Cd and mineral elements is potentially associated with rhizosphere soil bacteria. Taxa enriched in the LCHM rhizosphere (phyla Acidobacteriota and MBNT15) indicated the high nutrient characteristics of the soil and reduced activity of Cd in soil. The HCLM rhizosphere was highly colonized by metal-activating bacteria (Actinobacteria), lignin-degrading bacteria (Actinobacteria and Chlorofexi), and bacteria scavenging nutrients and trace elements (Anaerolinea and Ketobacter). Moreover, the differences in the uptake of Cd and mineral elements affected predicted functions of microbial communities, including sulfur oxidation and sulfur derivative formation, human or plant pathogen, and functions related to the iron oxidation and nitrate reduction. The results indicate a potential association of Cd and mineral elements uptake and accumulation with rhizosphere bacteria in rice, thus providing theoretical basis and a new perspective on the maintenance of rice security and high quality simultaneously.
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Affiliation(s)
- Shuangshuang Li
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Guangxian Li
- Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xianmin Huang
- Shandong General Station of Agricultural Environmental Protection and Rural Energy, Jinan 250100, China
| | - Yihui Chen
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Cheng Lv
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Liyong Bai
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Ke Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Huan He
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jiulan Dai
- Environment Research Institute, Shandong University, Qingdao 266237, China.
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Koner S, Chen JS, Rathod J, Hussain B, Hsu BM. Unravelling the ultramafic rock-driven serpentine soil formation leading to the geo-accumulation of heavy metals: An impact on the resident microbiome, biogeochemical cycling and acclimatized eco-physiological profiles. ENVIRONMENTAL RESEARCH 2023; 216:114664. [PMID: 36336091 DOI: 10.1016/j.envres.2022.114664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
In the present study, we have underpinned the serpentine rock, serpentinized ultramafic soil and rhizosphere's microbial communities, signifying their heavy metals-exposed taxa signatures and functional repertoires in comparison to non-serpentine soils. The results revealed that the serpentine rock embedded soil highlighted the geo-accumulation of higher amount of Cr and Ni impacting soil microbial diversity negatively by metal stress-driven selection. Biolog Ecoplate CLPP defined a restricted spectrum of C-utilization in the higher heavy metal-containing serpentine samples compared to non-serpentine. The linear discriminant analysis (LDA) score identified a higher abundance of Desulfobacterota, Opitutales, and Bacteroidales in low Cr and Ni-stressed non-serpentine-exposed samples. Whereas the abundance of Propionibacteriales and Actinobacteriota were significantly enriched in the serpentine niche. Further, the C, N, S, Fe, and methane biogeochemical cycles linked functional members were identified, and showing higher functional diversity in low Cr and Ni concentration-containing rhizosphere JS-soils. The Pearson correlation coefficient (r) value confirmed the abundance of functional members linked to specific biogeochemical cycle, positively correlated with relevant pathway enrichment. Ultimately, this study highlighted the heavy metal stress within a serpentine setting that could limit the resident microbial community's metabolic diversity and further select the bacteria that could thrive in the serpentine-associated heavy metal-stressed soils. These acclimatized microbes could pave the way for the future applications in the soil conservation and management.
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Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, 382355, Gujarat, India
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
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11
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Luo X, Huang L, Cai X, Zhou L, Zhou S, Yuan Y. Structure and core taxa of bacterial communities involved in extracellular electron transfer in paddy soils across China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157196. [PMID: 35810886 DOI: 10.1016/j.scitotenv.2022.157196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities with extracellular electron transfer (EET) activity are capable of driving geochemical changes and cycles, but a comprehensive understanding of the key microbiota responsible for EET in complex soil matrices is still lacking. Herein, the EET activities, in terms of maximum current density (jmax) and accumulated charge output (Cout), of 41 paddy soils across China were evaluated from the exoelectrogenic properties with a conventional bioelectrochemical system (BES). The jmax with a range of 8.85 × 10-4 to 0.41 A/m2 and Cout with a range of 0.27 to 172.21C were obtained from these soil-based BESs. The bacterial community analyses revealed that the most abundant phylum, order, and genus were Firmicutes, Clostridiales, and Clostridum-sensus-stricto 10, respectively. Bacterial network analysis displayed the positive correlations between the majority of electroactive bacteria-containing genera and multiple other genera, indicating their underlying cooperation for the EET. Partial least squares regression (PLSR) model showed remarkable performance in describing the EET activity with 75 most abundant genera as input variables, identified that 32 genera were very important for governing the EET activities. Multiple linear regression (MLR) analyses further prioritized that the genera norank-c-Berkelbacteria and Fonticella were the key contributors, while the genus Paenibacillus was the key competitor against bacterial exoelectrogenesis in paddy soils. Moreover, the spearman analysis showed that the abundance of these keystone taxa was mainly influenced by the carbon content and pH. This approach provides a promising avenue to monitor the microbial activities in paddy soils as well as the links between microbial community composition and ecological function.
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Affiliation(s)
- Xiaoshan Luo
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Lingyan Huang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Xixi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Lihua Zhou
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, School of Resources and Environment, Fujian Agriculture and Forestry, Fuzhou 350000, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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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: 0.5] [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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Lyu C, Li L, Liu X, Zhao Z. Rape straw application facilitates Se and Cd mobilization in Cd-contaminated seleniferous soils by enhancing microbial iron reduction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 310:119818. [PMID: 35870532 DOI: 10.1016/j.envpol.2022.119818] [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: 05/13/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Many naturally seleniferous soils are faced with Cd contamination problem, which severely limits crop cultivation in these areas. Straw returning has been widely applied in agricultural production due to its various benefits to soil physicochemical properties, soil fertility, and crops yield. However, effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils remain largely unclear. Therefore, the effects of straw application on the fates of Se and Cd in Cd-contaminated seleniferous soils were investigated in this study. The results showed that iron reduction driven by Clostridium and Anaeromyxbacter was responsible for the variations in Se and Cd fates in soil. Straw application respectively increased the gene copy numbers of Clostridium and Anaeromyxbacter by 19.5-56.3% and 33.6-39.8%, thus promoting iron reductive dissolution, eventually resulting in a high release amount of Se and Cd from Fe(III) (oxyhydr) oxides. Under reducing conditions, the released Cd was adsorbed by the newly formed metal sulfides or reacted with sulfides to generate CdS precipitates. Straw application decreased the soil exchangeable Se and soil exchangeable Cd concentration during flooding phase. However, straw application significantly increased Se/Cd in soil solution which had the highest bioavailability during flooding. In addition, straw application increased soil exchangeable Se concentration, but it had no significant effects on soil exchangeable Cd concentration after soil drainage. Taken together, straw application increased Se bioavailability and Cd mobility. Therefore, straw application is an effective method for improving Se bioavailability, but it is not suitable for the application to Cd-contaminated paddy soils. In the actual agricultural production, straw could be applied in seleniferous soils to improve Se bioavailability. At the same time, straw application should be cautious to avoid the release of Cd from Cd-contaminated soil.
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Affiliation(s)
- Chenhao Lyu
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan, 430070, China
| | - Lei Li
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan, 430070, China
| | - Xinwei Liu
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan, 430070, China
| | - Zhuqing Zhao
- Microelement Research Center, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan, 430070, China.
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14
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Solano-Arguedas AF, Boothman C, Newsome L, Pattrick RAD, Arguedas-Quesada D, Robinson CH, Lloyd JR. Geochemistry and microbiology of tropical serpentine soils in the Santa Elena Ophiolite, a landscape-biogeographical approach. GEOCHEMICAL TRANSACTIONS 2022; 23:2. [PMID: 36167930 PMCID: PMC9516835 DOI: 10.1186/s12932-022-00079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
The Santa Elena Ophiolite is a well-studied ultramafic system in Costa Rica mainly comprised of peridotites. Here, tropical climatic conditions promote active laterite formation processes, but the biogeochemistry of the resulting serpentine soils is still poorly understood. The aim of this study was to characterize the soil geochemical composition and microbial community of contrasting landscapes in the area, as the foundation to start exploring the biogeochemistry of metals occurring there. The soils were confirmed as Ni-rich serpentine soils but differed depending on their geographical location within the ophiolite area, showing three serpentine soil types. Weathering processes resulted in mountain soils rich in trace metals such as cobalt, manganese and nickel. The lowlands showed geochemical variations despite sharing similar landscapes: the inner ophiolite lowland soils were more like the surrounding mountain soils rather than the north lowland soils at the border of the ophiolite area, and within the same riparian basin, concentrations of trace metals were higher downstream towards the mangrove area. Microbial community composition reflected the differences in geochemical composition of soils and revealed potential geomicrobiological inputs to local metal biogeochemistry: iron redox cycling bacteria were more abundant in the mountain soils, while more manganese-oxidizing bacteria were found in the lowlands, with the highest relative abundance in the mangrove areas. The fundamental ecological associations recorded in the serpentine soils of the Santa Elena Peninsula, and its potential as a serpentinization endemism hotspot, demonstrate that is a model site to study the biogeochemistry, geomicrobiology and ecology of tropical serpentine areas.
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Affiliation(s)
- Agustín F Solano-Arguedas
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK.
- Forest Resources Unit (Reforesta), Engineering Research Institute (INII) and School of Chemistry, Universidad de Costa Rica, Montes de Oca, San José, 11501-2260, Costa Rica.
| | - Christopher Boothman
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Laura Newsome
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK
- Camborne School of Mines and Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Richard A D Pattrick
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Daniel Arguedas-Quesada
- Sociedad Civil Pro Ambiente Verdiazul CR, Playa Junquillal de Santa Cruz, Guanacaste, 50303, Costa Rica
| | - Clare H Robinson
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Williamson Research Centre, Department of Earth and Environmental Sciences, School of Natural Sciences, University of Manchester, Manchester, M13 9PL, UK.
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15
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Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
- *Correspondence: Josefa Antón,
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16
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Hall SJ, Huang W, Napieralski SA, Roden E. Shared Microbial Taxa Respond Predictably to Cyclic Time-Varying Oxygen Limitation in Two Disparate Soils. Front Microbiol 2022; 13:866828. [PMID: 35722278 PMCID: PMC9203030 DOI: 10.3389/fmicb.2022.866828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022] Open
Abstract
Periodic oxygen (O2) limitation in humid terrestrial soils likely influences microbial composition, but whether communities share similar responses in disparate environments remains unclear. To test if specific microbial taxa share consistent responses to anoxia in radically different soils, we incubated a rainforest Oxisol and cropland Mollisol under cyclic, time-varying anoxic/oxic cycles in the laboratory. Both soils are known to experience anoxic periods of days to weeks under field conditions; our incubation treatments consisted of anoxic periods of 0, 2, 4, 8, or 12 d followed by 4 d of oxic conditions, repeated for a total of 384 d. Taxa measured by 16S rRNA gene sequences after 48 d and 384 d of experimental treatments varied strongly with increasing anoxic period duration, and responses to anoxia often differed between soils at multiple taxonomic levels. Only 19% of the 30,356 operational taxonomic units (OTUs) occurred in both soils, and most OTUs did not respond consistently to O2 treatments. However, the OTUs present in both soils were disproportionally abundant, comprising 50% of sequences, and they often had a similar response to anoxic period duration in both soils (p < 0.0001). Overall, 67 OTUs, 36 families, 15 orders, 10 classes, and two phyla had significant and directionally consistent (positive or negative) responses to anoxic period duration in both soils. Prominent OTUs and taxonomic groups increasing with anoxic period duration in both soils included actinomycetes (Micromonosporaceae), numerous Ruminococcaceae, possible metal reducers (Anaeromyxobacter) or oxidizers (Candidatus Koribacter), methanogens (Methanomicrobia), and methanotrophs (Methylocystaceae). OTUs decreasing with anoxic duration in both soils included nitrifiers (Nitrospira) and ubiquitous unidentified Bradyrhizobiaceae and Micromonosporaceae. Even within the same genus, different OTUs occasionally showed strong positive or negative responses to anoxic duration (e.g., Dactylosporangium in the Actinobacteria), highlighting a potential for adaptation or niche partitioning in variable-O2 environments. Overall, brief anoxic periods impacted the abundance of certain microbial taxa in predictable ways, suggesting that microbial community data may partially reflect and integrate spatiotemporal differences in O2 availability within and among soils.
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Affiliation(s)
- Steven J. Hall
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Steven J. Hall,
| | - Wenjuan Huang
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | | | - Eric Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI, United States
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17
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Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality. mSystems 2022; 7:e0104721. [PMID: 35229646 PMCID: PMC8941939 DOI: 10.1128/msystems.01047-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soil microbiota plays fundamental roles in maintaining ecosystem functions and services, including biogeochemical processes and plant productivity. Despite the ubiquity of soil microorganisms from the topsoil to deeper layers, their vertical distribution and contribution to element cycling in subsoils remain poorly understood. Here, nine soil profiles (0 to 135 cm) were collected at the local scale (within 300 km) from two canonical paddy soil types (Fe-accumuli and Hapli stagnic anthrosols), representing redoximorphic and oxidative soil types, respectively. Variations with depth in edaphic characteristics and soil bacterial and diazotrophic community assemblies and their associations with element cycling were explored. The results revealed that nitrogen and iron status were the most distinguishing edaphic characteristics of the two soil types throughout the soil profile. The acidic Fe-accumuli stagnic anthrosols were characterized by lower concentrations of free iron oxides and total iron in topsoil and ammonia in deeper layers compared with the Hapli stagnic anthrosols. The bacterial and diazotrophic community assemblies were mainly shaped by soil depth, followed by soil type. Random forest analysis revealed that nitrogen and iron cycling were strongly correlated in Fe-accumuli stagnic anthrosol, whereas in Hapli soil, available sulfur was the most important variable predicting both nitrogen and iron cycling. The distinctive biogeochemical processes could be explained by the differences in enrichment of microbial taxa between the two soil types. The main discriminant clades were the iron-oxidizing denitrifier Rhodanobacter, Actinobacteria, and diazotrophic taxa (iron-reducing Geobacter, Nitrospirillum, and Burkholderia) in Fe-accumuli stagnic anthrosol and the sulfur-reducing diazotroph Desulfobacca in Hapli stagnic anthrosol. IMPORTANCE Rice paddy ecosystems support nearly half of the global population and harbor remarkably diverse microbiomes and functions in a variety of soil types. Diazotrophs provide significant bioavailable nitrogen in paddy soil, priming nitrogen transformation and other biogeochemical processes. This study provides a novel perspective on the vertical distribution of bacterial and diazotrophic communities in two hydragric anthrosols. Microbiome analysis revealed divergent biogeochemical processes in the two paddy soil types, with a dominance of nitrogen-iron cycling processes in Fe-accumuli stagnic anthrosol and sulfur-nitrogen-iron coupling in Hapli stagnic anthrosol. This study advances our understanding of the multiple significant roles played by soil microorganisms, especially diazotrophs, in biogeochemical element cycles, which have important ecological and biogeochemical ramifications.
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18
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Wunder LC, Aromokeye DA, Yin X, Richter-Heitmann T, Willis-Poratti G, Schnakenberg A, Otersen C, Dohrmann I, Römer M, Bohrmann G, Kasten S, Friedrich MW. Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments. THE ISME JOURNAL 2021; 15:3587-3604. [PMID: 34155335 PMCID: PMC8630232 DOI: 10.1038/s41396-021-01014-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.
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Affiliation(s)
- Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Graciana Willis-Poratti
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Instituto Antártico Argentino, Buenos Aires, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carolin Otersen
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ingrid Dohrmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Miriam Römer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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19
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Wang H, Li X, Li X, Li F, Su Z, Zhang H. Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China. MICROBIAL ECOLOGY 2021; 82:961-970. [PMID: 33660069 DOI: 10.1007/s00248-021-01716-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.
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Affiliation(s)
- Huanhuan Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China.
| | - Fuli Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
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Bhat MA, Mishra AK, Bhat MA, Banday MI, Bashir O, Rather IA, Rahman S, Shah AA, Jan AT. Myxobacteria as a Source of New Bioactive Compounds: A Perspective Study. Pharmaceutics 2021; 13:1265. [PMID: 34452226 PMCID: PMC8401837 DOI: 10.3390/pharmaceutics13081265] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Myxobacteria are unicellular, Gram-negative, soil-dwelling, gliding bacteria that belong to class δ-proteobacteria and order Myxococcales. They grow and proliferate by transverse fission under normal conditions, but form fruiting bodies which contain myxospores during unfavorable conditions. In view of the escalating problem of antibiotic resistance among disease-causing pathogens, it becomes mandatory to search for new antibiotics effective against such pathogens from natural sources. Among the different approaches, Myxobacteria, having a rich armor of secondary metabolites, preferably derivatives of polyketide synthases (PKSs) along with non-ribosomal peptide synthases (NRPSs) and their hybrids, are currently being explored as producers of new antibiotics. The Myxobacterial species are functionally characterized to assess their ability to produce antibacterial, antifungal, anticancer, antimalarial, immunosuppressive, cytotoxic and antioxidative bioactive compounds. In our study, we have found their compounds to be effective against a wide range of pathogens associated with the concurrence of different infectious diseases.
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Affiliation(s)
- Mudasir Ahmad Bhat
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | | | - Mujtaba Aamir Bhat
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Mohammad Iqbal Banday
- Department of Microbiology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Ommer Bashir
- Department of School Education, Jammu 181205, Jammu and Kashmir, India;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia;
| | - Safikur Rahman
- Department of Botany, MS College, BR Ambedkar Bihar University, Muzaffarpur 845401, Bihar, India;
| | - Ali Asghar Shah
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
| | - Arif Tasleem Jan
- Department of Botany, Baba Ghulam Shah Badshah University, Rajouri 185234, Jammu and Kashmir, India;
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21
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Wang C, Huang Y, Zhang C, Zhang Y, Yuan K, Xue W, Liu Y, Liu Y, Liu Z. Inhibition effects of long-term calcium-magnesia phosphate fertilizer application on Cd uptake in rice: Regulation of the iron-nitrogen coupling cycle driven by the soil microbial community. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125916. [PMID: 34492849 DOI: 10.1016/j.jhazmat.2021.125916] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) pollution in paddy soil seriously endangers food safety production. To investigate the effects and microbiological mechanisms of calcium-magnesium-phosphate (CMP) fertilizer application on Cd reduction in rice, field experiments were conducted in Cd-contaminated paddy soil. Compared with conventional compound fertilizer, CMP fertilizer treatments inhibited Cd uptake through plant roots, significantly decreasing Cd content in rice grains from 0.340 to 0.062 mg/kg. Soil pH and total Ca, Mg and P contents increased after CMP fertilizer application, resulting in a further decrease in soil available Cd content from 0.246 to 0.181 mg/kg. Specific extraction analysis recorded a decrease in both available Fe content and the ratio of nitrate to ammonium nitrogen, indicating that the soil Fe-N cycle was affected by the addition of CMP fertilizer. This finding was also recorded using soil bacterial community sequencing, with CMP fertilizer promoting the progress of nitrate-dependent Fe-oxidation driven by Thiobacillus (1.60-2.83%) and subsequent dissimilatory nitrate reduction to ammonium (DNRA) driven by Ignavibacteriae (1.01-1.92%); Fe-reduction driven by Anaeromyxobacter (3.09-2.23%) was also inhibited. Our results indicate that CMP fertilizer application regulates the Fe-N coupling cycle driven by the soil microbial community to benefit remediation of Cd contaminated paddy soil.
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Affiliation(s)
- Changrong Wang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China
| | - Yongchun Huang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China
| | - Changbo Zhang
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China
| | - Yahui Zhang
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, People's Republic of China
| | - Kai Yuan
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China
| | - Weijie Xue
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China
| | - Yaping Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, People's Republic of China
| | - Yuemin Liu
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, People's Republic of China
| | - Zhongqi Liu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, People's Republic of China.
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Glodowska M, Schneider M, Eiche E, Kontny A, Neumann T, Straub D, Kleindienst S, Kappler A. Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 281:117012. [PMID: 33813189 DOI: 10.1016/j.envpol.2021.117012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Fe(III) minerals play a crucial role for arsenic (As) mobility in aquifers as they usually represent the main As-bearing phases. Microbial reductive dissolution of As-bearing Fe(III) minerals is responsible for the release of As and the resulting groundwater contamination in many sites worldwide. So far, in most studies mainly abiogenic iron minerals have been considered. Yet, biogenic minerals that possess different properties to their abiogenic counterparts are also present in the environment. In some environments they dominate the iron mineral inventory but so far, it is unclear what this means for the As mobility. We, therefore, performed an in-situ aquifer Fe(III) minerals exposure experiment i) to evaluate how different biogenic and abiogenic Fe(III) minerals are transformed in a strongly reducing, As-contaminated aquifer (25 m) compared to As-free moderately reducing aquifer (32 m) and ii) to assess which microbial taxa are involved in these Fe(III) minerals transformations. We found that higher numbers of bacteria and archaea were associated with the minerals incubated in the As-contaminated compared to the non-contaminated aquifer and that all Fe(III) minerals were mainly colonized by Fe(III)-reducing bacteria, with Geobacter being the most abundant taxon. Additionally, fermenting microorganisms were abundant on minerals incubated in the As-contaminated aquifer, while methanotrophs were identified on the minerals incubated in the As-free moderately reducing aquifer, implying involvement of these microorganisms in Fe(III) reduction. We observed that biogenic Fe(III) minerals generally tend to become more reduced and when incubated in the As-contaminated aquifer sorbed more As than the abiogenic ones. Most of abiogenic and biogenic Fe(III) minerals were transformed into magnetite while biogenic more crystalline mixed phases were not subjected to visible transformation. This in-situ Fe(III) minerals incubation approach shows that biogenic minerals are more prone to be colonized by (Fe(III)-reducing) microorganisms and bind more As, although ultimately produce similar minerals during Fe(III) reduction.
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Affiliation(s)
- Martyna Glodowska
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Germany; Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany; Department of Microbiology, IWWR, Radboud University, the Netherlands.
| | - Magnus Schneider
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, KIT, Germany
| | - Elisabeth Eiche
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, KIT, Germany
| | - Agnes Kontny
- Karlsruhe Institute of Technology, Institute of Applied Geosciences, KIT, Germany
| | - Thomas Neumann
- Technical University of Berlin, Institute for Applied Geosciences, Berlin, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Germany
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Park Y, Yu J, Nguyen VK, Park S, Kim J, Lee T. Understanding complete ammonium removal mechanism in single-chamber microbial fuel cells based on microbial ecology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144231. [PMID: 33385649 DOI: 10.1016/j.scitotenv.2020.144231] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
The removal of organics and ammonium from domestic wastewater was successfully achieved by a flat-panel air-cathode microbial fuel cell (FA-MFC). To elucidate the reason for complete ammonium removal in the single-chamber MFCs, microbial communities were analyzed in biofilms on the surface of each anode, separator, and cathode of separator-electrode assemblies (SEAs). The spatial distribution of bacterial families related to the nitrogen cycle varied based on local conditions. Since oxygen diffusing from the air-cathode created a locally aerobic condition, ammonia-oxidizing bacteria (AOB) Nitrosomonadacea and nitrite-oxidizing bacteria (NOB) Nitrospiraceae were present near the cathode. NOB (~12.1%) was more abundant than AOB (~4.4%), suggesting that the nitrate produced by NOB may be reduced back to nitrite by heterotrophic denitrifiers such as Rhodocyclaceae (~21.7%) and Comamonadaceae (~5%) in the anoxic zone close to the NOB layer. Near that zone, the "nitrite loop" also substantially enriched two nitrite-reducing bacterial families: Ignavibacteriaceae (~18.1%), facultative heterotrophs, and Brocadiaceae (~11.2%), anaerobic ammonium oxidizing autotrophs. A larger inner area of biofilm contained abundant heterotrophic denitrifiers and fermentation bacteria. These results indicate that the large-surface SEA of FA-MFC allows counter-diffusion between substrates and oxygen, resulting in interactions of bacteria involved in the nitrogen cycle for complete ammonium removal.
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Affiliation(s)
- Younghyun Park
- Korea Testing & Research Institute, Ulsan 44412, Republic of Korea
| | - Jaecheul Yu
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Van Khanh Nguyen
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Seonghwan Park
- Future Environmental Research Center, Gyeongnam Department of Environmental Toxicology & Chemistry, Korea Institute of Toxicology, Jinju 52834, Republic of Korea
| | - Jeongmi Kim
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea
| | - Taeho Lee
- Department of Civil and Environmental Engineering, Pusan National University, Busan 46241, Republic of Korea.
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24
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Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.
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Sun Q, Guo S, Wang R, Song J. Responses of bacterial communities and their carbon dynamics to subsoil exposure on the Loess Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:144146. [PMID: 33298321 DOI: 10.1016/j.scitotenv.2020.144146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Subsoil exposure due to factors including erosion and terracing, evidently decreases soil organic carbon storage and productivity, but the responses of bacterial communities and their carbon dynamics remain unclear. Soils from 0-20 cm, 20-60 cm and 60-100 cm were collected from three 100 cm profiles in bare land on the Loess Plateau, and incubated in buried pots for a year (July 2016 to July 2017) to simulate subsoil exposure, with ongoing monitoring of the microbial mineralization rate of soil organic carbon (Kc), using Li-Cor 8100. At the end of the incubation period, the exposed soil and the in situ control soil were sampled to investigate changes in bacterial community composition, as represented by 16S rRNA, and the activities of enzymes involved in soil carbon cycling. Both copiotrophic (Actinobacteria and Alphaproteobacteria) and oligotrophic (Thermoleophilia) groups were stimulated in the exposed vs. control soil at 20-60 and 60-100 cm. The exposed vs. control soil from 60 to 100 cm produced the greatest bacterial responses, such as greater diversity and altered keystone groups (Thermoleophilia vs. unidentified Acidobacteria). Enzyme activities were greater in the exposed vs. control soil at both 20-60 cm (β-D-xylosidase and cellobiohydrolase) and 60-100 cm (β-D-xylosidase and β-D-glucosidase). The exposed soil from 20-60 cm and 60-100 cm had lower Kc and Q10 values than those at 0-20 cm. Our findings revealed the existence of bacterial depth-specific responses to subsoil exposure, and highlight the effect of anthropogenic soil redistribution on soil carbon flux and its potential responses to future climate change.
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Affiliation(s)
- Qiqi Sun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China; Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China
| | - Shengli Guo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China
| | - Rui Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shannxi 712100, PR China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, PR China.
| | - Jinming Song
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China.
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Qiu H, Gu L, Sun B, Zhang J, Zhang M, He S, An S, Leng X. Metagenomic Analysis Revealed that the Terrestrial Pollutants Override the Effects of Seasonal Variation on Microbiome in River Sediments. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 105:892-898. [PMID: 33152096 DOI: 10.1007/s00128-020-03033-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Researching the structure and function of sediment microbiome contribute to understanding the response of microbiome to external disturbances. However, seasonal changes in sediment microbiome with different terrestrial pollutants input have not yet been clearly understood. Metagenomic sequencing was used to evaluate the effects of seasonal variations and different land use types on sediment microbiome. Results showed that the differences in structure and functions of sediment microbiome among different land use types were obviously greater than different seasons. This indicated that the terrestrial pollutants weakened the effects of seasonal variations on shaping the sediment microbiome. The significant differences in sediment properties under the input of different terrestrial pollutants was observed, but no obvious differences between seasons, which may be the reason why terrestrial pollutants override the effects of seasonal variation on the sediment microbiome. Overall, the results extended our understanding of the impacts of seasonal variation and terrestrial pollutants on river sediment microbiome.
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Affiliation(s)
- Han Qiu
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, 210093, China
- Nanjing University Ecology Research Institute of Changshu, Changshu, 215500, Jiangsu, China
| | - Likun Gu
- College of Resources and Environment, Henan University of Engineering, Zhengzhou, 451191, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bo Sun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianyun Zhang
- College of Resources and Environment, Henan University of Engineering, Zhengzhou, 451191, China
| | - Miao Zhang
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, 210093, China
| | - Shanshan He
- Sino-Japan Friendship Center for Environmental Protection, No. 1 Yu Hui Nan Road, Beijing, 100029, China
| | - Shuqing An
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, 210093, China
- Nanjing University Ecology Research Institute of Changshu, Changshu, 215500, Jiangsu, China
| | - Xin Leng
- School of Life Science and Institute of Wetland Ecology, Nanjing University, Nanjing, 210093, China.
- Nanjing University Ecology Research Institute of Changshu, Changshu, 215500, Jiangsu, China.
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27
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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: 33] [Impact Index Per Article: 8.3] [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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28
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Kapili BJ, Barnett SE, Buckley DH, Dekas AE. Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment. ISME JOURNAL 2020; 14:971-983. [PMID: 31907368 PMCID: PMC7082343 DOI: 10.1038/s41396-019-0584-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using 15N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
| | - Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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Li H, Yu Y, Guo J, Li X, Rensing C, Wang G. Dynamics of the rice rhizosphere microbial community under continuous and intermittent flooding treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 249:109326. [PMID: 31421482 DOI: 10.1016/j.jenvman.2019.109326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 07/11/2019] [Accepted: 07/28/2019] [Indexed: 06/10/2023]
Abstract
Flooding regime is an important agronomic strategy, and widely applied in heavy metal-contaminated soil for controlling heavy metal uptake through biochemical processes. However, the dynamics of the microbial community in the rhizosphere of rice under different flooding systems are not well understood. In the present study, we investigated the dynamics between the microbial community and heavy metal ions under continuous flooding (CF) and intermittent flooding (IF) conditions to decipher the relationship between microbial community and environmental factors. The results showed that, for the complex Cd, Pb, and Zn contaminated soil under CF treatment did not significantly suppress Cd uptake, but promoted Pb and Ni accumulation into the rice root. Soil pH and bio-available phosphate content appeared to be the key factors impacting heavy metal mobility. When observing the microbial community in the rhizosphere, long term flooding resulted in an abundance of Anaeromyxobactersp., Geobacter and Desulfovibrio, and the abundance of these taxa displayed a significant relationship to Pb and Zn content of rice roots. From the study, we observed that the flooding regime could have a significant impact on concentrations of Cd, Pb and Ni in rice roots, and the different richness of SRB and FeRB may contribute to uptake of these heavy metals. In future work, the impact of Fe cycling on heavy metal bioavailability in the plant rhizosphere should be investigated further.
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Affiliation(s)
- HaiLong Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Yu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - JingXia Guo
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiangzhen Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
| | - Guo Wang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Roth H, Gallo S, Badger P, Hillwig M. Changes in microbial communities of a passive coal mine drainage bioremediation system. Can J Microbiol 2019; 65:775-782. [DOI: 10.1139/cjm-2018-0612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%–43%), Bacteroidetes (12%–37%), Firmicutes (3%–11%), and Verrucomicrobia (6%–11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.
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Affiliation(s)
- Hannah Roth
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
| | - Samantha Gallo
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
| | - Paul Badger
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
| | - Melissa Hillwig
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
- Department of Science, Robert Morris University, Moon Township, PA 15108, USA
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31
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Li H, Su JQ, Yang XR, Zhu YG. Distinct rhizosphere effect on active and total bacterial communities in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:422-430. [PMID: 30176455 DOI: 10.1016/j.scitotenv.2018.08.373] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/24/2018] [Accepted: 08/26/2018] [Indexed: 05/11/2023]
Abstract
Rhizosphere microbes are critical for plant health and biogeochemical cycles. Understanding the diversity of active microorganisms in the rhizosphere is key to enhancing plant growth and productivity. We examined rhizosphere bacterial communities of rice by comparison of the 16S ribosomal subunit amplicons generated from both the total (DNA-based, 16S rRNA gene) and the active (RNA-based, 16S rRNA) soil microbiota. Analysis based on the 16S rRNA gene showed a higher microbial diversity, but with little change in bacterial populations across the growth stages of the plant. Analysis of 16S rRNA recovered much less diversity, demonstrating that much of the 16S signal was derived from free DNA, dead or inactive cells. The rRNA analysis showed a stable microbial population present in the rhizosphere, and this was distinct from that in the bulk soil, which was also stable across the growth period. Root exudates (e.g., acetate, lactate, oxalate and succinate), which are major components contributing to the rhizosphere effect, appeared to shape the bacterial community, with some taxa (e.g., Oxobacter, Lachnospiraceae, Coprococcus and α-Proteobacteria) being enhanced in the rhizosphere. Soil compartments (rhizosphere vs. bulk) had a greater effect on the bacterial communities than did the plant phenological stages, especially at the rRNA level. These results suggest that the rhizosphere effect plays a key role in structuring the bacterial communities in rhizosphere soils with a distinct effect on active and total bacterial communities.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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32
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Shuai W, Jaffé PR. Anaerobic ammonium oxidation coupled to iron reduction in constructed wetland mesocosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:984-992. [PMID: 30340310 DOI: 10.1016/j.scitotenv.2018.08.189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Acidimicrobiaceae sp. A6 (referred to as A6) was recently identified as playing a key role in the Feammox process (ammonium oxidation coupled to iron reduction). Two constructed wetlands (CW) were built and bioaugmented with A6 to determine if, under the right conditions, Feammox can be enhanced in CWs by having strata with higher iron content. Hence, the solid stratum in the CWs was sand, and one CW was augmented with ferrihydrite. Vertical ammonium (NH4+) concentration profiles in the CW mesocosms were monitored regularly. After four months of operation, when reducing conditions were established in the CWs, they were inoculated with an enrichment culture containing A6 and monitored for an additional four months, after which they were dismantled and analyzed. During the four-month period after the A6 enrichment culture injection, 25.0 ± 7.3% of NH4+ was removed from the CW with the high iron substrate whereas 11.0 ± 9.7% was removed from the CW with the low iron substrate on average. Since the CW with high NH4+ removal had the same plant density, same bacterial biomass, same fraction of ammonium oxidizing bacteria (AOB), a higher biomass of A6, and a higher pH (NH4+ oxidation by Feammox raises pH, whereas NH4+ oxidation by aerobic AOB decreases pH), this difference in NH4+ removal is attributed to the Feammox process, indicating that wetlands can be constructed to take advantage of the Feammox process for increased NH4+ removal.
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Affiliation(s)
- Weitao Shuai
- Department of Civil and Environmental Engineering, Princeton University, NJ 08540, USA.
| | - Peter R Jaffé
- Department of Civil and Environmental Engineering, Princeton University, NJ 08540, USA.
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33
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Mohr KI. Diversity of Myxobacteria-We Only See the Tip of the Iceberg. Microorganisms 2018; 6:E84. [PMID: 30103481 PMCID: PMC6164225 DOI: 10.3390/microorganisms6030084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany.
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34
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Huang Y, Xiao X, Huang H, Jing J, Zhao H, Wang L, Long XE. Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry. Appl Microbiol Biotechnol 2018; 102:5717-5729. [PMID: 29704041 DOI: 10.1007/s00253-018-9013-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 02/26/2018] [Accepted: 04/05/2018] [Indexed: 01/25/2023]
Abstract
Soil weakness across consecutive cropping fields can be partially explained by the changes in microbial community diversity and structure. Succession patterns and co-occurrence mechanisms of bacteria and fungi, especially beneficial or pathogenic memberships in continuous cropping strawberry fields and their response to edaphic factors remained unclear. In this study, Illumina sequencing of bacterial 16S ribosomal RNA and fungal internal transcribed spacer genes was applied in three time-course (1, 5, and 10 years) fields across spring and winter. Results showed that the richness and diversity of bacterial and fungal communities increased significantly (p < 0.05) in 1-year field and decreased afterwards across two seasons. Network analysis revealed beneficial bacterial and fungal genus (Bacillus and Trichoderma) dominated under 1-year field whereas Fusarium accumulated under 10-year field at either season. Moreover, Trichoderma harzianum and Bacillus subtilis that have been reported to effectively control Fusarium wilt in strawberries accumulated significantly under 1-year field. Canonical correspondence analysis showed that beneficial bacterial Rhodospirillales and Rhizobiales and fungal Glomerales accumulated in 1-year field and their distributions were significantly affected by soil pH, microbial biomass C (MBC), and moisture. On the contrary, fungal pathogenic species Fusarium oxysporum strongly increased under 10-year field at the winter sample and the abundance was positively (p < 0.01) correlated with soil moisture. Our study suggested that the potential of microcosm under 1-year field stimulates the whole microbial diversity and favors different beneficial taxa across two seasons. Soil pH, moisture, and MBC were the most important edaphic factors leading to contrasting beneficial and pathogenic memberships across consecutive strawberry cropping fields.
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Affiliation(s)
- Ying Huang
- Laboratory for Agricultural Wastes Treatment and Recycling, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Xuanwu District, Nanjing, 210014, Jiangsu Province, China.,Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No.6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Xu Xiao
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No.6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Hongying Huang
- Laboratory for Agricultural Wastes Treatment and Recycling, Circular Agriculture Research Center, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Xuanwu District, Nanjing, 210014, Jiangsu Province, China.
| | - Jinquan Jing
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No.6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Hejuan Zhao
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No.6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Lin Wang
- Nanjing Institute of Agricultural Sciences in Jiangsu Hilly Area, No.6 Xianyin South Road, Qixia District, Nanjing, 210046, Jiangsu Province, China
| | - Xi-En Long
- College of Environment Science and Engineering, Central South University of Forestry and Technology, Changsha, 410004, China.
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35
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Qiao JT, Li XM, Li FB. Roles of different active metal-reducing bacteria in arsenic release from arsenic-contaminated paddy soil amended with biochar. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:958-967. [PMID: 29197791 DOI: 10.1016/j.jhazmat.2017.11.025] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/23/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Although biochar has great potential for heavy metal removal from sediments or soils, its impact on arsenic biogeochemistry in contaminated paddy fields remains poorly characterized. In this study, anaerobic microcosms were established with arsenic-contaminated paddy soil to investigate arsenic transformation as well as the potentially active microbial community and their transcriptional activities in the presence of biochar. The results demonstrated that biochar can simultaneously stimulate microbial reduction of As(V) and Fe(III), releasing high levels of As(III) into the soil solution relative to the control. Total RNAs were extracted to profile the potentially active microbial communities, which suggested that biochar increased the abundance of arsenic- and iron-related bacteria, such as Geobacter, Anaeromyxobacter and Clostridium compared to the control. Reverse transcription, quantitative PCR (RT-qPCR) showed that the abundance of Geobacter transcripts were significantly stimulated by biochar throughout the incubation. Furthermore, significant positive correlations were observed between the abundance of Geobacter transcripts and As(V) concentrations, and between that of Clostridium transcripts and Fe(III) concentrations in biochar-amended microcosms. Our findings suggest that biochar can stimulate the activity of metal-reducing bacteria to promote arsenic mobility. The Geobacter may contribute to As(V) reduction in the presence of biochar, while Clostridium has a role in Fe(III) reduction.
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Affiliation(s)
- Jiang-Tao Qiao
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiao-Min Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China
| | - Fang-Bai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, PR China.
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36
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Sun W, Xiao E, Pu Z, Krumins V, Dong Y, Li B, Hu M. Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:884-893. [PMID: 28886540 DOI: 10.1016/j.scitotenv.2017.08.275] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/22/2017] [Accepted: 08/28/2017] [Indexed: 05/21/2023]
Abstract
UNLABELLED Rice paddies are a significant source of the greenhouse gas methane, which mainly originates from microbial activity. Methane generation in anaerobic systems involves complex interactions of multiple functional microbial groups. Rice paddies installed in hilly terrain are often terraced, providing multiple quasi-independent plots differing primarily in their elevation up a hillside. This represents an excellent study site to explore the influence of environmental factors on microbial communities and interactions among microbial populations. In this study, we used a combination of geochemical analyses, high-throughput amplicon sequencing, and statistical methods to elucidate these interactions. Sulfate, total nitrogen, total iron, and total organic carbon were determined to be critical factors in steering the ecosystem composition and function. Sulfate-reducing bacteria predominated in the rice terrace microbial communities, and Fe(III)-reducing and methane-oxidizing bacteria were abundant as well. Biotic interactions indicated by co-occurrence network analysis suggest mutualistic interactions among these three functional groups. Paddy-scale methane production may be affected by competition among methanogens and sulfate- and Fe(III)-reducing bacteria, or by direct methane oxidation by methane-oxidizing bacteria. CAPSULE Microbial communities were characterized in rice terrace. The environment- and microbe-microbe interactions indicated the mitigation of sulfate and Fe on methane production.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China.
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zilun Pu
- Yingrui Biotechnology Ltd., Guangzhou 510006, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Yiran Dong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Baoqin Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
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37
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Zecchin S, Corsini A, Martin M, Cavalca L. Influence of water management on the active root-associated microbiota involved in arsenic, iron, and sulfur cycles in rice paddies. Appl Microbiol Biotechnol 2017; 101:6725-6738. [DOI: 10.1007/s00253-017-8382-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/25/2017] [Accepted: 06/09/2017] [Indexed: 11/28/2022]
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38
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Blake JM, De Vore CL, Avasarala S, Ali AM, Roldan C, Bowers F, Spilde MN, Artyushkova K, Kirk MF, Peterson E, Rodriguez-Freire L, Cerrato JM. Uranium mobility and accumulation along the Rio Paguate, Jackpile Mine in Laguna Pueblo, NM. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:605-621. [PMID: 28352908 DOI: 10.1039/c6em00612d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The mobility and accumulation of uranium (U) along the Rio Paguate, adjacent to the Jackpile Mine, in Laguna Pueblo, New Mexico was investigated using aqueous chemistry, electron microprobe, X-ray diffraction and spectroscopy analyses. Given that it is not common to identify elevated concentrations of U in surface water sources, the Rio Paguate is a unique site that concerns the Laguna Pueblo community. This study aims to better understand the solid chemistry of abandoned mine waste sediments from the Jackpile Mine and identify key hydrogeological and geochemical processes that affect the fate of U along the Rio Paguate. Solid analyses using X-ray fluorescence determined that sediments located in the Jackpile Mine contain ranges of 320 to 9200 mg kg-1 U. The presence of coffinite, a U(iv)-bearing mineral, was identified by X-ray diffraction analyses in abandoned mine waste solids exposed to several decades of weathering and oxidation. The dissolution of these U-bearing minerals from abandoned mine wastes could contribute to U mobility during rain events. The U concentration in surface waters sampled closest to mine wastes are highest during the southwestern monsoon season. Samples collected from September 2014 to August 2016 showed higher U concentrations in surface water adjacent to the Jackpile Mine (35.3 to 772 μg L-1) compared with those at a wetland 4.5 kilometers downstream of the mine (5.77 to 110 μg L-1). Sediments co-located in the stream bed and bank along the reach between the mine and wetland had low U concentrations (range 1-5 mg kg-1) compared to concentrations in wetland sediments with higher organic matter (14-15%) and U concentrations (2-21 mg kg-1). Approximately 10% of the total U in wetland sediments was amenable to complexation with 1 mM sodium bicarbonate in batch experiments; a decrease of U concentration in solution was observed over time in these experiments likely due to re-association with sediments in the reactor. The findings from this study provide new insights about how hydrologic events may affect the reactivity of U present in mine waste solids exposed to surface oxidizing conditions, and the influence of organic-rich sediments on U accumulation in the Rio Paguate.
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Affiliation(s)
- Johanna M Blake
- Department of Chemistry, MSC03 2060, University of New Mexico, Albuquerque, New Mexico 87131, USA.
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39
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Bolanz RM, Grauer C, Cooper RE, Göttlicher J, Steininger R, Perry S, Küsel K. Incorporation of molybdenum(vi) in akaganéite (β-FeOOH) and the microbial reduction of Mo–akaganéite by Shewanella loihica PV-4. CrystEngComm 2017. [DOI: 10.1039/c7ce01569k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Among all highly-crystalline iron oxides present in the environment, akaganéite (β-FeO(OH, Cl)) possesses one of the most unconventional structural setups and is a known scavenger for large quantitates of molybdenum (Mo6+).
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Affiliation(s)
- Ralph M. Bolanz
- Friedrich-Schiller-University Jena
- Institute for Geosciences
- 07745 Jena
- Germany
| | - Christoph Grauer
- Friedrich-Schiller-University Jena
- Institute for Geosciences
- 07745 Jena
- Germany
| | - Rebecca E. Cooper
- Friedrich-Schiller-University Jena
- Aquatic Geomicrobiology
- 07743 Jena
- Germany
| | - Jörg Göttlicher
- Karlsruhe Institute of Technology
- ANKA Synchrotron Radiation Facility
- D-76344 Eggenstein-Leopoldshafen
- Germany
| | - Ralph Steininger
- Karlsruhe Institute of Technology
- ANKA Synchrotron Radiation Facility
- D-76344 Eggenstein-Leopoldshafen
- Germany
| | - Stephen Perry
- Diamond Light Source Ltd
- Harwell Science and Innovation Campus
- Didcot
- UK
| | - Kirsten Küsel
- Friedrich-Schiller-University Jena
- Aquatic Geomicrobiology
- 07743 Jena
- Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
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40
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Jin Q, Kirk MF. Thermodynamic and Kinetic Response of Microbial Reactions to High CO 2. Front Microbiol 2016; 7:1696. [PMID: 27909425 PMCID: PMC5112241 DOI: 10.3389/fmicb.2016.01696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.
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Affiliation(s)
- Qusheng Jin
- Department of Earth Sciences, University of Oregon Eugene, OR, USA
| | - Matthew F Kirk
- Department of Geology, Kansas State University Manhattan, KS, USA
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41
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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Reyes C, Dellwig O, Dähnke K, Gehre M, Noriega-Ortega BE, Böttcher ME, Meister P, Friedrich MW. Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing. FEMS Microbiol Ecol 2016; 92:fiw054. [DOI: 10.1093/femsec/fiw054] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 11/13/2022] Open
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Breidenbach B, Blaser MB, Klose M, Conrad R. Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community. Environ Microbiol 2015; 18:2868-85. [PMID: 26337675 DOI: 10.1111/1462-2920.13041] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 11/27/2022]
Abstract
Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison with flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae and Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. On the contrary, members of soil crenarchaeotic group, mainly Candidatus Nitrososphaera, were higher in the rotational fields, possibly indicating increasing importance of ammonia oxidation during drainage. In contrast, minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields, whereas members of anaerobic Chloroflexi and sulfate-reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative polymerase chain reaction and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
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Affiliation(s)
| | - Martin B Blaser
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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Lopes AR, Bello D, Prieto-Fernández Á, Trasar-Cepeda C, Manaia CM, Nunes OC. Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:11690-11699. [PMID: 25850741 DOI: 10.1007/s11356-015-4410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.
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Affiliation(s)
- Ana R Lopes
- LEPABE, Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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Cabezas A, Pommerenke B, Boon N, Friedrich MW. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:489-497. [PMID: 25683328 DOI: 10.1111/1758-2229.12277] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 01/31/2015] [Indexed: 06/04/2023]
Abstract
Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.
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Affiliation(s)
- Angela Cabezas
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, Marburg, D-35043, Germany
| | - Bianca Pommerenke
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, Marburg, D-35043, Germany
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Michael W Friedrich
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, Marburg, D-35043, Germany
- Microbial Ecophysiology, Faculty of Biology/Chemistry, University of Bremen, Bremen, D-28334, Germany
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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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Wegner CE, Liesack W. Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil. Environ Microbiol 2015; 18:2825-42. [PMID: 25712035 DOI: 10.1111/1462-2920.12815] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/04/2015] [Accepted: 02/11/2015] [Indexed: 12/01/2022]
Abstract
We used paddy soil slurries amended with rice straw to identify the microbial populations involved in the methanogenic breakdown of plant polymers. Rice straw greatly stimulated microbial activity over the 28-day incubation period. On day 7, the transient peak concentration of acetate (24 mM) coincided with the onset of increased methane production. Microbial 16S rRNA transcript numbers increased by one to two orders of magnitude, but not the 16S rRNA gene copy numbers. Using metatranscriptomic rRNA, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, Veillonellaceae and Pseudomonadaceae were identified to be the most abundant and the most dynamic bacterial groups. Changes in methanogen rRNA and mRNA abundances corresponded well with methanogenic activity. Acetate determined the abundance ratio between Methanosarcinaceae and Methanosaetaceae. Methanocellaceae dominated hydrogenotrophic methanogenesis. Transcript levels of mRNA families involved in plant polymer breakdown increased slightly with time. Glycosyl hydrolase (GH) transcripts involved in cellulose and chitin breakdown were predominantly expressed by the Firmicutes, whereas those involved in hemicellulose breakdown exhibited more diverse taxonomic sources, including Acidobacteria, Bacteriodetes and Chloroflexi. Taken together, we observed strong population dynamics and the expression of taxonomically diverse GH families, suggesting that not only Firmicutes, but also less abundant groups play a major functional role in the decomposition of rice straw.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg (Lahn), Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg (Lahn), Germany.
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Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment. PLoS One 2015; 10:e0119465. [PMID: 25742617 PMCID: PMC4351183 DOI: 10.1371/journal.pone.0119465] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/29/2015] [Indexed: 12/21/2022] Open
Abstract
Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world's largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.
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Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01449-14. [PMID: 25614562 PMCID: PMC4319575 DOI: 10.1128/genomea.01449-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium’s genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.
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Breidenbach B, Conrad R. Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage. Front Microbiol 2015; 5:752. [PMID: 25620960 PMCID: PMC4288041 DOI: 10.3389/fmicb.2014.00752] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/11/2014] [Indexed: 01/13/2023] Open
Abstract
We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity) under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.
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Affiliation(s)
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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