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Wang B, Stirling E, He Z, Ma B, Zhang H, Zheng X, Xiao F, Yan Q. Pollution alters methanogenic and methanotrophic communities and increases dissolved methane in small ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149723. [PMID: 34438138 DOI: 10.1016/j.scitotenv.2021.149723] [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: 07/19/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 05/28/2023]
Abstract
Small ponds have become a hotspot of greenhouse gas emissions, but our understanding of methane (CH4) cycling and its biological regulation in small polluted ponds remains limited. To assess how pollution affects CH4 content, we investigated dissolved CH4 concentrations, water and sediments properties, methanogenic and methanotrophic communities in two types of small polluted ponds. Compared with low pollution (LP) ponds, high pollution (HP) ponds showed significantly (P < 0.05) higher dissolved CH4 in water. Sequencing of methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) genes showed that HP led to significant (P < 0.05) shifts of CH4-cycling microbial communities, with increased Shannon index of sediment methanogenic communities and water methanotrophic communities. There were also strong negative associations (P < 0.05) between dissolved CH4 concentrations and interdomain methanogen-methanotroph network connectivity in water and sediments, respectively. The partial least squares path modeling indicated that dissolved oxygen, total organic carbon, ammonium nitrogen and nitrate nitrogen of water, and total nitrogen and total carbon of sediment, and CH4-cycling microbes could regulate the CH4 content. This study clarified the effects of environmental deterioration on CH4 cycling in small ponds, highlighting the use of methanogen-methanotroph network connectivity to assess the CH4 production.
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Affiliation(s)
- Binhao Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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2
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Compte-Port S, Borrego CM, Moussard H, Jeanbille M, Restrepo-Ortiz CX, de Diego A, Rodriguez-Iruretagoiena A, Gredilla A, Fdez-Ortiz de Vallejuelo S, Galand PE, Kalenitchenko D, Rols JL, Pokrovsky OS, Gonzalez AG, Camarero L, Muñiz S, Navarro-Navarro E, Auguet JC. Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes. Environ Microbiol 2018; 20:2422-2437. [PMID: 29687572 DOI: 10.1111/1462-2920.14252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/22/2022]
Abstract
Using the 16S rRNA and mcrA genes, we investigated the composition, abundance and activity of sediment archaeal communities within 18 high-mountain lakes under contrasted metal levels from different origins (bedrock erosion, past-mining activities and atmospheric depositions). Bathyarchaeota, Euryarchaeota and Woesearchaeota were the major phyla found at the meta-community scale, representing 48%, 18.3% and 15.2% of the archaeal community respectively. Metals were equally important as physicochemical variables in explaining the assemblage of archaeal communities and their abundance. Methanogenesis appeared as a process of central importance in the carbon cycle within sediments of alpine lakes as indicated by the absolute abundance of methanogen 16S rRNA and mcrA gene transcripts (105 to 109 copies g-1 ). We showed that methanogen abundance and activity were significantly reduced with increasing concentrations of Pb and Cd, two indicators of airborne metal contaminations. Considering the ecological importance of methanogenesis in sediment habitats, these metal contaminations may have system wide implications even in remote area such as alpine lakes. Overall, this work was pioneer in integrating the effect of long-range atmospheric depositions on archaeal communities and indicated that metal contamination might significantly compromise the contribution of Archaea to the carbon cycling of the mountain lake sediments.
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Affiliation(s)
- Sergi Compte-Port
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain
| | - Carles M Borrego
- Group of Quality and Microbial Diversity, Catalan Institute for Water research (ICRA), Girona, Spain.,Group of Molecular Microbial Ecology (gEMM), Institute of Aquatic Ecology, University of Girona (UdG), Girona, Spain
| | - Hélène Moussard
- Equipe Environnement et Microbiologie (IPREM-EEM), UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Mathilde Jeanbille
- Department of plant pathology and forest mycology Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
| | | | - Alberto de Diego
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Ainara Gredilla
- Department of analytical chemistry, Faculty of science and technology, University of Basque Country, Bilbao, Spain
| | | | - Pierre E Galand
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Dimitri Kalenitchenko
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique, Banyuls/Mer, F-66650, France
| | - Jean-Luc Rols
- EcoLab, UMR CNRS 5245, Observatory of Midi-Pyrénées, University Paul Sabatier, Toulouse, France
| | - Oleg S Pokrovsky
- Geosciences and Environment Toulouse, UMR 5563 CNRS, 14 Avenue Edouard Belin 31400, Toulouse, France.,BIO-GEO-CLIM Laboratory, Tomsk State University, Tomsk, Russia
| | - Aridane G Gonzalez
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Lluis Camarero
- Group of integrative freshwater ecology, Department of continental ecology, Center of advanced studies of Blanes (CEAB-CSIC), Blanes, Spain
| | - Selene Muñiz
- Pyrenean institute of ecology (IPE-CSIC), Zaragoza, Spain
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3
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Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS. High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. Environ Microbiol 2017; 19:2192-2209. [DOI: 10.1111/1462-2920.13703] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Adrienne B. Narrowe
- Department of Integrative Biology; University of Colorado Denver; Denver CO USA
| | - Jordan C. Angle
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Rebecca A. Daly
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Kay C. Stefanik
- School of Environment and Natural Resources; The Ohio State University; Columbus OH USA
| | - Kelly C. Wrighton
- Department of Microbiology; The Ohio State University; Columbus OH USA
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Šimonovičová A, Ferianc P, Vojtková H, Pangallo D, Hanajík P, Kraková L, Feketeová Z, Čerňanský S, Okenicová L, Žemberyová M, Bujdoš M, Pauditšová E. Alkaline Technosol contaminated by former mining activity and its culturable autochthonous microbiota. CHEMOSPHERE 2017; 171:89-96. [PMID: 28006667 PMCID: PMC5267631 DOI: 10.1016/j.chemosphere.2016.11.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 05/31/2023]
Abstract
Technosols or technogenic substrates contaminated by potentially toxic elements as a result of iron mining causes not only contamination of the surrounding ecosystem but may also lead to changes of the extent, abundance, structure and activity of soil microbial community. Microbial biomass were significantly inhibited mainly by exceeding limits of potentially toxic metals as arsenic (in the range of 343-511 mg/kg), copper (in the range of 7980-9227 mg/kg), manganese (in the range of 2417-2670 mg/kg), alkaline and strong alkaline pH conditions and minimal contents of organic nutrients. All of the 14 bacterial isolates, belonged to 4 bacterial phyla, Actinobacteria, Firmicutes; β- and γ-Proteobacteria. Thirteen genera and 20 species of microscopic filamentous fungi were recovered. The most frequently found species belonged to genera Aspergillus (A. clavatus, A. niger, A. flavus, A. versicolor, Aspergillus sp.) with the dominating A. niger in all samples, and Penicillium (P. canescens, P. chrysogenum, P. spinulosum, Penicillium sp.). Fungal plant pathogens occurred in all surface samples. These included Bjerkandera adustata, Bionectria ochloleuca with anamorph state Clonostachys pseudochloleuca, Lewia infectoria, Phoma macrostoma and Rhizoctonia sp.
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Affiliation(s)
- A Šimonovičová
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic.
| | - P Ferianc
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - H Vojtková
- Institute of Environmental Engineering, Faculty of Mining and Geology, VŠB - Technical University of Ostrava, Czech Republic
| | - D Pangallo
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - P Hanajík
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - L Kraková
- Institut of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovak Republic
| | - Z Feketeová
- Department of Soil Science, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - S Čerňanský
- Department of Environmental Ecology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - L Okenicová
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - M Žemberyová
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - M Bujdoš
- Institute of Laboratory Research on Geomaterials, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
| | - E Pauditšová
- Department of Landscape Ecology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovak Republic
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5
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Vaksmaa A, Jetten MSM, Ettwig KF, Lüke C. McrA primers for the detection and quantification of the anaerobic archaeal methanotroph 'Candidatus Methanoperedens nitroreducens'. Appl Microbiol Biotechnol 2017; 101:1631-1641. [PMID: 28084539 PMCID: PMC5266762 DOI: 10.1007/s00253-016-8065-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of ‘Candidatus M. nitroreducens’. The first primer pair produces a fragment of 186-bp that can be used to quantify ‘Candidatus M. nitroreducens’ cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the ‘Candidatus M. nitroreducens’ mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106 copies g−1 wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102 copies g−1 wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104 copies g−1 wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known ‘Candidatus M. nitroreducens’ archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of ‘Candidatus M. nitroreducens’ sequences, which have been only poorly captured by general methanogenic mcrA primers.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands
| | - Katharina F Ettwig
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
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6
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Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, Jetten MSM, Lüke C, Reimann J. Nitrate- and nitrite-dependent anaerobic oxidation of methane. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:941-955. [PMID: 27753265 DOI: 10.1111/1758-2229.12487] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens. They were named 'Candidatus Methanoperedens nitroreducens' and use reverse methanogenesis with the key enzyme methyl-coenzyme M (methyl-CoM) reductase for methane activation. Their major end product is nitrite which can be taken up by nitrite-dependent methanotrophs. Nitrite-dependent AOM is performed by the NC10 bacterium 'Candidatus Methylomirabilis oxyfera' that probably utilizes an intra-aerobic pathway through the dismutation of NO to N2 and O2 for aerobic methane activation by methane monooxygenase, yet being a strictly anaerobic microbe. Environmental distribution, physiological and biochemical aspects are discussed in this article as well as the cooperation of the microorganisms involved.
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Affiliation(s)
- Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
- Netherlands Earth Systems Science Center, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
| | - Joachim Reimann
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, Nijmegen, AJ, 6525, The Netherlands
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7
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Abstract
Anaerobic oxidation of methane (AOM) is crucial for controlling the emission of this potent greenhouse gas to the atmosphere. Nitrite-, nitrate-, and sulfate-dependent methane oxidation is well-documented, but AOM coupled to the reduction of oxidized metals has so far been demonstrated only in environmental samples. Here, using a freshwater enrichment culture, we show that archaea of the order Methanosarcinales, related to "Candidatus Methanoperedens nitroreducens," couple the reduction of environmentally relevant forms of Fe3+ and Mn4+ to the oxidation of methane. We obtained an enrichment culture of these archaea under anaerobic, nitrate-reducing conditions with a continuous supply of methane. Via batch incubations using [13C]methane, we demonstrated that soluble ferric iron (Fe3+, as Fe-citrate) and nanoparticulate forms of Fe3+ and Mn4+ supported methane-oxidizing activity. CO2 and ferrous iron (Fe2+) were produced in stoichiometric amounts. Our study connects the previous finding of iron-dependent AOM to microorganisms detected in numerous habitats worldwide. Consequently, it enables a better understanding of the interaction between the biogeochemical cycles of iron and methane.
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Besaury L, Ghiglione JF, Quillet L. Abundance, activity, and diversity of archaeal and bacterial communities in both uncontaminated and highly copper-contaminated marine sediments. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:230-242. [PMID: 24072336 DOI: 10.1007/s10126-013-9542-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 09/10/2013] [Indexed: 06/02/2023]
Abstract
We analyzed the impact of copper mine tailing discharges on benthic Archaea and Bacteria around the city of Chanaral in northern Chile. Quantitative PCR (Q-PCR) showed that the bacteria dominated the prokaryotic community at both sites, but only the bacteria showed a decrease in abundance in the copper-contaminated site. Q-PCR on reverse transcripts indicated a higher activity of both bacterial and archaeal communities in the contaminated site, suggesting an adaptation of the two communities to copper. This hypothesis was reinforced by the concomitant augmentation of the copper-resistant copA gene coding for a P-type ATP-ase pump in the contaminated site. The metabolically active bacterial community of the contaminated site was dominated by Gammaproteobacteria related to Ectothiorhodospiraceae and Chromatiaceae and by Alphaproteobacteria phylum related to Rhodobacteraceae. The metabolically active archaeal community was dominated by one lineage belonging to unclassified Euryarchaeota and to methanogenic Archaea.
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Affiliation(s)
- Ludovic Besaury
- Faculté des Sciences, CNRS UMR 6143-M2C, Groupe de Microbiologie, Université de Rouen, Place Emile Blondel, 76821, Mont Saint Aignan Cedex, France,
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9
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Chen LX, Li JT, Chen YT, Huang LN, Hua ZS, Hu M, Shu WS. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ Microbiol 2013; 15:2431-44. [PMID: 23574280 DOI: 10.1111/1462-2920.12114] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/20/2013] [Indexed: 11/29/2022]
Abstract
In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.
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Affiliation(s)
- Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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10
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Lymperopoulou DS, Kormas KA, Karagouni AD. Variability of prokaryotic community structure in a drinking water reservoir (Marathonas, Greece). Microbes Environ 2011; 27:1-8. [PMID: 21971081 PMCID: PMC4036031 DOI: 10.1264/jsme2.me11253] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H′ 0.81–3.28 and 1.36–1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning.
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Affiliation(s)
- Despoina S Lymperopoulou
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, Microbiology Group, Athens, Greece.
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11
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Rastogi G, Barua S, Sani RK, Peyton BM. Investigation of microbial populations in the extremely metal-contaminated Coeur d'Alene River sediments. MICROBIAL ECOLOGY 2011; 62:1-13. [PMID: 21331609 DOI: 10.1007/s00248-011-9810-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 01/17/2011] [Indexed: 05/30/2023]
Abstract
The deposition of mine tailings generated from 125 years of sulfidic ore mining resulted in the enrichment of Coeur d'Alene River (CdAR) sediments with significant amounts of toxic heavy metals. A review of literature suggests that microbial populations play a pivotal role in the biogeochemical cycling of elements in such mining-impacted sedimentary environments. To assess the indigenous microbial communities associated with metal-enriched sediments of the CdAR, high-density 16S microarray (PhyloChip) and clone libraries specific to bacteria (16S rRNA), ammonia oxidizers (amoA), and methanogens (mcrA) were analyzed. PhyloChip analysis provided a comprehensive assessment of bacterial populations and detected the largest number of phylotypes in Proteobacteria followed by Firmicutes and Actinobacteria. Furthermore, PhyloChip and clone libraries displayed considerable metabolic diversity in indigenous microbial populations by capturing several chemolithotrophic groups such as ammonia oxidizers, iron-reducers and -oxidizers, methanogens, and sulfate-reducers in the CdAR sediments. Twenty-two phylotypes detected on PhyloChip could not be classified even at phylum level thus suggesting the presence of novel microbial populations in the CdAR sediments. Clone libraries demonstrated very limited diversity of ammonia oxidizers and methanogens in the CdAR sediments as evidenced by the fact that only Nitrosospira- and Methanosarcina-related phylotypes were retrieved in amoA and mcrA clone libraries, respectively.
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Affiliation(s)
- Gurdeep Rastogi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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12
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Wang H, Wang FY, Wei ZQ, Hu HY. Quinone profiles of microbial communities in sediments of Haihe River-Bohai Bay as influenced by heavy metals and environmental factors. ENVIRONMENTAL MONITORING AND ASSESSMENT 2011; 176:157-167. [PMID: 20568008 DOI: 10.1007/s10661-010-1573-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Accepted: 06/04/2010] [Indexed: 05/29/2023]
Abstract
A total of 11 sediment samples were collected from the sites along Haihe River-Bohai Bay, with site 1 at the beginning of Haihe River and site 11 in Bohai Bay, about 150 km away from site 1. Quinone profiles were used for the analysis of microbial community as influenced by pollutants in water and sediments, such as heavy metals, and other environmental factors. Nineteen species of quinones were found at site 1 while only six species at sites 10 and 11. Both the diversity of quinone species (DQ) and the number of quinones were higher in the sediments from Haihe River and the near-sea area of Bohai Bay than in those from the deep-sea area. The β diversity values were significantly higher, while Jaccard indexes of similarity were much lower among non-contiguous pairs of sites as compared with the contiguous ones. Cluster analysis indicated that quinone profiles may be grouped into two main clusters (sites 1-7 and sites 8-11), and there were higher similarities within the groups than between groups. Quinone species composition varied at different sites. Ubiquinones such as UQ-8, UQ-9, and UQ-10 and menaquinones such as MK-6, MK-7, MK-8 were isolated from all the sites and accounted for the largest proportions. Pearson correlation analysis revealed that both the number of quinone species and DQ correlated positively with total organic carbon contents in water and sediments, but negatively correlated with salinity and electroconductivity and did not correlate significantly with heavy metal contents in water.
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Affiliation(s)
- Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Department of Environmental Science and Engineering, Tsinghua University, Beijing, 100084, China.
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Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. MICROBIAL ECOLOGY 2010; 60:784-95. [PMID: 20725722 PMCID: PMC2974187 DOI: 10.1007/s00248-010-9734-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 08/01/2010] [Indexed: 05/22/2023]
Abstract
Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.
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Affiliation(s)
- Iris Porat
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | | | - Jennifer J. Mosher
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Craig C. Brandt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Scott C. Brooks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Liyuan Liang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Meghan M. Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Anthony V. Palumbo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
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Rastogi G, Osman S, Kukkadapu R, Engelhard M, Vaishampayan PA, Andersen GL, Sani RK. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota. MICROBIAL ECOLOGY 2010; 60:539-550. [PMID: 20386898 DOI: 10.1007/s00248-010-9657-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Accepted: 03/13/2010] [Indexed: 05/29/2023]
Abstract
A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines.
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Affiliation(s)
- Gurdeep Rastogi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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15
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Rastogi G, Stetler LD, Peyton BM, Sani RK. Molecular analysis of prokaryotic diversity in the deep subsurface of the former Homestake gold mine, South Dakota, USA. J Microbiol 2009; 47:371-84. [PMID: 19763410 DOI: 10.1007/s12275-008-0249-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Accepted: 04/10/2009] [Indexed: 11/29/2022]
Abstract
A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.
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Affiliation(s)
- Gurdeep Rastogi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA. J Ind Microbiol Biotechnol 2009; 36:585-98. [PMID: 19189143 DOI: 10.1007/s10295-009-0528-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022]
Abstract
The present study investigated the cultivable mesophilic (37 degrees C) and thermophilic (60 degrees C) cellulose-degrading bacterial diversity in a weathered soil-like sample collected from the deep subsurface (1.5 km depth) of the Homestake gold mine in Lead, South Dakota, USA. Chemical characterization of the sample by X-ray fluorescence spectroscopy revealed a high amount of toxic heavy metals such as Cu, Cr, Pb, Ni, and Zn. Molecular community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from enrichment cultures growing in presence of microcrystalline cellulose as the sole source of carbon. All phylotypes retrieved from enrichment cultures were affiliated to Firmicutes. Cellulose-degrading mesophilic and thermophilic pure cultures belonging to the genera Brevibacillus, Paenibacillus, Bacillus, and Geobacillus were isolated from enrichment cultures, and selected cultures were studied for enzyme activities. For a mesophilic isolate (DUSELG12), the optimum pH and temperature for carboxymethyl cellulase (CMCase) were 5.5 and 55 degrees C, while for a thermophilic isolate (DUSELR7) they were 5.0 and 75 degrees C, respectively. Furthermore, DUSELG12 retained about 40% CMCase activity after incubation at 60 degrees C for 8 h. Most remarkably, thermophilic isolate, DUSELR7 retained 26% CMCase activity at 60 degrees C up to a period of 300 h. Overall, the present work revealed the presence of different cellulose-degrading bacterial lineages in the unique deep subsurface environment of the mine. The results also have strong implications for biological conversion of cellulosic agricultural and forestry wastes to commodity chemicals including sugars.
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