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Shen L, Wu L, Wei W, Yang Y, MacLeod MJ, Lin J, Song G, Yuan J, Yang P, Wu L, Li M, Zhuang M. Marine aquaculture can deliver 40% lower carbon footprints than freshwater aquaculture based on feed, energy and biogeochemical cycles. NATURE FOOD 2024:10.1038/s43016-024-01004-y. [PMID: 38907010 DOI: 10.1038/s43016-024-01004-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/17/2024] [Indexed: 06/23/2024]
Abstract
Freshwater aquaculture is an increasingly important source of blue foods but produces substantial methane and nitrous oxide emissions. Marine aquaculture, also known as mariculture, is a smaller sector with a large growth potential, but its climate impacts are challenging to accurately quantify. Here we assess the greenhouse gas emissions from mariculture's aquatic environment in global potentially suitable areas at 10 km resolution on the basis of marine biogeochemical cycles, greenhouse gas measurements from research cruises and satellite-observed net primary productivity. Mariculture's aquatic emissions intensities are estimated to be 1-6 g CH4 kg-1 carcass weight and 0.05-0.2 g N2O kg-1 carcass weight, >98% and >80% lower than freshwater systems. Using a life-cycle assessment approach, we show that mariculture's carbon footprints are ~40% lower than those of freshwater aquaculture based on feed, energy use and the aquatic environment emissions. Adoption of mariculture alongside freshwater aquaculture production could offer considerable climate benefits to meet future dietary protein and nutritional needs.
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Affiliation(s)
- Lu Shen
- Department of Atmospheric and Oceanic Sciences, School of Physics, Peking University, Beijing, China.
- Institute of Carbon Neutrality, Peking University, Beijing, China.
| | - Lidong Wu
- Chinese Academy of Fishery Sciences, Beijing, China
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Wei Wei
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China
| | - Yi Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China
| | - Michael J MacLeod
- Department of Rural Economy, Environment and Society, Scotland's Rural College, Edinburgh, UK
| | - Jintai Lin
- Department of Atmospheric and Oceanic Sciences, School of Physics, Peking University, Beijing, China
| | - Guodong Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and Key Laboratory of Marine Chemistry Theory and Technology (Ministry of Education), Ocean University of China, Qingdao, China
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ping Yang
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Lin Wu
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Mingwei Li
- Institute of Energy, Environment and Economy, Tsinghua University, Beijing, China
| | - Minghao Zhuang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
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Baur PA, Henry Pinilla D, Glatzel S. Is ebullition or diffusion more important as methane emission pathway in a shallow subsaline lake? THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169112. [PMID: 38072262 DOI: 10.1016/j.scitotenv.2023.169112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/11/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023]
Abstract
Methane (CH4) emissions via ebullition contribute significantly to greenhouse gas emissions from freshwater bodies. According to the literature, the ebullition pathway may even be the most important pathway in some cases, particularly in shallow lakes. Ebullition rates are not often estimated because of the high uncertainty associated with episodic releases, leading to difficulties in their determination. This study provides an estimate of such emissions in a large, shallow, subsaline lake in eastern Austria, Lake Neusiedl, and compares them to the diffusion pathway. Ebullition gas sampling was conducted every 5-10 days over a period of 107 days from late March to mid-July 2021, using ebullition traps placed in three distinct locations: Reed belt, Channel and Open water/Lake. The aim was to study the temporal and spatial heterogeneity of ebullition and its contribution to total emissions. At the same time, several water quality and other environmental parameters were measured and then tested against the CH4 ebullition rates to explore them as potential drivers for this pathway. The carbon isotope fractionation factor (αC) of the measured CH4 ebullition gas, ranging from 1.03 to 1.06, indicates a dominance of the acetoclastic methanogenesis in the sediments of Lake Neusiedl, regardless of the location. The Reed belt location showed the highest mean CH4 ebullition rate (17 ± 28 mg CH4 m-2 d-1), which is >340-fold higher than the mean of the other two locations, and demonstrated also a strong temperature dependency. In all locations at Lake Neusiedl, the median CH4 fluxes via diffusion are significantly higher than via ebullition. Our analyses do not confirm the dominance of the ebullition pathway in any of the studied locations. Whereas at the Reed belt, ebullition accounts for 48 % of the CH4 emissions, in the other two locations, is responsible only for about 1 %.
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Affiliation(s)
- Pamela Alessandra Baur
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Geography and Regional Research, Working group Geoecology, Josef-Holaubek-Platz 2, Vienna 1090, Austria; University of Vienna, Faculty of Life Sciences, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, Vienna 1030, Austria.
| | - Daniela Henry Pinilla
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Geography and Regional Research, Working group Geoecology, Josef-Holaubek-Platz 2, Vienna 1090, Austria.
| | - Stephan Glatzel
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Geography and Regional Research, Working group Geoecology, Josef-Holaubek-Platz 2, Vienna 1090, Austria; University of Vienna, Faculty of Life Sciences, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, Vienna 1030, Austria.
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3
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Bueno de Mesquita CP, Hartman WH, Ardón M, Tringe SG. Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland. ISME COMMUNICATIONS 2024; 4:ycae040. [PMID: 38628812 PMCID: PMC11020224 DOI: 10.1093/ismeco/ycae040] [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: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Seawater intrusion into freshwater wetlands causes changes in microbial communities and biogeochemistry, but the exact mechanisms driving these changes remain unclear. Here we use a manipulative laboratory microcosm experiment, combined with DNA sequencing and biogeochemical measurements, to tease apart the effects of sulfate from other seawater ions. We examined changes in microbial taxonomy and function as well as emissions of carbon dioxide, methane, and nitrous oxide in response to changes in ion concentrations. Greenhouse gas emissions and microbial richness and composition were altered by artificial seawater regardless of whether sulfate was present, whereas sulfate alone did not alter emissions or communities. Surprisingly, addition of sulfate alone did not lead to increases in the abundance of sulfate reducing bacteria or sulfur cycling genes. Similarly, genes involved in carbon, nitrogen, and phosphorus cycling responded more strongly to artificial seawater than to sulfate. These results suggest that other ions present in seawater, not sulfate, drive ecological and biogeochemical responses to seawater intrusion and may be drivers of increased methane emissions in soils that received artificial seawater addition. A better understanding of how the different components of salt water alter microbial community composition and function is necessary to forecast the consequences of coastal wetland salinization.
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Affiliation(s)
- Clifton P Bueno de Mesquita
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Wyatt H Hartman
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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4
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Brown AM, Bass AM, Garnett MH, Skiba UM, Macdonald JM, Pickard AE. Sources and controls of greenhouse gases and heavy metals in mine water: A continuing climate legacy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167371. [PMID: 37758145 DOI: 10.1016/j.scitotenv.2023.167371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/11/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Water pollution arising from abandoned coal mines, is second only to sewage as a source of freshwater pollution and in coalfield catchments mine water can be the dominant pollutant, with oxidised iron smothering the bed of receiving rivers. This study measured greenhouse gases in mine water outflows from sixteen sites across the Midland Valley in Scotland. Radiogenic and stable carbon isotopes measurements (Δ14C and δ13C) were used to determine the sources of both methane (CH4) and carbon dioxide (CO2) produced within the flooded mine environment. Concentrations of CH4-C ranged from 20 to 215 μg l-1 and CO2-C from 30 to 120 mg l-1, with CO2 accounting for 97 % of the mine water global warming potential. Methane origins included 51 % modern biogenic, 41 % thermogenic and 8 % from hydrogenotrophic methanogenesis of coal. The most significant inverse impact on biogenic CH4 concentrations was sulphate, most likely due to sulphate reducing bacteria outcompeting methanogens. Carbon dioxide origins included 64 % from the dissolution of limestone, 21 % from terrestrial organic carbon and 15 % from coal. The limestone derived CO2 was positively correlated with high sulphate concentrations, which resulted in sulphuric acid and caused the dissolution of carbonate from limestone. The mine waters experienced significant carbonate buffering becoming only slightly acidic (pH 6-7), but with significant loss of inorganic carbon. The mine waters had low dissolved oxygen (6-25 %) and high dissolved iron (2 to 65 mg l-1) and manganese (0.5 to 5 mg l-1) concentrations. Dissolved greenhouse gases from abandoned mines were estimated as 0.27 +0.31-0.18% of Scotland's global warming potential. This novel work has contributed information about the sources and controls of greenhouse gas fluxes in mine waters and identified the need to quantify and report this emissions term.
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Affiliation(s)
- Alison M Brown
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian EH26 0QB, UK; School of Geographical & Earth Science, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Adrian M Bass
- School of Geographical & Earth Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Mark H Garnett
- NEIF Radiocarbon Laboratory, Rankine Ave, East Kilbride, Glasgow G75 0QF, UK
| | - Ute M Skiba
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian EH26 0QB, UK
| | - John M Macdonald
- School of Geographical & Earth Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Amy E Pickard
- UK Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian EH26 0QB, UK
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5
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Pavia MJ, Finn D, Macedo-Tafur F, Tello-Espinoza R, Penaccio C, Bouskill N, Cadillo-Quiroz H. Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients. Environ Microbiol 2023; 25:2388-2403. [PMID: 37501535 DOI: 10.1111/1462-2920.16469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.
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Affiliation(s)
- Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Damien Finn
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Franco Macedo-Tafur
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Rodil Tello-Espinoza
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
- School of Forestry, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Christa Penaccio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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6
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Karadagli F, Marcus A, Rittmann BE. Microbiological hydrogen (H 2 ) thresholds in anaerobic continuous-flow systems: Effects of system characteristics. Biotechnol Bioeng 2023. [PMID: 37148477 DOI: 10.1002/bit.28415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
Hydrogen (H2 ) concentrations that were associated with microbiological respiratory processes (RPs) such as sulfate reduction and methanogenesis were quantified in continuous-flow systems (CFSs) (e.g., bioreactors, sediments). Gibbs free energy yield (ΔǴ ~ 0) of the relevant RP has been proposed to control the observed H2 concentrations, but most of the reported values do not align with the proposed energetic trends. Alternatively, we postulate that system characteristics of each experimental design influence all system components including H2 concentrations. To analyze this proposal, a Monod-based mathematical model was developed and used to design a gas-liquid bioreactor for hydrogenotrophic methanogenesis with Methanobacterium bryantii M.o.H. Gas-to-liquid H2 mass transfer, microbiological H2 consumption, biomass growth, methane formation, and Gibbs free energy yields were evaluated systematically. Combining model predictions and experimental results revealed that an initially large biomass concentration created transients during which biomass consumed [H2 ]L rapidly to the thermodynamic H2 -threshold (≤1 nM) that triggerred the microorganisms to stop H2 oxidation. With no H2 oxidation, continuous gas-to-liquid H2 transfer increased [H2 ]L to a level that signaled the methanogens to resume H2 oxidation. Thus, an oscillatory H2 -concentration profile developed between the thermodynamic H2 -threshold (≤1 nM) and a low [H2 ]L (~10 nM) that relied on the rate of gas-to-liquid H2 -transfer. The transient [H2 ]L values were too low to support biomass synthesis that could balance biomass losses through endogenous oxidation and advection; thus, biomass declined continuously and disappeared. A stable [H2 ]L (1807 nM) emerged as a result of abiotic H2 -balance between gas-to-liquid H2 transfer and H2 removal via advection of liquid-phase.
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Affiliation(s)
- Fatih Karadagli
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
| | - Andrew Marcus
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Skyology Inc., San Francisco, California, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
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Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
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Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
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Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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9
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Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps. mSystems 2023; 8:e0117922. [PMID: 36927099 PMCID: PMC10134854 DOI: 10.1128/msystems.01179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.
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10
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Zhao J, Chakrabarti S, Chambers R, Weisenhorn P, Travieso R, Stumpf S, Standen E, Briceno H, Troxler T, Gaiser E, Kominoski J, Dhillon B, Martens-Habbena W. Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159865. [PMID: 36461566 DOI: 10.1016/j.scitotenv.2022.159865] [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] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Randolph Chambers
- College of William and Mary, W.M. Keck Environmental Field Laboratory, P.O. Box 8795, Williamsburg, VA, USA
| | | | - Rafael Travieso
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Sandro Stumpf
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Emily Standen
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Henry Briceno
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Tiffany Troxler
- Department of Earth and Environment and Sea Level Solutions Center in the Institute of Environment, Florida International University, Miami, FL, USA
| | - Evelyn Gaiser
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - John Kominoski
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Braham Dhillon
- Fort Lauderdale Research and Education Center and Department of Plant Pathology, University of Florida, Davie, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA.
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11
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Botti A, Biagi E, Musmeci E, Breglia A, Degli Esposti M, Fava F, Zanaroli G. Effect of polyhydroxyalkanoates on the microbial reductive dechlorination of polychlorinated biphenyls and competing anaerobic respirations in a marine microbial culture. MARINE POLLUTION BULLETIN 2023; 186:114458. [PMID: 36493518 DOI: 10.1016/j.marpolbul.2022.114458] [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: 07/08/2022] [Revised: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The effect of polyhydroxyalkanoates (PHAs) with different composition on the reductive dechlorination activity of a polychlorinated biphenyls (PCBs) dechlorinating marine microbial community and on the activity of sulfate-reducing (SRB) and methanogenic bacteria (MB), were investigated in marine sediment microcosms and compared with the main monomer, 3-hydroxybutyric acid (3HB). Despite PHAs were fermented more slowly than 3HB, all electron donors stimulated constantly sulfate-reduction, methanogenesis and, only transiently, PCB reductive dechlorination. No relevant differences were observed with different compositions of PHAs. According to electron balances, the majority of the supplied electrons (50 %) were consumed by SRB and to less extent by MB (9-31 %), while a small percentage (0.01 %) was delivered to OHRB. In the studied conditions PHAs were confirmed as potential slow‑hydrogen releasing compounds in marine environment but their fermentation rate was sufficiently high to mainly stimulate the competitors of organohalide respring bacteria for electron donors.
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Affiliation(s)
- Alberto Botti
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Elena Biagi
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Eliana Musmeci
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Alessia Breglia
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Micaela Degli Esposti
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Fabio Fava
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy
| | - Giulio Zanaroli
- Dept. of Civil, Chemical, Environmental and Material Engineering (DICAM), Alma Mater Studiorum University of Bologna, Via Terracini 28, 40131 Bologna, Italy.
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12
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Spietz RL, Payne D, Szilagyi R, Boyd ES. Reductive biomining of pyrite by methanogens. Trends Microbiol 2022; 30:1072-1083. [PMID: 35624031 DOI: 10.1016/j.tim.2022.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/13/2023]
Abstract
Pyrite (FeS2) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS2 has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS2 via direct contact with the mineral. Reduction of FeS2 occurs through a multistep process that generates aqueous sulfide (HS-) and FeS2-associated pyrrhotite (Fe1-xS). Subsequent dissolution of Fe1-xS provides Fe(II)(aq), but not HS-, that rapidly complexes with HS-(aq) generated from FeS2 reduction to form soluble iron sulfur clusters [nFeS(aq)]. Cells assimilate nFeS(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS2. As such, reductive dissolution of FeS2 by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.
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Affiliation(s)
- Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Robert Szilagyi
- Department of Chemistry, University of British Columbia - Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
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13
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Wu Q, Guthrie MJ, Jin Q. Physiological Acclimation Extrapolates the Kinetics and Thermodynamics of Methanogenesis From Laboratory Experiments to Natural Environments. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.838487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions. We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions.
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14
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Kwon MJ, Tripathi BM, Göckede M, Shin SC, Myeong NR, Lee YK, Kim M. Disproportionate microbial responses to decadal drainage on a Siberian floodplain. GLOBAL CHANGE BIOLOGY 2021; 27:5124-5140. [PMID: 34216067 DOI: 10.1111/gcb.15785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.
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Affiliation(s)
- Min Jung Kwon
- Korea Polar Research Institute, Incheon, Republic of Korea
| | | | | | | | - Nu Ri Myeong
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, Republic of Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, Republic of Korea
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15
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Roland FAE, Borges AV, Darchambeau F, Llirós M, Descy JP, Morana C. The possible occurrence of iron-dependent anaerobic methane oxidation in an Archean Ocean analogue. Sci Rep 2021; 11:1597. [PMID: 33452366 PMCID: PMC7810693 DOI: 10.1038/s41598-021-81210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 11/24/2022] Open
Abstract
In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L-1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L-1 d-1, respectively, were put in evidence. In the Fe oxidation-reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.
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Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, Liège, Belgium.
| | | | | | - Marc Llirós
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Girona Biomedical Research Institute, Salt, Catalunya, Spain
| | | | - Cédric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
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16
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Tyne RL, Barry PH, Lawson M, Byrne DJ, Warr O, Xie H, Hillegonds DJ, Formolo M, Summers ZM, Skinner B, Eiler JM, Ballentine CJ. Rapid microbial methanogenesis during CO 2 storage in hydrocarbon reservoirs. Nature 2021; 600:670-674. [PMID: 34937895 PMCID: PMC8695373 DOI: 10.1038/s41586-021-04153-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023]
Abstract
Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO2) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO2 geological sequestration1,2. Depleted hydrocarbon reservoirs have substantial CO2 storage potential1,3, and numerous hydrocarbon reservoirs have undergone CO2 injection as a means of enhanced oil recovery (CO2-EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO2-EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13-19% of the injected CO2 to methane (CH4) and up to an additional 74% of CO2 was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73-109 millimoles of CH4 per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO2 fields suggest that microbial methanogenesis may be an important subsurface sink of CO2 globally. For CO2 sequestration sites within the environmental window for microbial methanogenesis, conversion to CH4 should be considered in site selection.
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Affiliation(s)
- R. L. Tyne
- grid.4991.50000 0004 1936 8948Department of Earth Sciences, University of Oxford, Oxford, UK
| | - P. H. Barry
- grid.4991.50000 0004 1936 8948Department of Earth Sciences, University of Oxford, Oxford, UK ,grid.56466.370000 0004 0504 7510Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - M. Lawson
- grid.421234.20000 0004 1112 1641ExxonMobil Upstream Business Development, Spring, TX USA ,grid.497051.e0000 0004 5997 8548Present Address: Aker BP, Stavanger, Norway
| | - D. J. Byrne
- grid.29172.3f0000 0001 2194 6418CRPG-CNRS, Université de Lorraine, Nancy, France
| | - O. Warr
- grid.17063.330000 0001 2157 2938Department of Earth Sciences, University of Toronto, Toronto, Ontario Canada
| | - H. Xie
- grid.20861.3d0000000107068890Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA USA
| | - D. J. Hillegonds
- grid.4991.50000 0004 1936 8948Department of Earth Sciences, University of Oxford, Oxford, UK
| | - M. Formolo
- grid.421234.20000 0004 1112 1641ExxonMobil Upstream Integrated Solutions, Spring, TX USA
| | - Z. M. Summers
- ExxonMobil Research and Engineering Co., Virginia, NJ USA
| | - B. Skinner
- grid.421234.20000 0004 1112 1641ExxonMobil Upstream Integrated Solutions, Spring, TX USA
| | - J. M. Eiler
- grid.20861.3d0000000107068890Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA USA
| | - C. J. Ballentine
- grid.4991.50000 0004 1936 8948Department of Earth Sciences, University of Oxford, Oxford, UK
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17
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Williamson AJ, Engelbrektson AL, Liu Y, Huang LL, Kumar A, Menon AR, Thieme J, Carlson HK, Coates JD. Tungstate Control of Microbial Sulfidogenesis and Souring of the Engineered Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:16119-16127. [PMID: 33253556 DOI: 10.1021/acs.est.0c04682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sulfide accumulation in oil reservoir fluids (souring) from the activity of sulfate-reducing microorganisms (SRM) is of grave concern because of the associated health and facility failure risks. Here, we present an assessment of tungstate as a selective and potent inhibitor of SRM. Dose-response inhibitor experiments were conducted with a number of SRM isolates and enrichments at 30-80 °C and an increase in the effectiveness of tungstate treatment at higher temperatures was observed. To explore mixed inhibitor treatment modes, we tested synergy or antagonism between several inhibitors with tungstate, and found synergism between WO42- and NO2-, while additive effects were observed with ClO4- and NO3-. We also evaluated SRM inhibition by tungstate in advective upflow oil-sand-packed columns. Although 2 mM tungstate was initially sufficient to inhibit sulfidogenesis, subsequent temporal CaWO4 precipitation resulted in loss of the bioavailable inhibitor from solution and a concurrent increase in effluent sulfide. Mixing 4 mM sodium carbonate with the 2 mM tungstate was enough to promote tungstate solubility to reach inhibitory concentrations, without precipitation, and completely inhibit SRM activity. Overall, we demonstrate the effectiveness of tungstate as a potent SRM inhibitor, particularly at higher temperatures, and propose a novel carbonate-tungstate formulation for application to soured oil reservoirs.
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Affiliation(s)
- Adam J Williamson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Anna L Engelbrektson
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Yi Liu
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Leah L Huang
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aarti Kumar
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Aruna R Menon
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
| | - Juergen Thieme
- NSLS-II Brookhaven National Laboratory, Brookhaven, New York 11973, United States
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John D Coates
- Energy Biosciences Institute, 2151 Berkeley Way, California 94704, United States
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18
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Peterson BD, McDaniel EA, Schmidt AG, Lepak RF, Janssen SE, Tran PQ, Marick RA, Ogorek JM, DeWild JF, Krabbenhoft DP, McMahon KD. Mercury Methylation Genes Identified across Diverse Anaerobic Microbial Guilds in a Eutrophic Sulfate-Enriched Lake. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15840-15851. [PMID: 33228362 PMCID: PMC9741811 DOI: 10.1021/acs.est.0c05435] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mercury (Hg) methylation is a microbially mediated process that converts inorganic Hg into bioaccumulative, neurotoxic methylmercury (MeHg). The metabolic activity of methylating organisms is highly dependent on biogeochemical conditions, which subsequently influences MeHg production. However, our understanding of the ecophysiology of methylators in natural ecosystems is still limited. Here, we identified potential locations of MeHg production in the anoxic, sulfidic hypolimnion of a freshwater lake. At these sites, we used shotgun metagenomics to characterize microorganisms with the Hg-methylation gene hgcA. Putative methylators were dominated by hgcA sequences divergent from those in well-studied, confirmed methylators. Using genome-resolved metagenomics, we identified organisms with hgcA (hgcA+) within the Bacteroidetes and the recently described Kiritimatiellaeota phyla. We identified hgcA+ genomes derived from sulfate-reducing bacteria, but these accounted for only 22% of hgcA+ genome coverage. The most abundant hgcA+ genomes were from fermenters, accounting for over half of the hgcA gene coverage. Many of these organisms also mediate hydrolysis of polysaccharides, likely from cyanobacterial blooms. This work highlights the distribution of the Hg-methylation genes across microbial metabolic guilds and indicate that primary degradation of polysaccharides and fermentation may play an important but unrecognized role in MeHg production in the anoxic hypolimnion of freshwater lakes.
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Affiliation(s)
- Benjamin D. Peterson
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- Corresponding author:
| | - Elizabeth A. McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Anna G. Schmidt
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Ryan F. Lepak
- Environmental Science & Technology Program, University of Wisconsin - Madison, 660 N. Park Street, Madison, WI 53706, USA
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
- U.S. Environmental Protection Agency Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Sarah E. Janssen
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Integrative Biology, University of Wisconsin - Madison, 250 N. Mills St.Madison, WI 53706, USA
| | - Robert A. Marick
- Department of Biochemistry, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Jacob M. Ogorek
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - John F. DeWild
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - David P. Krabbenhoft
- U.S. Geological Survey, Upper Midwest Water Science Center, Mercury Research Laboratory, 8505 Research Way, Middleton, WI 53562, USA
| | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin - Madison, 1550 Linden Drive, Madison, WI 53706, USA
- Department of Civil and Environmental Engineering, University of Wisconsin – Madison, 1415 Engineering Drive, Madison WI 53706, USA
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19
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Michas A, Harir M, Lucio M, Vestergaard G, Himmelberg A, Schmitt-Kopplin P, Lueders T, Hatzinikolaou DG, Schöler A, Rabus R, Schloter M. Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt. Front Microbiol 2020; 11:556793. [PMID: 33133031 PMCID: PMC7550536 DOI: 10.3389/fmicb.2020.556793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/09/2020] [Indexed: 01/23/2023] Open
Abstract
Sulfate-reducing microorganisms (SRMs) often compete with methanogens for common substrates. Due to thermodynamic reasons, SRMs should outcompete methanogens in the presence of sulfate. However, many studies have documented coexistence of these microbial groups in natural environments, suggesting that thermodynamics alone cannot explain the interactions among them. In this study, we investigated how SRMs compete with the established methanogenic communities in sediment from a long-term, electron acceptor-depleted, asphalt-exposed ecosystem and how they affect the composition of the organic material. We hypothesized that, upon addition of sulfate, SRMs (i) outcompete the methanogenic communities and (ii) markedly contribute to transformations of the organic material. We sampled sediments from the test and proximate control sites under anoxic conditions and incubated them in seawater medium with or without sulfate. Abundance and activity pattern of SRMs and methanogens, as well as the total prokaryotic community, were followed for 6 weeks by using qPCR targeting selected marker genes. Some of these genes were also subjected to amplicon sequencing to assess potential shifts in diversity patterns. Alterations of the organic material in the microcosms were determined by mass spectrometry. Our results indicate that the competition of SRMs with methanogens upon sulfate addition strongly depends on the environment studied and the starting microbiome composition. In the asphalt-free sediments (control), the availability of easily degradable organic material (mainly plant-derived) allows SRMs to use a larger variety of substrates, reducing interspecies competition with methanogens. In contrast, the abundant presence of recalcitrant compounds in the asphalt-exposed sediment was associated with a strong competition between SRMs and methanogens, ultimately detrimental for the latter. Our data underpin the importance of the quality of bioavailable organic materials in anoxic environments as a driver for microbial community structure and function.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany.,Chair of Soil Science, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany.,Chair of Analytical Food Chemistry, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Anne Himmelberg
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany.,Chair of Analytical Food Chemistry, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Tillmann Lueders
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Dimitris G Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Attica, Greece
| | - Anne Schöler
- Institute for Neuropathology, Charité University Hospital Berlin, Berlin, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Helmholtz Association of German Research Centers, Neuherberg, Germany.,Chair of Soil Science, Technical University of Munich, Freising-Weihenstephan, Germany
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Zaporski J, Jamison M, Zhang L, Gu B, Yang Z. Mercury methylation potential in a sand dune on Lake Michigan's eastern shoreline. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138879. [PMID: 32371207 DOI: 10.1016/j.scitotenv.2020.138879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Lake Michigan hosts the largest freshwater sand dune system in the world and is economically important for the fishery industry and tourism. Due to industrial pollution and atmospheric mercury (Hg) deposition, toxic levels of methylmercury (MeHg) have been found in the Lake biota, but little information is known regarding MeHg sources and Hg methylation potential in the shoreline sand dunes. We conducted anaerobic incubation experiments with beach sands collected from Ludington, Michigan, and examined the effects of organic carbon substrate addition, inorganic nitrogen, and mineral magnetite on Hg methylation. Despite nutrient poor and low-organic carbon conditions, appreciable Hg methylation activity coupled with carbon degradation was observed in the sands. Addition of acetate as a carbon source substantially increased MeHg production from 2 to 380 ng/kg sediment while acetate was rapidly degraded in the first 19 days of incubation. Ammonium addition showed little influence on carbon degradation or Hg methylation, whereas iron oxide addition (~1% dry weight) significantly inhibited both carbon degradation and MeHg production (by up to 90%), highlighting strongly coupled interactions between microbes, carbon substrates, and minerals. This research demonstrates the potential of microbial Hg methylation in the sand dunes, which may play a role in MeHg input and bioaccumulation in the Lake Michigan ecosystem.
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Affiliation(s)
- Jared Zaporski
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Megan Jamison
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA
| | - Lijie Zhang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA.
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21
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Compte-Port S, Fillol M, Gich F, Borrego CM. Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources. PLoS One 2020; 15:e0231238. [PMID: 32267873 PMCID: PMC7141681 DOI: 10.1371/journal.pone.0231238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/19/2020] [Indexed: 12/25/2022] Open
Abstract
Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.
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Affiliation(s)
- Sergi Compte-Port
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Frederic Gich
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Carles M. Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
- * E-mail:
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22
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Zhang Y, Li Q, Dai Q, Kang Y. Microbial mechanism underlying high and stable methane oxidation rates during mudflat reclamation with long-term rice cultivation: Illumina high-throughput sequencing-based data analysis. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:332-341. [PMID: 30856444 DOI: 10.1016/j.jhazmat.2019.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/10/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
This study aimed to determine the methane oxidation rates (MOR), pmoA gene abundance and diversity, and microbial community composition using Illumina high-throughput sequencing. Mudflats located within Yancheng City, divided into different plots with 0-, 11-, and 20-year successive rice planting histories, were selected and sampled. The study found that the relative MOR (normalized with the 16S rRNA gene) increased dramatically after 11-year cultivation and remained stable in 20-year treatment, indicating that long-term rice cultivation in mudflats promoted MOR. The sequencing data analysis revealed that high MOR was related to the synergistic growth of methane-producing archaea (MPA) and aerobic and facultative methane-consuming bacteria (MCB) mainly belonging to Proteobacteria. Redundancy and correlation analyses showed that Methylophilaceae and Methylococcaceae affiliated within β- and γ-Proteobacterial methanotrophs were closely related to the relative MOR. Methane-oxidizing archaea (MOA) coupled to sulfate and nitrite reductions contributed more to the high and stable MOR compared with Proteobacterial MCB. Chloroflexi and Geobacter were the potential hydrogen donors for hydrogenotrophic MPA. The results showed that long-term rice cultivation in mudflats promoted the relative MOR. The unknown MOA coupled to sulfate and nitrite reductions, besides the necessary hydrogenotrophic MPA and their hydrogen donors (Chloroflexi and Geobacter) collectively contributed to methane cycling.
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Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China.
| | - Yijun Kang
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China.
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23
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Parro V, Puente-Sánchez F, Cabrol NA, Gallardo-Carreño I, Moreno-Paz M, Blanco Y, García-Villadangos M, Tambley C, Tilot VC, Thompson C, Smith E, Sobrón P, Demergasso CS, Echeverría-Vega A, Fernández-Martínez MÁ, Whyte LG, Fairén AG. Microbiology and Nitrogen Cycle in the Benthic Sediments of a Glacial Oligotrophic Deep Andean Lake as Analog of Ancient Martian Lake-Beds. Front Microbiol 2019; 10:929. [PMID: 31130930 PMCID: PMC6509559 DOI: 10.3389/fmicb.2019.00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
Potential benthic habitats of early Mars lakes, probably oligotrophic, could range from hydrothermal to cold sediments. Dynamic processes in the water column (such as turbidity or UV penetration) as well as in the benthic bed (temperature gradients, turbation, or sedimentation rate) contribute to supply nutrients to a potential microbial ecosystem. High altitude, oligotrophic, and deep Andean lakes with active deglaciation processes and recent or past volcanic activity are natural models to assess the feasibility of life in other planetary lake/ocean environments and to develop technology for their exploration. We sampled the benthic sediments (down to 269 m depth) of the oligotrophic lake Laguna Negra (Central Andes, Chile) to investigate its ecosystem through geochemical, biomarker profiling, and molecular ecology studies. The chemistry of the benthic water was similar to the rest of the water column, except for variable amounts of ammonium (up to 2.8 ppm) and nitrate (up to 0.13 ppm). A life detector chip with a 300-antibody microarray revealed the presence of biomass in the form of exopolysaccharides and other microbial markers associated to several phylogenetic groups and potential microaerobic and anaerobic metabolisms such as nitrate reduction. DNA analyses showed that 27% of the Archaea sequences corresponded to a group of ammonia-oxidizing archaea (AOA) similar (97%) to Nitrosopumilus spp. and Nitrosoarchaeum spp. (Thaumarchaeota), and 4% of Bacteria sequences to nitrite-oxidizing bacteria from the Nitrospira genus, suggesting a coupling between ammonia and nitrite oxidation. Mesocosm experiments with the specific AOA inhibitor 2-Phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) demonstrated an AOA-associated ammonia oxidation activity with the simultaneous accumulation of nitrate and sulfate. The results showed a rich benthic microbial community dominated by microaerobic and anaerobic metabolisms thriving under aphotic, low temperature (4°C), and relatively high pressure, that might be a suitable terrestrial analog of other planetary settings.
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Affiliation(s)
- Victor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | - Nathalie A. Cabrol
- SETI Institute, Carl Sagan Center, Mountain View, CA, United States
- NASA Ames Research Center, Mountain View, CA, United States
| | | | | | | | | | | | - Virginie C. Tilot
- Instituto Español de Oceanografía (IEO), Málaga, Spain
- Muséum National d’Histoire Naturelle, Paris, France
| | - Cody Thompson
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Eric Smith
- SETI Institute, Carl Sagan Center, Mountain View, CA, United States
| | - Pablo Sobrón
- SETI Institute, Carl Sagan Center, Mountain View, CA, United States
| | | | - Alex Echeverría-Vega
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, Chile
| | | | - Lyle G. Whyte
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada
| | - Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca, NY, United States
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24
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Wu Q, Bao X, Guo W, Wang B, Li Y, Luo H, Wang H, Ren N. Medium chain carboxylic acids production from waste biomass: Current advances and perspectives. Biotechnol Adv 2019; 37:599-615. [PMID: 30849433 DOI: 10.1016/j.biotechadv.2019.03.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 11/29/2022]
Abstract
Alternative chemicals to diverse fossil-fuel-based products is urgently needed to mitigate the adverse impacts of fossil fuel depletion on human development. To this end, researchers have focused on the production of biochemical from readily available and affordable waste biomass. This is consistent with current guidelines for sustainable development and provides great advantages related to economy and environment. The search for suitable biochemical products is in progress worldwide. Therefore, this review recommends a biochemical (i.e., medium chain carboxylic acids (MCCAs)) utilizing an emerging biotechnological production platform called the chain elongation (CE) process. This work covers comprehensive introduction of the CE mechanism, functional microbes, available feedstock types and corresponding utilization strategies, major methods to enhance the performance of MCCAs production, and the challenges that need to be addressed for practical application. This work is expected to provide a thorough understanding of the CE technology, to guide and inspire researchers to solve existing problems in depth, and motivate large-scale MCCAs production.
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Affiliation(s)
- Qinglian Wu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Xian Bao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Wanqian Guo
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Bing Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Yunxi Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Haichao Luo
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Huazhe Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China
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25
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Yang LW, Liu C, Yang T. An evaluation on the extraction capability of anion exchange membranes for high-precision sulfur isotope measurement by multiple-collector inductively coupled plasma mass spectrometry. RSC Adv 2019; 9:31224-31232. [PMID: 35527964 PMCID: PMC9072498 DOI: 10.1039/c9ra04121d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022] Open
Abstract
Anion exchange membranes (AEMs) are adept at extracting sulfate for sulfur isotope analyses by multiple-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) from natural samples typically with low sulfate concentrations.
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Affiliation(s)
- Liu Willow Yang
- State Key Laboratory for Mineral Deposits Research
- School of Earth Sciences and Engineering
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Chenhui Liu
- State Key Laboratory for Mineral Deposits Research
- School of Earth Sciences and Engineering
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Tao Yang
- State Key Laboratory for Mineral Deposits Research
- School of Earth Sciences and Engineering
- Nanjing University
- Nanjing 210093
- P. R. China
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26
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Goopy JP. Creating a low enteric methane emission ruminant: what is the evidence of success to the present and prospects for developing economies? ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an18457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Enteric methane emissions from livestock constitute a greater part of anthropogenic greenhouse gases (GHGs) in Africa, than in more industrialised economies, providing a strong incentive for the development of low methane phenotype ruminants. Although dietary and husbandry options already exist for lowering methane production, means of changing ‘methane status’ of animals enduringly has a strong appeal. This paper is a critical review the empirical success to date of attempts to alter this status. Introduction of reductive acetogens, defaunation, anti-methanogen vaccines, early life programming and genetic selection at both the rumen and animal level are considered in turn. It is concluded that to date, there is little in vivo evidence to support the practical success of any of these strategies, save selective breeding, and this at a high cost with unknown efficacy. Finally, it is suggested that for developing economies management and nutritional strategies to reduce emissions will have the greatest and most immediate impact, at the lowest cost.
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27
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Effect of pretreatment solutions and conditions on decomposition and anaerobic digestion of lignocellulosic biomass in rice straw. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation. ISME JOURNAL 2018; 13:632-650. [PMID: 30323265 PMCID: PMC6461797 DOI: 10.1038/s41396-018-0296-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 11/24/2022]
Abstract
Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of 13C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.
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29
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Holmes DE, Orelana R, Giloteaux L, Wang LY, Shrestha P, Williams K, Lovley DR, Rotaru AE. Potential for Methanosarcina to Contribute to Uranium Reduction during Acetate-Promoted Groundwater Bioremediation. MICROBIAL ECOLOGY 2018; 76:660-667. [PMID: 29500492 PMCID: PMC6132540 DOI: 10.1007/s00248-018-1165-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/16/2018] [Indexed: 05/06/2023]
Abstract
Previous studies of acetate-promoted bioremediation of uranium-contaminated aquifers focused on Geobacter because no other microorganisms that can couple the oxidation of acetate with U(VI) reduction had been detected in situ. Monitoring the levels of methyl CoM reductase subunit A (mcrA) transcripts during an acetate-injection field experiment demonstrated that acetoclastic methanogens from the genus Methanosarcina were enriched after 40 days of acetate amendment. The increased abundance of Methanosarcina corresponded with an accumulation of methane in the groundwater. In order to determine whether Methanosarcina species could be participating in U(VI) reduction in the subsurface, cell suspensions of Methanosarcina barkeri were incubated in the presence of U(VI) with acetate provided as the electron donor. U(VI) was reduced by metabolically active M. barkeri cells; however, no U(VI) reduction was observed in inactive controls. These results demonstrate that Methanosarcina species could play an important role in the long-term bioremediation of uranium-contaminated aquifers after depletion of Fe(III) oxides limits the growth of Geobacter species. The results also suggest that Methanosarcina have the potential to influence uranium geochemistry in a diversity of anaerobic sedimentary environments.
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Affiliation(s)
- Dawn E Holmes
- Department of Physical and Biological Science, Western New England University, Springfield, MA, USA.
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Roberto Orelana
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Ludovic Giloteaux
- Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Pravin Shrestha
- Energy Biosciences Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
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30
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Habtewold J, Gordon R, Voroney P, Sokolov V, VanderZaag A, Wagner-Riddle C, Dunfield K. Sodium Persulfate and Potassium Permanganate Inhibit Methanogens and Methanogenesis in Stored Liquid Dairy Manure. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:786-794. [PMID: 30025063 DOI: 10.2134/jeq2018.01.0054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Stored liquid dairy manure is a hotspot for methane (CH) emission, thus effective mitigation strategies are required. We assessed sodium persulfate (NaSO), potassium permanganate (KMnO), and sodium hypochlorite (NaOCl) for impacts on the abundance of microbial communities and CH production in liquid dairy manure. Liquid dairy manure treated with different rates (1, 3, 6, and 9 g or mL L slurry) of these chemicals or their combinations were incubated under anoxic conditions at 22.5 ± 1.3°C for 120 d. Untreated and sodium 2-bromoethanesulfonate (BES)-treated manures were included as negative and positive controls, respectively, whereas sulfuric acid (HSO)-treated manure was used as a reference. Quantitative real-time polymerase chain reaction was used to quantify the abundances of bacteria and methanogens on Days 0, 60, and 120. Headspace CH/CO ratios were used as a proxy to determine CH production. Unlike bacterial abundance, methanogen abundance and CH/CO ratios varied with treatments. Addition of 1 to 9 g L slurry of NaSO and KMnO reduced methanogen abundance (up to ∼28%) and peak CH/CO ratios (up to 92-fold). Except at the lowest rate, chemical combinations also reduced the abundance of methanogens (up to ∼17%) and CH/CO ratios (up to ninefold), although no impacts were observed when 3% NaOCl was used alone. With slurry acidification, the ratios reduced up to twofold, whereas methanogen abundance was unaffected. Results suggest that NaSO and KMnO may offer alternative options to reduce CH emission from stored liquid dairy manure, but this warrants further assessment at larger scales for environmental impacts and characteristics of the treated manure.
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31
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Ancient Microbial Activity in Deep Hydraulically Conductive Fracture Zones within the Forsmark Target Area for Geological Nuclear Waste Disposal, Sweden. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8060211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Parro V, Blanco Y, Puente-Sánchez F, Rivas LA, Moreno-Paz M, Echeverría A, Chong-Díaz G, Demergasso C, Cabrol NA. Biomarkers and Metabolic Patterns in the Sediments of Evolving Glacial Lakes as a Proxy for Planetary Lake Exploration. ASTROBIOLOGY 2018; 18:586-606. [PMID: 27893284 DOI: 10.1089/ast.2015.1342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Oligotrophic glacial lakes in the Andes Mountains serve as models to study the effects of climate change on natural biological systems. The persistent high UV regime and evolution of the lake biota due to deglaciation make Andean lake ecosystems potential analogues in the search for life on other planetary bodies. Our objective was to identify microbial biomarkers and metabolic patterns that represent time points in the evolutionary history of Andean glacial lakes, as these may be used in long-term studies as microscale indicators of climate change processes. We investigated a variety of microbial markers in shallow sediments from Laguna Negra and Lo Encañado lakes (Región Metropolitana, Chile). An on-site immunoassay-based Life Detector Chip (LDChip) revealed the presence of sulfate-reducing bacteria, methanogenic archaea, and exopolymeric substances from Gammaproteobacteria. Bacterial and archaeal 16S rRNA gene sequences obtained from field samples confirmed the results from the immunoassays and also revealed the presence of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, as well as cyanobacteria and methanogenic archaea. The complementary immunoassay and phylogenetic results indicate a rich microbial diversity with active sulfate reduction and methanogenic activities along the shoreline and in shallow sediments. Sulfate inputs from the surrounding volcanic terrains during deglaciation may explain the observed microbial biomarker and metabolic patterns, which differ with depth and between the two lakes. A switch from aerobic and heterotrophic metabolisms to anaerobic ones such as sulfate reduction and methanogenesis in the shallow shores likely reflects the natural evolution of the lake sediments due to deglaciation. Hydrodynamic deposition of sediments creates compartmentalization (e.g., sediments with different structure and composition surrounded by oligotrophic water) that favors metabolic transitions. Similar phenomena would be expected to occur on other planetary lakes, such as those of Titan, where watery niches fed by depositional events would be surrounded by a "sea" of hydrocarbons. Key Words: Glacier lakes-Sedimentation-Prokaryotic metabolisms and biomarkers-Deglaciation-Life detection-Planetary exploration. Astrobiology 18, 586-606.
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Affiliation(s)
- Víctor Parro
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Yolanda Blanco
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | | | - Luis A Rivas
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Mercedes Moreno-Paz
- 1 Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC) , Madrid, Spain
| | - Alex Echeverría
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Guillermo Chong-Díaz
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Cecilia Demergasso
- 2 Centro de Biotecnología "Profesor Alberto Ruiz," Universidad Católica del Norte , Antofagasta, Chile
| | - Nathalie A Cabrol
- 3 The SETI Institute , Carl Sagan Center, Mountain View, California, and NASA Ames Research Center, Moffett Field, California, USA
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33
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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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Strickman RJ, Mitchell CPJ. Mercury methylation in stormwater retention ponds at different stages in the management lifecycle. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2018; 20:595-606. [PMID: 29376168 DOI: 10.1039/c7em00486a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Stormwater retention ponds effectively manage erosion, flooding, and pollutant loadings, but are also sources of methylmercury (MeHg), a bioaccumulative neurotoxin which is produced by anaerobic aquatic microorganisms. Stormwater retention ponds have a 10-15 year working life, after which they are dredged and reflooded. In this study, we related MeHg biogeochemistry to the different stages of the management lifecycle. In a new, a dredged, and a mature stormwater retention pond, we measured MeHg and inorganic mercury (IHg) concentrations, and the potential for MeHg formation (Kmeth), during the early summer, peak summer, and fall of 2013. In our study sites, MeHg concentrations appear to be driven by mercury (Hg) methylation, indicated by significant correlations between Kmeth values and MeHg concentrations and the percent of Hg present as MeHg. Relationships between Hg variables and ancillary biogeochemistry suggest that Hg methylation is carried out by sulfate reducing bacteria, but that the process is modulated by the supply of IHg substrate, sediment total and labile organic carbon, and possibly competition with nitrate reducers. Wetlands at different points in the management lifecycle differ in terms of their MeHg biogeochemistry. The organic matter-poor new wetland had low MeHg production (mean Kmeth 0.014 per day) and sediment concentrations (mean 0.015 ng g-1), while the mature wetland both produced and accumulated MeHg about five times more actively. Methylmercury production capacity was only temporarily reduced in the reflooded sediments of the dredged wetland, which experienced rapid increases in Kmeth values from low (mean 0.015 per day) immediately after dredging, to values similar to those in the mature wetland after five months. This pattern may have been related to recolonization of the sediments with mercury methylators or increased microbial activities in response to the addition of fresh organic matter. Additional studies should focus on the applicability of these patterns to stormwater retention ponds in other areas, and particularly investigate the effects of stormwater pond dredging on their microbial ecology and MeHg biogeochemistry.
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Affiliation(s)
- R J Strickman
- University of Toronto Scarborough, Department of Physical and Environmental Sciences, 1285 Military Trail, Toronto, Ontario M4C 1A4, Canada.
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Liu ZH, Yin H, Lin Z, Dang Z. Sulfate-reducing bacteria in anaerobic bioprocesses: basic properties of pure isolates, molecular quantification, and controlling strategies. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/21622515.2018.1437783] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ze-hua Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
- Key Lab Pollution Control and Ecosystem Restoration in Industry Cluster, Ministry of Education, Guangzhou, People’s Republic of China
- Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou, People’s Republic of China
- Guangdong Provincial Engineering and Technology Research Center for Environment Risk Prevention and Emergency Disposal, South China University of Technology, Guangzhou, People’s Republic of China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhang Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
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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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Noronha MF, Lacerda Júnior GV, Gilbert JA, de Oliveira VM. Taxonomic and functional patterns across soil microbial communities of global biomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1064-1074. [PMID: 28787780 DOI: 10.1016/j.scitotenv.2017.07.159] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 05/24/2023]
Affiliation(s)
- Melline Fontes Noronha
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil; Institute of Biology, Campinas University, Brazil.
| | - Gileno Vieira Lacerda Júnior
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil; Institute of Biology, Campinas University, Brazil
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA; The Microbiome Center, Bioscience Division, Argonne National Laboratory, Lemont, IL, USA
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Multidisciplinary Center for Chemistry, Biology and Agriculture Research (CPQBA), Campinas University, Brazil
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Ma TT, Liu LY, Rui JP, Yuan Q, Feng DS, Zhou Z, Dai LR, Zeng WQ, Zhang H, Cheng L. Coexistence and competition of sulfate-reducing and methanogenic populations in an anaerobic hexadecane-degrading culture. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:207. [PMID: 28878822 PMCID: PMC5584521 DOI: 10.1186/s13068-017-0895-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Over three-fifths of the world's known crude oil cannot be recovered using state-of-the-art techniques, but microbial conversion of petroleum hydrocarbons trapped in oil reservoirs to methane is one promising path to increase the recovery of fossil fuels. The process requires cooperation between syntrophic bacteria and methanogenic archaea, which can be affected by sulfate-reducing prokaryotes (SRPs). However, the effects of sulfate on hydrocarbon degradation and methane production remain elusive, and the microbial communities involved are not well understood. RESULTS In this study, a methanogenic hexadecane-degrading enrichment culture was treated with six different concentrations of sulfate ranging from 0.5 to 25 mM. Methane production and maximum specific methane production rate gradually decreased to 44 and 56% with sulfate concentrations up to 25 mM, respectively. There was a significant positive linear correlation between the sulfate reduction/methane production ratio and initial sulfate concentration, which remained constant during the methane production phase. The apparent methanogenesis fractionation factor (αapp) gradually increased during the methane production phase in each treatment, the αapp for the treatments with lower sulfate (0.5-4 mM) eventually plateaued at ~1.047, but that for the treatment with 10-25 mM sulfate only reached ~1.029. The relative abundance levels of Smithella and Methanoculleus increased almost in parallel with the increasing sulfate concentrations. Furthermore, the predominant sulfate reducer communities shifted from Desulfobacteraceae in the low-sulfate cultures to Desulfomonile in the high-sulfate cultures. CONCLUSION The distribution of hexadecane carbon between methane-producing and sulfate-reducing populations is dependent on the initial sulfate added, and not affected during the methane production period. There was a relative increase in hydrogenotrophic methanogenesis activity over time for all sulfate treatments, whereas the total activity was inhibited by sulfate addition. Both Smithella and Methanoculleus, the key alkane degraders and methane producers, can adapt to sulfate stress. Specifically, different SRP populations were stimulated at various sulfate concentrations. These results could help to evaluate interactions between sulfate-reducing and methanogenic populations during anaerobic hydrocarbon degradation in oil reservoirs.
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Affiliation(s)
- Ting-Ting Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Lai-Yan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Jun-Peng Rui
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology of Chinese Academy of Sciences, Section 4-9, Renmin South Road, Chengdu, 610041 People's Republic of China
- Environmental Microbiology Key Laboratory of Sichuan Province, Section 4-9, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 99 Lincheng West Road, Guanshanhu District, Guiyang, 550081 People's Republic of China
| | - Ding-Shan Feng
- Anhui Normal University, 1 Beijing East Road, Wuhu, 241000 People's Republic of China
| | - Zheng Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Li-Rong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Wan-Qiu Zeng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
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Amenabar MJ, Shock EL, Roden EE, Peters JW, Boyd ES. Microbial substrate preference dictated by energy demand, not supply. NATURE GEOSCIENCE 2017; 10:577-581. [PMID: 30944580 PMCID: PMC6443248 DOI: 10.1038/ngeo2978] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/02/2017] [Indexed: 06/08/2023]
Abstract
Growth substrates that maximize energy yield are widely thought to be utilized preferentially by microorganisms. However, observed distributions of microorganisms and their activities often deviate from predictions based solely on thermodynamic considerations of substrate energy supply. Here we present observations of the bioenergetics and growth yields of a metabolically flexible, thermophilic strain of the archaeon Acidianus when grown autotrophically on minimal medium with hydrogen (H2) or elemental sulfur (S°) as an electron donor, and S° or ferric iron (Fe3+) as an electron acceptor. Thermodynamic calculations indicate that S°/Fe3+ and H2/Fe3+ yield three- and four-fold more energy per mol electron transferred, respectively, than the H2/S° couple. However, biomass yields in Acidianus cultures provided with H2/S° were eight-fold greater than when provided S°/Fe3+ or H2/Fe3+, indicating the H2/S° redox couple is preferred. Indeed, cells provided with all three growth substrates (H2, Fe3+, and S°) grew preferentially by reduction of S° with H2. We conclude that substrate preference is dictated by differences in the energy demand of electron transfer reactions in Acidianus when grown with different substrates, rather than substrate energy supply.
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Affiliation(s)
| | - Everett L. Shock
- School of Earth & Space Exploration and School of Molecular Sciences, Arizona State University, Tempe, Arizona
- NASA Astrobiology Institute, Mountain View, California
| | - Eric E. Roden
- Department of Geosciences, University of Wisconsin, Madison, Wisconsin
- NASA Astrobiology Institute, Mountain View, California
| | - John W. Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana
| | - Eric S. Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana
- NASA Astrobiology Institute, Mountain View, California
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Dalcin Martins P, Hoyt DW, Bansal S, Mills CT, Tfaily M, Tangen BA, Finocchiaro RG, Johnston MD, McAdams BC, Solensky MJ, Smith GJ, Chin YP, Wilkins MJ. Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands. GLOBAL CHANGE BIOLOGY 2017; 23:3107-3120. [PMID: 28117550 DOI: 10.1111/gcb.13633] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/02/2016] [Indexed: 05/04/2023]
Abstract
Inland waters are increasingly recognized as critical sites of methane emissions to the atmosphere, but the biogeochemical reactions driving such fluxes are less well understood. The Prairie Pothole Region (PPR) of North America is one of the largest wetland complexes in the world, containing millions of small, shallow wetlands. The sediment pore waters of PPR wetlands contain some of the highest concentrations of dissolved organic carbon (DOC) and sulfur species ever recorded in terrestrial aquatic environments. Using a suite of geochemical and microbiological analyses, we measured the impact of sedimentary carbon and sulfur transformations in these wetlands on methane fluxes to the atmosphere. This research represents the first study of coupled geochemistry and microbiology within the PPR and demonstrates how the conversion of abundant labile DOC pools into methane results in some of the highest fluxes of this greenhouse gas to the atmosphere ever reported. Abundant DOC and sulfate additionally supported some of the highest sulfate reduction rates ever measured in terrestrial aquatic environments, which we infer to account for a large fraction of carbon mineralization in this system. Methane accumulations in zones of active sulfate reduction may be due to either the transport of free methane gas from deeper locations or the co-occurrence of methanogenesis and sulfate reduction. If both respiratory processes are concurrent, any competitive inhibition of methanogenesis by sulfate-reducing bacteria may be lessened by the presence of large labile DOC pools that yield noncompetitive substrates such as methanol. Our results reveal some of the underlying mechanisms that make PPR wetlands biogeochemical hotspots, which ultimately leads to their critical, but poorly recognized role in regional greenhouse gas emissions.
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Affiliation(s)
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Richland, WA, 99350, USA
| | - Sheel Bansal
- United States Geological Survey - Northern Prairie Wildlife Research Center, Jamestown, ND, 58401, USA
| | - Christopher T Mills
- United States Geological Survey, Crustal Geophysics and Geochemistry Science Center, Building 20, Denver Federal Center, Denver, CO, 80225, USA
| | - Malak Tfaily
- Environmental Molecular Sciences Laboratory, Richland, WA, 99350, USA
| | - Brian A Tangen
- United States Geological Survey - Northern Prairie Wildlife Research Center, Jamestown, ND, 58401, USA
| | - Raymond G Finocchiaro
- United States Geological Survey - Northern Prairie Wildlife Research Center, Jamestown, ND, 58401, USA
| | - Michael D Johnston
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Brandon C McAdams
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew J Solensky
- United States Geological Survey - Northern Prairie Wildlife Research Center, Jamestown, ND, 58401, USA
| | - Garrett J Smith
- Microbiology Department, The Ohio State University, Columbus, OH, 43210, USA
| | - Yu-Ping Chin
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael J Wilkins
- Microbiology Department, The Ohio State University, Columbus, OH, 43210, USA
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
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Pozo G, Lu Y, Pongy S, Keller J, Ledezma P, Freguia S. Selective cathodic microbial biofilm retention allows a high current-to-sulfide efficiency in sulfate-reducing microbial electrolysis cells. Bioelectrochemistry 2017; 118:62-69. [PMID: 28719849 DOI: 10.1016/j.bioelechem.2017.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/03/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022]
Abstract
Selective microbial retention is of paramount importance for the long-term performance of cathodic sulfate reduction in microbial electrolysis cells (MECs) due to the slow growth rate of autotrophic sulfate-reducing bacteria. In this work, we investigate the biofilm retention and current-to-sulfide conversion efficiency using carbon granules (CG) or multi-wall carbon nanotubes deposited on reticulated vitreous carbon (MWCNT-RVC) as electrode materials. For ~2months, the MECs were operated at sulfate loading rates of 21 to 309gSO4 -S/m2/d. Although MWCNT-RVC achieved a current density of 57±11A/m2, greater than the 32±9A/m2 observed using CG, both materials exhibited similar sulfate reduction rates (SRR), with MWCNT-RVC reaching 104±16gSO4 -S/m2/d while 110±13gSO4 -S/m2/d were achieved with CG. Pyrosequencing analysis of the 16S rRNA at the end of experimentation revealed a core community dominated by Desulfovibrio (28%), Methanobacterium (19%) and Desulfomicrobium (14%), on the MWCNT-RVC electrodes. While a similar Desulfovibrio relative abundance of 29% was found in CG-biofilms, Desulfomicrobium was found to be significantly less abundant (4%) and Methanobacterium practically absent (0.2%) on CG electrodes. Surprisingly, our results show that CG can achieve higher current-to-sulfide efficiencies at lower power consumption than the nano-modified three-dimensional MWCNT-RVC.
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Affiliation(s)
- Guillermo Pozo
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia.
| | - Yang Lu
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia
| | - Sebastien Pongy
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia; Département Génie Energétique et Environnement, INSA Lyon, 69621 Villeurbanne Cedex, France
| | - Jürg Keller
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia
| | - Pablo Ledezma
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia
| | - Stefano Freguia
- Advanced Water Management Centre, the University of Queensland, St Lucia, QLD 4072, Australia
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Xiao KQ, Beulig F, Kjeldsen KU, Jørgensen BB, Risgaard-Petersen N. Concurrent Methane Production and Oxidation in Surface Sediment from Aarhus Bay, Denmark. Front Microbiol 2017; 8:1198. [PMID: 28713339 PMCID: PMC5492102 DOI: 10.3389/fmicb.2017.01198] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/12/2017] [Indexed: 12/26/2022] Open
Abstract
Marine surface sediments, which are replete with sulfate, are typically considered to be devoid of endogenous methanogenesis. Yet, methanogenic archaea are present in those sediments, suggesting a potential for methanogenesis. We used an isotope dilution method based on sediment bag incubation and spiking with 13C-CH4 to quantify CH4 turnover rates in sediment from Aarhus Bay, Denmark. In two independent experiments, highest CH4 production and oxidation rates (>200 pmol cm-3 d-1) were found in the top 0-2 cm, below which rates dropped below 100 pmol cm-3 d-1 in all other segments down to 16 cm. This drop in overall methane turnover with depth was accompanied by decreasing rates of organic matter mineralization with depth. Molecular analyses based on quantitative PCR and MiSeq sequencing of archaeal 16S rRNA genes showed that the abundance of methanogenic archaea also peaked in the top 0-2 cm segment. Based on the community profiling, hydrogenotrophic and methylotrophic methanogens dominated among the methanogenic archaea in general, suggesting that methanogenesis in surface sediment could be driven by both CO2 reduction and fermentation of methylated compounds. Our results show the existence of elevated methanogenic activity and a dynamic recycling of CH4 at low concentration in sulfate-rich marine surface sediment. Considering the common environmental conditions found in other coastal systems, we speculate that such a cryptic methane cycling can be ubiquitous.
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Affiliation(s)
- Ke-Qing Xiao
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
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Krohn J, Lozanovska I, Kuzyakov Y, Parvin S, Dorodnikov M. CH 4 and CO 2 production below two contrasting peatland micro-relief forms: An inhibitor and δ 13C study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 586:142-151. [PMID: 28169027 DOI: 10.1016/j.scitotenv.2017.01.192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 06/06/2023]
Abstract
Two peatland micro-relief forms (microforms) - hummocks and hollows - differ by their hydrological characteristics (water table level, i.e. oxic-anoxic conditions) and vegetation communities. We studied the CH4 and CO2 production potential and the localization of methanogenic pathways in both hummocks and hollows at depths of 15, 50, 100, 150 and 200cm in a laboratory incubation experiment. For this purpose, we measured CH4 and CO2 production rates, peat elemental composition, as well as δ13C values of gases and solids; the specific inhibitor of methanogenesis BES (2-bromo-ethane sulfonate, 1mM) was aimed to preferentially block the acetoclastic pathway. The cumulative CH4 production of all depths was almost one fold higher in hollows than in hummocks, with no differences in CO2. With depth, CO2 and CH4 production decreased, and the relative contribution of the hydrogenotrophic pathway of methanogenesis increased. The highest methanogenic activity among all depths and both microforms was measured at 15cm of hollows (91%) at which the highest relative contribution of acetoclastic vs. hydrogenotrophic pathway (92 and 8%, respectively) was detected. For hummocks, the CH4 production was the highest at 50cm (82%), where relative contribution of acetoclastic methanogenesis comprised 89%. The addition of 1mM BES was not selective and inhibited both methanogenic pathways in the soil. Thus, BES was less efficient in partitioning the pathways compared with the δ13C signature. We conclude that the peat microforms - dry hummocks and wet hollows - play an important role for CH4 but not for CO2 production when the effects of living vegetation are excluded.
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Affiliation(s)
- Johannes Krohn
- Department of Soil Science of Temperate Ecosystems, Faculty of Forest Sciences and Forest Ecology, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Ivana Lozanovska
- Department of Soil Science of Temperate Ecosystems, Faculty of Forest Sciences and Forest Ecology, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Faculty of Forest Sciences and Forest Ecology, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany; Department of Agricultural Soil Science, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Shahnaj Parvin
- Department of Soil Science of Temperate Ecosystems, Faculty of Forest Sciences and Forest Ecology, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Maxim Dorodnikov
- Department of Soil Science of Temperate Ecosystems, Faculty of Forest Sciences and Forest Ecology, Georg-August University Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
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Sela-Adler M, Ronen Z, Herut B, Antler G, Vigderovich H, Eckert W, Sivan O. Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments. Front Microbiol 2017; 8:766. [PMID: 28529500 PMCID: PMC5418336 DOI: 10.3389/fmicb.2017.00766] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/13/2017] [Indexed: 11/13/2022] Open
Abstract
The competition between sulfate reducing bacteria and methanogens over common substrates has been proposed as a critical control for methane production. In this study, we examined the co-existence of methanogenesis and sulfate reduction with shared substrates over a large range of sulfate concentrations and rates of sulfate reduction in estuarine systems, where these processes are the key terminal sink for organic carbon. Incubation experiments were carried out with sediment samples from the sulfate-methane transition zone of the Yarqon (Israel) estuary with different substrates and inhibitors along a sulfate concentrations gradient from 1 to 10 mM. The results show that methanogenesis and sulfate reduction can co-exist while the microbes share substrates over the tested range of sulfate concentrations and at sulfate reduction rates up to 680 μmol L-1 day-1. Rates of methanogenesis were two orders of magnitude lower than rates of sulfate reduction in incubations with acetate and lactate, suggesting a higher affinity of sulfate reducing bacteria for the available substrates. The co-existence of both processes was also confirmed by the isotopic signatures of δ34S in the residual sulfate and that of δ13C of methane and dissolved inorganic carbon. Copy numbers of dsrA and mcrA genes supported the dominance of sulfate reduction over methanogenesis, while showing also the ability of methanogens to grow under high sulfate concentration and in the presence of active sulfate reduction.
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Affiliation(s)
- Michal Sela-Adler
- Department of Geological and Environmental Sciences, Ben Gurion University of the NegevBeer-Sheva, Israel
| | - Zeev Ronen
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben Gurion University of the NegevBeer-Sheva, Israel
| | - Barak Herut
- Israel Oceanographic and Limnological ResearchHaifa, Israel
| | - Gilad Antler
- Department of Earth Sciences, University of CambridgeCambridge, UK
| | - Hanni Vigderovich
- Department of Geological and Environmental Sciences, Ben Gurion University of the NegevBeer-Sheva, Israel
| | - Werner Eckert
- The Yigal Allon Kinneret Limnological Laboratory, Israel Oceanographic and Limnological ResearchMigdal, Israel
| | - Orit Sivan
- Department of Geological and Environmental Sciences, Ben Gurion University of the NegevBeer-Sheva, Israel
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46
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Strickman RJS, Fulthorpe RR, Coleman Wasik JK, Engstrom DR, Mitchell CPJ. Experimental sulfate amendment alters peatland bacterial community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 566-567:1289-1296. [PMID: 27267720 DOI: 10.1016/j.scitotenv.2016.05.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 06/06/2023]
Abstract
As part of a long-term, peatland-scale sulfate addition experiment, the impact of varying sulfate deposition on bacterial community responses was assessed using 16S tag encoded pyrosequencing. In three separate areas of the peatland, sulfate manipulations included an eight year quadrupling of atmospheric sulfate deposition (experimental), a 3-year recovery to background deposition following 5years of elevated deposition (recovery), and a control area. Peat concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, were measured, the production of which is attributable to a growing list of microorganisms, including many sulfate-reducing Deltaproteobacteria. The total bacterial and Deltaproteobacterial community structures in the experimental treatment differed significantly from those in the control and recovery treatments that were either indistinguishable or very similar to one another. Notably, the relatively rapid return (within three years) of bacterial community structure in the recovery treatment to a state similar to the control, demonstrates significant resilience of the peatland bacterial community to changes in atmospheric sulfate deposition. Changes in MeHg accumulation between sulfate treatments correlated with changes in the Deltaproteobacterial community, suggesting that sulfate may affect MeHg production through changes in the community structure of this group.
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Affiliation(s)
- R J S Strickman
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - R R Fulthorpe
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada
| | - J K Coleman Wasik
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, MN, United States
| | - D R Engstrom
- St. Croix Watershed Research Station, Science Museum of Minnesota, Marine on St. Croix, MN, United States
| | - C P J Mitchell
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Scarborough, Ontario, Canada.
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Abstract
Pervasive anoxia in the subsurface ocean during the Proterozoic may have allowed large fluxes of biogenic CH4 to the atmosphere, enhancing the climatic significance of CH4 early in Earth's history. Indeed, the assumption of elevated pCH4 during the Proterozoic underlies most models for both anomalous climatic stasis during the mid-Proterozoic and extreme climate perturbation during the Neoproterozoic; however, the geologic record cannot directly constrain atmospheric CH4 levels and attendant radiative forcing. Here, we revisit the role of CH4 in Earth's climate system during Proterozoic time. We use an Earth system model to quantify CH4 fluxes from the marine biosphere and to examine the capacity of biogenic CH4 to compensate for the faint young Sun during the "boring billion" years before the emergence of metazoan life. Our calculations demonstrate that anaerobic oxidation of CH4 coupled to SO42- reduction is a highly effective obstacle to CH4 accumulation in the atmosphere, possibly limiting atmospheric pCH4 to less than 10 ppm by volume for the second half of Earth history regardless of atmospheric pO2 If recent pO2 constraints from Cr isotopes are correct, we predict that reduced UV shielding by O3 should further limit pCH4 to very low levels similar to those seen today. Thus, our model results likely limit the potential climate warming by CH4 for the majority of Earth history-possibly reviving the faint young Sun paradox during Proterozoic time and challenging existing models for the initiation of low-latitude glaciation that depend on the oxidative collapse of a steady-state CH4 greenhouse.
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Owen DDR, Shouakar-Stash O, Morgenstern U, Aravena R. Thermodynamic and hydrochemical controls on CH4 in a coal seam gas and overlying alluvial aquifer: new insights into CH4 origins. Sci Rep 2016; 6:32407. [PMID: 27578542 PMCID: PMC5006171 DOI: 10.1038/srep32407] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022] Open
Abstract
Using a comprehensive data set (dissolved CH4, δ13C-CH4, δ2H-CH4, δ13C-DIC, δ37Cl, δ2H-H2O, δ18O-H2O, Na, K, Ca, Mg, HCO3, Cl, Br, SO4, NO3 and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH4 from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ13C-CH4 data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO2 reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO4 concentrations and competition for reactants such as H2. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ2H-CH4 (<310‰) indicate acetoclastic methanogenesis where SO4 concentrations inhibit CO2 reduction. Evidence of CH4 migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH4 at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH4 within and between aquifers in these basins.
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Affiliation(s)
- D Des R Owen
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| | | | - U Morgenstern
- GNS Science, Lower Hutt 5014, P.O. Box 30368, New Zealand
| | - R Aravena
- Department of Earth and Environmental Sciences, University of Waterloo, Ontario N2L 3G1, Canada
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Li T, Xie B, Wang G, Zhang W, Zhang Q, Vesala T, Raivonen M. Field-scale simulation of methane emissions from coastal wetlands in China using an improved version of CH4MODwetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 559:256-267. [PMID: 27065445 DOI: 10.1016/j.scitotenv.2016.03.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/04/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Abstract
Coastal wetlands are important CH4 sources to the atmosphere. Coastal wetlands account for ~10% of the total area of natural wetlands in China, but the size of this potential CH4 source remains highly uncertain. We introduced the influence of salinity on CH4 production and CH4 diffusion into a biogeophysical model named CH4MODwetland so that it can be used in coastal wetlands. The improved model can generally simulate seasonal CH4 variations from tidal marshes dominated by Phragmites and Scirpus. However, the model underestimated winter CH4 fluxes from tidal marshes in the Yellow River Delta and YanCheng Estuary. It also failed to capture the accurate timing of the CH4 peaks in YanCheng Estuary and ChongMing Island in 2012. The improved model could generally simulate the difference between the annual mean CH4 fluxes from mangrove sites in GuangZhou and HaiKou city under different salinity and water table depth conditions, although fluxes were systematically underestimated in the mangrove site of HaiKou city. Using the improved model, the seasonal CH4 emissions simulated across all of the coastal wetlands ranged from 0.1 to 44.90gm(-2), with an average value of 7.89gm(-2), which is in good agreement with the observed values. The improved model significantly decreased the RMSE and RMD from 424% to 14% and 314% to -2%, respectively, and improved the EF from -18.30 to 0.99. Model sensitivity analysis showed that CH4 emissions were most sensitive to Pox in the tidal marshes and salinity in the mangroves. The results show that previous studies may have overestimated CH4 emissions on a regional or global scale by neglecting the influence of salinity. In general, the CH4MODwetland model can simulate seasonal CH4 emissions from different types of coastal wetlands under various conditions. Further improvements of CH4MODwetland should include the specific characteristics of CH4 processes in mangroves to decrease the uncertainty in estimating regional or global CH4 emissions from natural wetlands.
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Affiliation(s)
- Tingting Li
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, PR China.
| | - Baohua Xie
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Yantai, Shandong 264003, PR China; Shandong Provincial Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China.
| | - Guocheng Wang
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Wen Zhang
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Qing Zhang
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, PR China
| | - Timo Vesala
- Department of Physics, P.O. Box 48, FI-00014, University of Helsinki, Finland; Department of Forest Sciences, P.O. Box 27, FI-00014, University of Helsinki, Finland
| | - Maarit Raivonen
- Department of Physics, P.O. Box 48, FI-00014, University of Helsinki, Finland
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Turner TE, Billett MF, Baird AJ, Chapman PJ, Dinsmore KJ, Holden J. Regional variation in the biogeochemical and physical characteristics of natural peatland pools. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 545-546:84-94. [PMID: 26745296 DOI: 10.1016/j.scitotenv.2015.12.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/30/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
Natural open-water pools are a common feature of northern peatlands and are known to be an important source of atmospheric methane (CH4). Pool environmental variables, particularly water chemistry, vegetation community and physical characteristics, have the potential to exert strong controls on carbon cycling in pools. A total of 66 peatland pools were studied across three regions of the UK (northern Scotland, south-west Scotland, and Northern Ireland). We found that within-region variability of pool water chemistry was low; however, for many pool variables measured there were significant differences between regions. PCA analysis showed that pools in SW Scotland were strongly associated with greater vegetative cover and shallower water depth which is likely to increase dissolved organic carbon (DOC) mineralisation rates, whereas pools in N Scotland were more open and deeper. Pool water DOC, particulate organic carbon and dissolved CH4 concentrations were significantly different between regions. Pools in Northern Ireland had the highest concentrations of DOC (mean=14.5 mg L(-1)) and CH4 (mean=20.6 μg C L(-1)). Chloride and sulphate concentrations were significantly higher in the pools in N Scotland (mean values 26.3 and 2.40 mg L(-1), respectively) than elsewhere, due to a stronger marine influence. The ratio of UV absorbance at 465 nm to absorbance at 665 nm for pools in Northern Ireland indicated that DOC was sourced from poorly humified peat, potentially increasing the bioavailability and mineralisation of organic carbon in pools compared to the pools elsewhere. This study, which specifically aims to address a lack of basic biogeochemical knowledge about pool water chemistry, clearly shows that peatland pools are highly regionally variable. This is likely to be a reflection of significant regional-scale differences in peatland C cycling.
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Affiliation(s)
- T Edward Turner
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK.
| | - Michael F Billett
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, UK
| | - Andy J Baird
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
| | - Pippa J Chapman
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
| | | | - Joseph Holden
- water@leeds, School of Geography, University of Leeds, LS2 9JT, UK
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