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Yang R, Ji M, Zhang X, He F, Yu Z, Zeng J, Zhao D. Methane emissions and microbial communities under differing flooding conditions and seasons in littoral wetlands of urban lake. ENVIRONMENTAL RESEARCH 2024; 250:118390. [PMID: 38331139 DOI: 10.1016/j.envres.2024.118390] [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: 11/05/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Wetlands are the largest natural sources of methane (CH4) emissions worldwide. Littoral wetlands of urban lakes represent an ecotone between aquatic and terrestrial ecosystems and are strongly influenced by water levels, environmental conditions, and anthropogenic activities. Despite these littoral zones being potential "hotspots" of CH4 emissions, the status of CH4 emissions therein and the role of physicochemical properties and microbial communities regulating these emissions remain unclear. This study compared the CH4 fluxes, physicochemical properties, and CH4-cycling microbial communities (methanogens and methanotrophs) of three zones (a non-flooded supralittoral zone, a semi-flooded eulittoral zone, and a flooded infralittoral zone) in the littoral wetlands of Lake Pipa, Jiangsu Province, China, for two seasons (summer and winter). The eulittoral zone was a CH4 source (median: 11.49 and 0.02 mg m-2 h-1 in summer and winter, respectively), whereas the supralittoral zone acted as a CH4 sink (median: -0.78 and -0.09 mg m-2 h-1 in summer and winter, respectively). The infralittoral zone shifted from CH4 sink to source between the summer (median: -10.65 mg m-2 h-1) and winter (median: 0.11 mg m-2 h-1). The analysis of the functional genes of methanogenesis (mcrA) and methanotrophy (pmoA) and path analysis showed that CH4 fluxes were strongly regulated by biotic factors (abundance of the mcrA gene and alpha diversity of CH4-cycling microbial communities) and abiotic factors (ammonia nitrogen, moisture, and soil organic carbon). In particular, biotic factors had a major influence on the variation in the CH4 flux, whereas abiotic factors had a minor influence. Our findings provide novel insights into the spatial and seasonal variations in CH4-cycling microbial communities and identify the key factors influencing CH4 fluxes in littoral wetlands. These results are important for managing nutrient inputs and regulating the hydrological regimes of urban lakes.
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Affiliation(s)
- Runhan Yang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Mengting Ji
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Xiaomin Zhang
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fei He
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China; Ministry of Ecology and Environment, Nanjing Institute of Environment Sciences, Nanjing, 210042, China
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang, 332899, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing, 210098, China.
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Wen F, Biederman JA, Hao Y, Qian R, Zheng Z, Cui X, Zhao T, Xue K, Wang Y. Extreme drought alters methane uptake but not methane sink in semi-arid steppes of Inner Mongolia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169834. [PMID: 38190902 DOI: 10.1016/j.scitotenv.2023.169834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
Global climate change, particularly drought, is expected to alter grassland methane (CH4) oxidation, a key natural process against atmospheric greenhouse gas accumulation, yet the extent of this effect and its interaction with future atmospheric CH4 concentrations increases remains uncertain. To address this research gap, we measured CH4 flux during an imposed three-month rain-free period corresponding to a 100-year recurrence drought in soil mesocosms collected from 16 different Eurasian steppe sites. We also investigated the abundance and composition of methanotrophs. Additionally, we conducted a laboratory experiment to explore the impact of elevated CH4 concentration on the CH4 uptake capacity of grassland soil under drought conditions. We found that regardless of the type of grassland, CH4 flux was still being absorbed at its peak, meaning that all grasslands functioned as persistent CH4 sinks even when the soil water content (SWC) was <5 %. A bell-shaped relationship between SWC and CH4 uptake was observed in the soils. The average maximum CH4 oxidation rate in the meadow steppe was higher than that in the typical and desert steppe soils during extreme drought. The experimental elevation of atmospheric CH4 concentration counteracted the anticipated reduction in CH4 uptake related to physiological water stress on methanotrophic soil microbes under the drought stress. On the contrary, we found that across the regional scale, nitrogen, phosphorous, and total soil organic content played a crucial role in moderating the duration and magnitude of CH4 uptake with respect to SWC. USC-γ (Upland Soil Cluster γ) and JR-3 (Jasper Ridge Cluster) were the dominant group of soil methanotrophic bacteria in three types of grassland. However, the methanotrophic abundance, rather than the methanotrophic community composition, was the dominant microbiological factor governing CH4 uptake during the drought.
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Affiliation(s)
- Fuqi Wen
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Joel A Biederman
- Southwest Watershed Research Center, Agricultural Research Service, Tucson, AZ, USA
| | - Yanbin Hao
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China..
| | - Ruyan Qian
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Zheng
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China
| | - Xiaoyong Cui
- College of Life Sciences, University Chinese Academy of Sciences, Beijing, China; Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China
| | - Tong Zhao
- School of Mathematics Sciences, University Chinese Academy of Sciences, Beijing 101408, China
| | - Kai Xue
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China.; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining 810001, China; College of Resources and Environment, University Chinese Academy of Sciences, Beijing 101408, China
| | - Yanfen Wang
- Yanshan Earth Critical Zone and Surface Fluxes Research Station, Chinese Academy of Sciences, Beijing 101408, China.; College of Resources and Environment, University Chinese Academy of Sciences, Beijing 101408, China
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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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Dai W, Liu Y, Yao D, Wang N, Shao J, Ye X, Cui Z, Zong H, Tian L, Chen X, Wang H. Biogeographic distribution, assembly processes and potential nutrient cycling functions of myxobacteria communities in typical agricultural soils in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167255. [PMID: 37741390 DOI: 10.1016/j.scitotenv.2023.167255] [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: 07/15/2023] [Revised: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Predatory myxobacteria are important soil micropredators with the potential to regulate soil microbial community structure and ecosystem function. However, the biogeographic distribution patterns, assembly processes, and potential nutrient cycling functions of myxobacteria communities in typical agricultural soils in China are still poorly understood. High-throughput sequencing, phylogenetic zero modeling, and the multi-nutrient cycling index were used to assess the biogeographic distribution, assembly processes, and soil ecosystem functions of predation myxobacteria communities in typical agricultural soils of six long-term fertilization ecological experimental stations. The results demonstrated a hump-shaped distribution of myxobacteria α-diversity along the latitudinal gradient and significant differences in myxobacteria β-diversity in typical agricultural soils (P < 0.05). Bacterial richness, soil organic carbon, and pH were the most important predictors of myxobacteria α-diversity, whereas geographic factors and soil pH were the most significant ecological predictors of myxobacteria β-diversity. Myxobacteria community assembly is dominated by deterministic processes, especially homogeneous selection, primarily driven by soil pH and bacterial richness. In addition, we revealed the ecological significance of myxobacteria communities in typical agricultural soil microbial networks and the potential link between myxobacteria communities and soil nutrient cycling. These findings enhance our understanding of the biogeographic distribution, community assembly, ecological predictors, and relationships with soil nutrient cycling of myxobacteria communities in typical agricultural soils, paving the way for a more predictive understanding of the effect of predatory myxobacteria communities on soil ecosystem function, which is essential for the development of sustainable agriculture.
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Affiliation(s)
- Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Jinpeng Shao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Zong
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China
| | - Lei Tian
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China
| | - XiuZhai Chen
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China.
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China.
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Experimental erosion of microbial diversity decreases soil CH 4 consumption rates. Ecology 2023; 104:e4178. [PMID: 37782571 DOI: 10.1002/ecy.4178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/11/2023] [Accepted: 08/25/2023] [Indexed: 10/04/2023]
Abstract
Biodiversity-ecosystem functioning (BEF) experiments have predominantly focused on communities of higher organisms, in particular plants, with comparably little known to date about the relevance of biodiversity for microbially driven biogeochemical processes. Methanotrophic bacteria play a key role in Earth's methane (CH4 ) cycle by removing atmospheric CH4 and reducing emissions from methanogenesis in wetlands and landfills. Here, we used a dilution-to-extinction approach to simulate diversity loss in a methanotrophic landfill cover soil community. Replicate samples were diluted 101 -107 -fold, preincubated under a high CH4 atmosphere for microbial communities to recover to comparable size, and then incubated for 86 days at constant or diurnally cycling temperature. We hypothesize that (1) CH4 consumption decreases as methanotrophic diversity is lost, and (2) this effect is more pronounced under variable temperatures. Net CH4 consumption was determined by gas chromatography. Microbial community composition was determined by DNA extraction and sequencing of amplicons specific to methanotrophs and bacteria (pmoA and 16S gene fragments). The richness of operational taxonomic units (OTU) of methanotrophic and nonmethanotrophic bacteria decreased approximately linearly with log-dilution. CH4 consumption decreased with the number of OTUs lost, independent of community size. These effects were independent of temperature cycling. The diversity effects we found occured in relatively diverse communities, challenging the notion of high functional redundancy mediating high resistance to diversity erosion in natural microbial systems. The effects also resemble the ones for higher organisms, suggesting that BEF relationships are universal across taxa and spatial scales.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Martin Hartmann
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ruth Henneberger
- Institute of Molecular Health Science, ETH Zürich, Zürich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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Li Z, Ren L, Wang X, Chen M, Wang T, Dai R, Wang Z. Anaerobic hydrolysis of recalcitrant tetramethylammonium from semiconductor wastewater: Performance and mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132239. [PMID: 37567140 DOI: 10.1016/j.jhazmat.2023.132239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/23/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
The treatment of tetramethylammonium hydroxide (TMAH)-bearing wastewater, generated in the electronic and semiconductor industries, raises significant concerns due to the neurotoxic, recalcitrant, and bio-inhibiting effects of TMAH. In this study, we proposed the use of an anaerobic hydrolysis bioreactor (AHBR) for TMAH removal, achieving a high removal efficiency of approximately 85%, which greatly surpassed the performance of widely-used advanced oxidation processes (AOPs). Density functional theory calculations indicated that the unexpectedly poor efficiency (5.8-8.0%) of selected AOPs can be attributed to the electrostatic repulsion between oxidants and the tightly bound electrons of TMAH. Metagenomic analyses of the AHBR revealed that Proteobacteria and Euryarchaeota played a dominant role in the transformation of TMAH through processes such as methyl transfer, methanogenesis, and acetyl-coenzyme A synthesis, utilizing methyl-tetrahydromethanopterin as a substrate. Moreover, several potential functional genes (e.g., mprF, basS, bcrB, sugE) related to TMAH resistance have been identified. Molecular docking studies between five selected proteins and tetramethylammonium further provided evidence supporting the roles of these potential functional genes. This study demonstrates the superiority of AHBR as a pretreatment technology compared to several widely-researched AOPs, paving the way for the proper design of treatment processes to abate TMAH in semiconductor wastewater.
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Affiliation(s)
- Zhouyan Li
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lehui Ren
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xueye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control/College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tianlin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Zhang L, Sun X, Wang L, Zhang H, Chu H, Li Y. Soil edaphic factors and climate seasonality explain the turnover of methanotrophic communities in riparian wetlands. ENVIRONMENTAL RESEARCH 2023; 233:116447. [PMID: 37331554 DOI: 10.1016/j.envres.2023.116447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/20/2023]
Abstract
Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for the removal of atmospheric CH4, which is sensitive to the dynamics of water tables. However, little attention has been given to the turnover of methanotrophic communities across wet and dry periods in riparian wetlands. Here, by sequencing the pmoA gene, we investigated the turnover of soil methanotrophic communities across wet and dry periods in typical riparian wetlands that experience intensive agricultural practices. The results demonstrated that the methanotrophic abundance and diversity were significantly higher in the wet period than in the dry period, probably owing to the climatic seasonal succession and associated variation in soil edaphic factors. The co-occurrence patterns of the interspecies association analysis demonstrated that the key ecological clusters (i.e., Mod#1, Mod#2, Mod#4, Mod#5) showed contrasting correlations with soil edaphic properties between wet and dry periods. The linear regression slope of the relationships between the relative abundance of Mod#1 and the carbon to nitrogen ratio was higher in the wet period than in the dry period, whereas the linear regression slope of the relationships between the relative abundance of Mod#2 and soil nitrogen content (i.e., dissolved organic nitrogen, nitrate, and total nitrogen) was higher in the dry period than in the wet period. Moreover, Stegen's null model combined with phylogenetic group-based assembly analysis demonstrated that the methanotrophic community exhibited a higher proportion of drift (55.0%) and a lower contribution of dispersal limitation (24.5%) in the wet period than in the dry period (43.8% and 35.7%, respectively). Overall, these findings demonstrate that the turnover of methanotrophic communities across wet and dry periods were soil edaphic factors and climate dependent.
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Affiliation(s)
- Liyan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China.
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Jensen S, Siljanen HM, Dörsch P. Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:206-215. [PMID: 36786058 PMCID: PMC10464705 DOI: 10.1111/1758-2229.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 05/06/2023]
Abstract
Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2 h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.
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Affiliation(s)
- Sigmund Jensen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Henri M.P. Siljanen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandKuopioFinland
| | - Peter Dörsch
- Norwegian University of Life SciencesFaculty for Environmental Sciences and Natural Resource ManagementNorway
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Synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under methanethiol stress. Appl Microbiol Biotechnol 2023; 107:3099-3111. [PMID: 36933079 DOI: 10.1007/s00253-023-12472-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/25/2023] [Accepted: 03/03/2023] [Indexed: 03/19/2023]
Abstract
Methanotrophs are able to metabolize volatile organic sulfur compounds (VOSCs), excrete organic carbon during CH4 oxidation, and influence microbial community structure and function of the ecosystem. In return, microbial community structure and environmental factors can affect the growth metabolism of methanotrophs. In this study, Methylomonas koyamae and Hyphomicrobium methylovorum were used for model organisms, and methanethiol (MT) was chosen for a typical VOSC to investigate the synergy effects under VOSC stress. The results showed that when Hyphomicrobium methylovorum was co-cultured with Methylomonas koyamae in the medium with CH4 used as the carbon source, the co-culture had better MT tolerance relative to Methylomonas koyamae and oxidized all CH4 within 120 h, even at the initial MT concentration of 2000 mg m-3. The optimal co-culture ratios of Methylomonas koyamae to Hyphomicrobium methylovorum were 4:1-12:1. Although MT could be converted spontaneously to dimethyl disulfide (DMDS), H2S, and CS2 in air, faster losses of MT, DMDS, H2S, and CS2 were observed in each strain mono-culture and the co-culture. Compared with Hyphomicrobium methylovorum, MT was degraded more quickly in the Methylomonas koyamae culture. During the co-culture, the CH4 oxidation process of Methylomonas koyamae could provide carbon and energy sources for the growth of Hyphomicrobium methylovorum, while Hyphomicrobium methylovorum oxidized MT to help Methylomonas koyamae detoxify. These findings are helpful to understand the synergy effects of Methylomonas koyamae and Hyphomicrobium methylovorum under MT stress and enrich the role of methanotrophs in the sulfur biogeochemical cycle. KEY POINTS: • The co-culture of Methylomonas and Hyphomicrobium has better tolerance to CH3SH. • Methylomonas can provide carbon sources for the growth of Hyphomicrobium. • The co-culture of Methylomonas and Hyphomicrobium enhances the removal of CH4 and CH3SH.
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Wang X, Yin Y, Yu Z, Shen G, Cheng H, Tao S. Distinct distribution patterns of the abundant and rare bacteria in high plateau hot spring sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 863:160832. [PMID: 36521602 DOI: 10.1016/j.scitotenv.2022.160832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
The diversity and distribution patterns of the abundant and rare microbial sub-communities in hot spring ecosystems and their assembly mechanisms are poorly understood. The present study investigated the diversity and distribution patterns of the total, abundant, conditionally rare, and always rare taxa in the low- and moderate-temperature hot spring sediments on the Tibetan Plateau based on high-throughput 16S rRNA gene sequencing, and explored their major environmental drivers. The diversity of these four bacterial taxa showed no significant change between the low-temperature and moderate-temperature hot spring sediments, whereas the bacterial compositions were obviously different. Stochasticity dominated the bacterial sub-community assemblages, while heterogeneous selection also played an important role in shaping the abundant and conditionally rare taxa between the low-temperature and moderate-temperature hot spring sediments. No significant difference in the topological properties of co-occurrence networks was found between the conditionally rare and abundant taxa, and the connections between the paired operational taxonomic units (OTUs) were almost positive. The diversity of the total, abundant, and conditionally rare taxa was governed by the salinity of hot spring sediments, while that of the always rare taxa was determined by the content of S element. In contrast, temperature had significant direct effect on the composition of the total, abundant, and conditionally rare taxa, but relatively weak influence on that of the always rare taxa. Besides, salinity was another major environmental factor driving the composition of the abundant and rare sub-communities in the hot spring sediments. These results reveal the assembly processes and major environmental drivers that shaped different bacterial sub-communities in the hot spring sediments on the Tibetan Plateau, and indicate the importance of conditionally rare taxa in constructing bacterial communities. These findings enhance the current understanding of the ecological mechanisms maintaining the ecosystem stability and services in extreme environment.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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11
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Nijman TPA, Lemmens M, Lurling M, Kosten S, Welte C, Veraart AJ. Phosphorus control and dredging decrease methane emissions from shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157584. [PMID: 35882339 DOI: 10.1016/j.scitotenv.2022.157584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.
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Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maxime Lemmens
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Miquel Lurling
- Aquatic Ecology & Water Quality Management Group, Department of Environmental Sciences, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
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12
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Crevecoeur S, Prairie YT, del Giorgio PA. Tracking the upstream history of aquatic microbes in a boreal lake yields new insights on microbial community assembly. PNAS NEXUS 2022; 1:pgac171. [PMID: 36714827 PMCID: PMC9802056 DOI: 10.1093/pnasnexus/pgac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
Bacterial community structure can change rapidly across short spatial and temporal scales as environmental conditions vary, but the mechanisms underlying those changes are still poorly understood. Here, we assessed how a lake microbial community assembles by following its reorganization from the main tributary, which, when flowing into the lake, first traverses an extensive macrophyte-dominated vegetated habitat, before reaching the open water. Environmental conditions in the vegetated habitat changed drastically compared to both river and lake waters and represented a strong environmental gradient for the incoming bacteria. We used amplicon sequencing of the 16S rRNA gene and transcript to reconstruct the shifts in relative abundance of individual taxa and link this to their pattern in activity (here assessed with RNA:DNA ratios). Our results indicate that major shifts in relative abundance were restricted mostly to rare taxa (<0.1% of relative abundance), which seemed more responsive to environmental changes. Dominant taxa (>1% of relative abundance), on the other hand, traversed the gradient mostly unchanged with relatively low and stable RNA:DNA ratios. We also identified a high level of local recruitment and a seedbank of taxa capable of activating/inactivating, but these were almost exclusively associated with the rare biosphere. Our results suggest a scenario where the lake community results from a reshuffling of the rank abundance structure within the incoming rare biosphere, driven by selection and growth, and that numerical dominance is not a synonym of activity, growth rate, or environmental selection, but rather reflect mass effects structuring these freshwater bacterial communities.
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Affiliation(s)
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC H2×1Y4, Canada
| | - Paul A del Giorgio
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC H2×1Y4, Canada
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13
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Jia Y, Zhao S, Guo W, Peng L, Zhao F, Wang L, Fan G, Zhu Y, Xu D, Liu G, Wang R, Fang X, Zhang H, Kristiansen K, Zhang W, Chen J. Sequencing introduced false positive rare taxa lead to biased microbial community diversity, assembly, and interaction interpretation in amplicon studies. ENVIRONMENTAL MICROBIOME 2022; 17:43. [PMID: 35978448 PMCID: PMC9387074 DOI: 10.1186/s40793-022-00436-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by their inherent scarcity and the deficiency of currently available techniques. Sample-wise cross contaminations might be introduced by sample index misassignment in the most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control and clustering or denoising algorithms could remove sequencing errors and non-biological artifact reads, no algorithm could eliminate high quality reads from sample-wise cross contaminations introduced by index misassignment, making it difficult to distinguish between bona fide rare taxa and potential false positives in metabarcoding studies. RESULTS We thoroughly evaluated the rate of index misassignment of the widely used NovaSeq 6000 and DNBSEQ-G400 sequencing platforms using both commercial and customized mock communities, and observed significant lower (0.08% vs. 5.68%) fraction of potential false positive reads for DNBSEQ-G400 as compared to NovaSeq 6000. Significant batch effects could be caused by stochastically introduced false positive or false negative rare taxa. These false detections could also lead to inflated alpha diversity of relatively simple microbial communities and underestimated that of complex ones. Further test using a set of cow rumen samples reported differential rare taxa by different sequencing platforms. Correlation analysis of the rare taxa detected by each sequencing platform demonstrated that the rare taxa identified by DNBSEQ-G400 platform had a much higher possibility to be correlated with the physiochemical properties of rumen fluid as compared to NovaSeq 6000 platform. Community assembly mechanism and microbial network correlation analysis indicated that false positive or negative rare taxa detection could lead to biased community assembly mechanism and identification of fake keystone species of the community. CONCLUSIONS We highly suggest proper positive/negative/blank controls, technical replicate settings, and proper sequencing platform selection in future amplicon studies, especially when the microbial rare biosphere would be focused.
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Affiliation(s)
- Yangyang Jia
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wenjie Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ling Peng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Fang Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yuanfang Zhu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dayou Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Ruoqing Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, 266555, China.
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14
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Täumer J, Marhan S, Groß V, Jensen C, Kuss AW, Kolb S, Urich T. Linking transcriptional dynamics of CH 4-cycling grassland soil microbiomes to seasonal gas fluxes. THE ISME JOURNAL 2022; 16:1788-1797. [PMID: 35388141 PMCID: PMC9213473 DOI: 10.1038/s41396-022-01229-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/07/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Soil CH4 fluxes are driven by CH4-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. To date, a comprehensive understanding of underlying microbiome dynamics has rarely been obtained in situ. Using quantitative metatranscriptomics, we aimed to link CH4-cycling microbiomes to net surface CH4 fluxes throughout a year in two grassland soils. CH4 fluxes were highly dynamic: both soils were net CH4 sources in autumn and winter and sinks in spring and summer, respectively. Correspondingly, methanogen mRNA abundances per gram soil correlated well with CH4 fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer, when the soils acted as net CH4 sinks. CH4 uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH4 emissions from grassland soils. High methanotroph to methanogen ratios would indicate CH4 sink properties. Our study links for the first time the seasonal transcriptional dynamics of CH4-cycling soil microbiomes to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.
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Affiliation(s)
- Jana Täumer
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Verena Groß
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Corinna Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Steffen Kolb
- RA Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Tim Urich
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany.
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15
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Cerbin S, Pérez G, Rybak M, Wejnerowski Ł, Konowalczyk A, Helmsing N, Naus-Wiezer S, Meima-Franke M, Pytlak Ł, Raaijmakers C, Nowak W, Bodelier PLE. Methane-Derived Carbon as a Driver for Cyanobacterial Growth. Front Microbiol 2022; 13:837198. [PMID: 35432228 PMCID: PMC9010870 DOI: 10.3389/fmicb.2022.837198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.
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Affiliation(s)
- Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- *Correspondence: Slawek Cerbin,
| | - Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Michał Rybak
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Łukasz Wejnerowski
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Adam Konowalczyk
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Nico Helmsing
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Suzanne Naus-Wiezer
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Łukasz Pytlak
- Montanuniversität Leoben, Applied Geosciences and Geophysics, Leoben, Austria
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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16
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Liu X, Shi Y, Yang T, Gao GF, Zhang L, Xu R, Li C, Liu R, Liu J, Chu H. Distinct Co-occurrence Relationships and Assembly Processes of Active Methane-Oxidizing Bacterial Communities Between Paddy and Natural Wetlands of Northeast China. Front Microbiol 2022; 13:809074. [PMID: 35154054 PMCID: PMC8826055 DOI: 10.3389/fmicb.2022.809074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/04/2022] [Indexed: 11/27/2022] Open
Abstract
Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a 13C stable isotope-probing experiment and high-throughput sequencing to determine the structure profiling, co-occurrence relationships, and assembly processes of methanotrophic communities in four wetlands of Northeast China. There was a clear difference in community structure between paddy and natural wetlands. LEfSe analyses revealed that Methylobacter, FWs, and Methylosinus were enriched in natural wetlands, while Methylosarcina were prevailing in paddy, all identified as indicative methanotrophs. We observed distinct co-occurrence relationships between paddy and natural wetlands: more robust and complex connections in natural wetlands than paddy wetlands. Furthermore, the relative importance of stochastic processes was greater than that of deterministic processes, as stochastic processes explained >50% of the variation in communities. These results demonstrated that the co-occurrence relationships and assembly processes of active methanotrophic communities in paddy and natural wetlands were distinct. Overall, the results of this study enhance our understanding of the communities of methane-oxidizing bacteria in paddy and natural wetlands of Northeast China.
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Affiliation(s)
- Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liyan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Ruoyu Xu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Chenxin Li
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Ruiyang Liu
- High School Affiliated to Nanjing Normal University, Nanjing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
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17
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Martin G, Rissanen AJ, Garcia SL, Mehrshad M, Buck M, Peura S. Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes. Front Microbiol 2021; 12:669937. [PMID: 34456882 PMCID: PMC8397446 DOI: 10.3389/fmicb.2021.669937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.
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Affiliation(s)
- Gaëtan Martin
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Antti J. Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
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18
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Li C, Hambright KD, Bowen HG, Trammell MA, Grossart HP, Burford MA, Hamilton DP, Jiang H, Latour D, Meyer EI, Padisák J, Zamor RM, Krumholz LR. Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates. Environ Microbiol 2021; 23:6503-6519. [PMID: 34327792 DOI: 10.1111/1462-2920.15691] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.
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Affiliation(s)
- Chuang Li
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, The University of Oklahoma, Norman, Ok, USA
| | - K David Hambright
- Plankton Ecology and Limnology Laboratory, Program in Ecology and Evolutionary Biology, and the Geographical Ecology Group, Department of Biology, The University of Oklahoma, Norman, OK, USA
| | - Hannah G Bowen
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Majoi A Trammell
- Biomedical Research Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Stechlin, and Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Michele A Burford
- Australian Rivers Institute and School of Environment and Science, Griffith University, Nathan, Qld, Australia
| | - David P Hamilton
- Australian Rivers Institute, Griffith University, Nathan, Qld, Australia
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Delphine Latour
- Université Clermont Auvergne CNRS, LMGE, Aubière Cedex, France
| | - Elisabeth I Meyer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Judit Padisák
- Research Group of Limnology, Centre of Natural Sciences, University of Pannonia, Veszprém, Hungary
| | | | - Lee R Krumholz
- Department of Microbiology and Plant Biology, Institute for Energy and the Environment, The University of Oklahoma, Norman, Ok, USA
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19
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Horio K, Takahashi H, Kobori T, Watanabe K, Aki T, Nakashimada Y, Okamura Y. Visualization of Gene Reciprocity among Lactic Acid Bacteria in Yogurt by RNase H-Assisted Rolling Circle Amplification-Fluorescence In Situ Hybridization. Microorganisms 2021; 9:1208. [PMID: 34204984 PMCID: PMC8228470 DOI: 10.3390/microorganisms9061208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, we developed an in situ mRNA detection method termed RNase H-assisted rolling circle amplification-fluorescence in situ hybridization (RHa-RCA-FISH), which can detect even short mRNA in a bacterial cell. However, because this FISH method is sensitive to the sample condition, it is necessary to find a suitable cell permeabilization and collection protocol. Here, we demonstrate its further applicability for detecting intrinsic mRNA expression using lactic acid bacteria (LAB) as a model consortium. Our results show that this method can visualize functional gene expression in LAB cells and can be used for monitoring the temporal transition of gene expression. In addition, we also confirmed that data obtained from bulk analyses such as RNA-seq or microarray do not always correspond to gene expression in individual cells. RHa-RCA-FISH will be a powerful tool to compensate for insufficient data from metatranscriptome analyses while clarifying the carriers of function in microbial consortia. By extending this technique to capture spatiotemporal microbial gene expression at the single-cell level, it will be able to characterize microbial interactions in phytoplankton-bacteria interactions.
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Affiliation(s)
- Kyohei Horio
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan;
| | - Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
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20
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Zhang Y, Yao P, Sun C, Li S, Shi X, Zhang XH, Liu J. Vertical diversity and association pattern of total, abundant and rare microbial communities in deep-sea sediments. Mol Ecol 2021; 30:2800-2816. [PMID: 33960545 PMCID: PMC8251536 DOI: 10.1111/mec.15937] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.
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Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chuang Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Sanzhong Li
- Key Laboratory of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaochong Shi
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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21
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Ma RC, Chu YX, Wang J, Wang C, Leigh MB, Chen Y, He R. Stable-isotopic and metagenomic analyses reveal metabolic and microbial link of aerobic methane oxidation coupled to denitrification at different O 2 levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142901. [PMID: 33757249 DOI: 10.1016/j.scitotenv.2020.142901] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 06/12/2023]
Abstract
Aerobic methane (CH4) oxidation coupled to denitrification (AME-D) can not only mitigate CH4 emission into the atmosphere, but also potentially alleviate nitrogen pollution in surface waters and engineered ecosystems, and it has attracted substantial research interest. O2 concentration plays a key role in AME-D, yet little is understood about how it impacts microbial interactions. Here, we applied isotopically labeled K15NO3 and 13CH4 and metagenomic analyses to investigate the metabolic and microbial link of AME-D at different O2 levels. Among the four experimental O2 levels of 21%,10%, 5% and 2.5% and a CH4 concentration of 8% (i.e., the O2/CH4 ratios of 2.62, 1.26, 0.63 and 0.31), the highest NO3--N removal occurred in the AME-D system incubated at the O2 concentration of 10%. Methanol and acetate may serve as the trophic linkage between aerobic methanotrophs and denitrifers in the AME-D systems. Methylotrophs including Methylophilus, Methylovorus, Methyloversatilis and Methylotenera were abundant under the O2-sufficient condition with the O2 concentration of 21%, while denitrifiers such as Azoarcus, Thauera and Thiobacillus dominated in the O2-limited environment with the O2 concentration of 10%. The competition of denitrifiers and methylotrophs in the AME-D system for CH4-derived carbon, such as methanol and acetate, might be influenced by chemotactic responses. More methane-derived carbon flowed into methylotrophs under the O2-sufficient condition, while more methane-derived carbon was used for denitrification in the O2-limited environment. These findings can aid in evaluating the distribution and contribution of AME-D and in developing strategies for mitigating CH4 emission and nitrogen pollution in natural and engineered ecosystems.
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Affiliation(s)
- Ruo-Chan Ma
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Cheng Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, AK 99775, USA
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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22
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Wang J, Chu YX, Yao XZ, He R. Enhanced degradation of methanethiol in enrichment cultures in the presence of methane. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Cramm MA, Neves BDM, Manning CCM, Oldenburg TBP, Archambault P, Chakraborty A, Cyr-Parent A, Edinger EN, Jaggi A, Mort A, Tortell P, Hubert CRJ. Characterization of marine microbial communities around an Arctic seabed hydrocarbon seep at Scott Inlet, Baffin Bay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143961. [PMID: 33373752 DOI: 10.1016/j.scitotenv.2020.143961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
Seabed hydrocarbon seeps present natural laboratories for investigating responses of marine ecosystems to petroleum input. A hydrocarbon seep near Scott Inlet, Baffin Bay, was visited for in situ observations and sampling in the summer of 2018. Video evidence of an active hydrocarbon seep was confirmed by methane and hydrocarbon analysis of the overlying water column, which is 260 m at this site. Elevated methane concentrations in bottom water above and down current from the seep decreased to background seawater levels in the mid-water column >150 m above the seafloor. Seafloor microbial mats morphologically resembling sulfide-oxidizing bacteria surrounded areas of bubble ebullition. Calcareous tube worms, brittle stars, shrimp, sponges, sea stars, sea anemones, sea urchins, small fish and soft corals were observed near the seep, with soft corals showing evidence for hydrocarbon incorporation. Sediment microbial communities included putative methane-oxidizing Methyloprofundus, sulfate-reducing Desulfobulbaceae and sulfide-oxidizing Sulfurovum. A metabolic gene diagnostic for aerobic methanotrophs (pmoA) was detected in the sediment and bottom water above the seep epicentre and up to 5 km away. Both 16S rRNA gene and pmoA amplicon sequencing revealed that pelagic microbial communities oriented along the geologic basement rise associated with methane seepage (running SW to NE) differed from communities in off-axis water up to 5 km away. Relative abundances of aerobic methanotrophs and putative hydrocarbon-degrading bacteria were elevated in the bottom water down current from the seep. Detection of bacterial clades typically associated with hydrocarbon and methane oxidation highlights the importance of Arctic marine microbial communities in mitigating hydrocarbon emissions from natural geologic sources.
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Affiliation(s)
- Margaret A Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta T2N 1N4, Canada.
| | - Bárbara de Moura Neves
- Fisheries and Oceans Canada, Ecological Sciences Section, 80 East White Hills Road, P.O. Box 5667, St. John's, Newfoundland A1C 5X1, Canada
| | - Cara C M Manning
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Thomas B P Oldenburg
- Department of Geoscience, University of Calgary, 2500 University Dr NW, Calgary, Alberta T2N 1N4, Canada
| | - Philippe Archambault
- ArcticNet, Québec Océan, Takuvik Département de Biologie, Université Laval, Québec G1V 0A6, Canada
| | - Anirban Chakraborty
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta T2N 1N4, Canada
| | - Annie Cyr-Parent
- Department of Economic Development and Transportation, Government of Nunavut, Building 1104A, Inuksugait Plaza, PO Box 1000, Station 1500, Iqaluit, NU X0A 0H0, Canada
| | - Evan N Edinger
- Memorial University of Newfoundland, 230 Elizabeth Avenue, St. John's, Newfoundland A1C 5S7, Canada
| | - Aprami Jaggi
- Department of Geoscience, University of Calgary, 2500 University Dr NW, Calgary, Alberta T2N 1N4, Canada
| | - Andrew Mort
- Natural Resources Canada, 3303 33 Street NW, Calgary, Alberta T2L 2A7, Canada
| | - Philippe Tortell
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Casey R J Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta T2N 1N4, Canada
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24
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Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland. Microbiol Resour Announc 2021; 10:10/9/e01438-20. [PMID: 33664141 PMCID: PMC7936639 DOI: 10.1128/mra.01438-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here. Wetlands are important sources of methane emissions, and the impacts of these emissions can be mitigated by methanotrophic bacteria. The genomes of methanotrophs Methylomonas sp. strain LL1 and Methylosinus sp. strain H3A, as well as Methylocystis sp. strains H4A, H15, H62, and L43, were sequenced and are reported here.
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25
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Razzak A, Shafiquzzaman M, Haider H, Alresheedi M. Arsenic removal by iron-oxidizing bacteria in a fixed-bed coconut husk column: Experimental study and numerical modeling. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:115977. [PMID: 33172698 DOI: 10.1016/j.envpol.2020.115977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/04/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
Groundwater in several parts of the world, particularly in developing countries, has been contaminated with Arsenic (As). In search of low-cost As removal methods, the biological oxidation of As(III) and Fe(II) followed by co-precipitation requires detailed investigation for the practical implementation of this technology. The present study investigated the biological oxidation of As(III) and Fe(II) through a combination of laboratory experiments and reactive transport modeling. Batch experiments were conducted to evaluate the As(III) oxidation by Fe-oxidizing bacteria, mainly Leptothrix spp. A fixed-bed down-flow biological column containing inexpensive and readily available coconut husk support media was used to evaluate the combined removal of As(III) and Fe(II) from synthetic groundwater. Oxidation and co-precipitation processes effectively reduced the concentration of As(III) from 500 μg/L to < 10 μg/L with a hydraulic retention time of 120 min. A one-dimensional reactive transport model was developed based on the microbially mediated biochemical reactions of As(III) and Fe(II). The model successfully reproduced the observed As(III) and Fe(II) removal trends in the column experiments. The modeling results showed that the top 20 cm aerobic layer of the column played a primary role in the microbial oxidation of Fe(II) and As(III). The model calibration identified the hydraulic residence time as the most significant process parameter for the removal of Fe and As in the column. The developed model can effectively predict As concentrations in the effluent and provide design guidelines for the biological treatment of As. The model would also be useful for understanding the biogeochemical behavior of Fe and As under aerobic conditions.
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Affiliation(s)
- Abdur Razzak
- Department of Environmental Engineering, Pusan National University, 30, Jangjeon-Dong, Geumjeong-Gu, Busan, 609-735, South Korea; Transportation Engineering Branch, Highways and Public Works, Government of Yukon, 461 Range Road, Whitehorse, Y1A 3A4, Canada
| | - Md Shafiquzzaman
- Department of Civil Engineering, College of Engineering, Qassim University, Buraidah, 51452, Saudi Arabia.
| | - Husnain Haider
- Department of Civil Engineering, College of Engineering, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Mohammad Alresheedi
- Department of Civil Engineering, College of Engineering, Qassim University, Buraidah, 51452, Saudi Arabia
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26
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Cai Y, Zhou X, Shi L, Jia Z. Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China. MICROBIAL ECOLOGY 2020; 80:859-871. [PMID: 32803363 DOI: 10.1007/s00248-020-01570-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 08/03/2020] [Indexed: 05/25/2023]
Abstract
Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a direct link of pmoA genes to 16S rRNA genes based on their isolated strain or draft genomes. However, whether the results of pmoA-based assays could be largely represented by 16S rRNA gene sequencing in upland soils remains unclear. In this study, we collected 20 forest soils across China and compared methane-oxidizing bacterial (MOB) communities by high-throughput sequencing of 16S rRNA and pmoA genes using different primer sets. The results showed that 16S rRNA gene sequencing and the semi-nested polymerase chain reaction (PCR) of the pmoA gene (A189/A682r nested with a mixture of mb661 and A650) consistently revealed the dominance of USCα (accounting for more than 50% of the total MOB) in 12 forest soils. A189f/A682r successfully amplified pmoA genes (mainly RA14 of USCα) in only three forest soils. A189f/mb661 could amplify USCα (mainly JR1) in several forest soils but showed a strong preferential amplification of Methylocystis and many other type I MOB groups. A189f/A650 almost exclusively amplified USCα (mainly JR1) and largely discriminated against Methylocystis and most of the other MOB groups. The semi-nested PCR approach weakened the bias of A189f/mb661 and A189f/A650 for JR1 and balanced the coverage of all USCα members. The canonical correspondence analysis indicated that soil NH4+-N and pH were the main environmental factors affecting the MOB community of Chinese forest soils. The RA14 of the USCα group prefers to live in soils with low pH, low temperature, low elevation, high precipitation, and rich in nitrogen. JR1's preferences for temperature and elevation were opposite to RA14. Our study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.
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Affiliation(s)
- Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | - Xue Zhou
- College of agricultural science and engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Limei Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China.
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27
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Semrau JD, DiSpirito AA, Obulisamy PK, Kang-Yun CS. Methanobactin from methanotrophs: genetics, structure, function and potential applications. FEMS Microbiol Lett 2020; 367:5804726. [PMID: 32166327 DOI: 10.1093/femsle/fnaa045] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | | | - Christina S Kang-Yun
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA 48109-2125
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28
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Adyasari D, Hassenrück C, Montiel D, Dimova N. Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD). PLoS One 2020; 15:e0235235. [PMID: 32598345 PMCID: PMC7323985 DOI: 10.1371/journal.pone.0235235] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/10/2020] [Indexed: 11/18/2022] Open
Abstract
Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.
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Affiliation(s)
- Dini Adyasari
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Daniel Montiel
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
- Geosyntec Consultants, Clearwater, FL, United States of America
| | - Natasha Dimova
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
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29
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Meyer KM, Hopple AM, Klein AM, Morris AH, Bridgham SD, Bohannan BJM. Community structure - Ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function. Mol Ecol 2020; 29:1806-1819. [PMID: 32285532 DOI: 10.1111/mec.15442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 02/28/2020] [Accepted: 04/02/2020] [Indexed: 11/30/2022]
Abstract
Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here, we argue that this stems from at least three issues: (a) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge; (b) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge; and (c) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4 )-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and statistically control for environmental covariates to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Anya M Hopple
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Scott D Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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Xiu W, Lloyd J, Guo H, Dai W, Nixon S, Bassil NM, Ren C, Zhang C, Ke T, Polya D. Linking microbial community composition to hydrogeochemistry in the western Hetao Basin: Potential importance of ammonium as an electron donor during arsenic mobilization. ENVIRONMENT INTERNATIONAL 2020; 136:105489. [PMID: 31991235 DOI: 10.1016/j.envint.2020.105489] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 05/25/2023]
Abstract
Various functional groups of microorganisms and related biogeochemical processes are likely to control arsenic (As) mobilization in groundwater systems. However, spatially-dependent correlations between microbial community composition and geochemical zonation along groundwater flow paths are not fully understood, especially with respect to arsenic mobility. The western Hetao Basin was selected as the study area to address this limitation, where groundwater flows from a proximal fan (geochemical-group I: low As, oxidizing), through a transition area (geochemical-group II: moderate As, moderately-reducing) and then to a flat plain (geochemical-group III: high As, reducing). High-throughput Illumina 16S rRNA gene sequencing showed that the microbial community structure in the proximal fan included bacteria affiliated with organic carbon degradation and nitrate-reduction or even nitrate-dependant Fe(II)-oxidation, mainly resulting in As immobilization. In contrast, for the flat plain, high As groundwater contained Fe(III)- and As(V)-reducing bacteria, consistent with current models on As mobilization driven via reductive dissolution of Fe(III)/As(V) mineral assemblages. However, Spearman correlations between hydrogeochemical data and microbial community compositions indicated that ammonium as a possible electron donor induced reduction of Fe oxide minerals, suggesting a wider range of metabolic pathways (including ammonium oxidation coupled with Fe(III) reduction) driving As mobilization in high As groundwater systems.
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Affiliation(s)
- Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China; Institute of Earth Sciences, China University of Geosciences (Beijing), Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Jonathan Lloyd
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, the University of Manchester, Manchester, United Kingdom
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China.
| | - Wei Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Sophie Nixon
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, the University of Manchester, Manchester, United Kingdom
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, the University of Manchester, Manchester, United Kingdom
| | - Cui Ren
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Chaoran Zhang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Tiantian Ke
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - David Polya
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, the University of Manchester, Manchester, United Kingdom
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31
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He R, Su Y, Leewis MC, Chu YX, Wang J, Ma RC, Wu D, Zhan LT, Herriott IC, Leigh MB. Low O 2 level enhances CH 4-derived carbon flow into microbial communities in landfill cover soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113676. [PMID: 31818614 DOI: 10.1016/j.envpol.2019.113676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/07/2019] [Accepted: 11/24/2019] [Indexed: 06/10/2023]
Abstract
CH4 oxidation in landfill cover soils plays a significant role in mitigating CH4 release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH4 oxidation rate and the fate of CH4-derived carbon. In this study, microbial populations that oxidize CH4 and the subsequent conversion of CH4-derived carbon into CO2, soil organic C and biomass C were investigated in landfill cover soils at two O2 tensions, i.e., O2 concentrations of 21% ("sufficient") and 2.5% ("limited") with and without toluene. CH4-derived carbon was primarily converted into CO2 and soil organic C in the landfill cover soils, accounting for more than 80% of CH4 oxidized. Under the O2-sufficient condition, 52.9%-59.6% of CH4-derived carbon was converted into CO2 (CECO2-C), and 29.1%-39.3% was converted into soil organic C (CEorganic-C). A higher CEorganic-C and lower CECO2-C occurred in the O2-limited environment, relative to the O2-sufficient condition. With the addition of toluene, the carbon conversion efficiency of CH4 into biomass C and organic C increased slightly, especially in the O2-limited environment. A more complex microbial network was involved in CH4 assimilation in the O2-limited environment than under the O2-sufficient condition. DNA-based stable isotope probing of the community with 13CH4 revealed that Methylocaldum and Methylosarcina had a higher relative growth rate than other type I methanotrophs in the landfill cover soils, especially at the low O2 concentration, while Methylosinus was more abundant in the treatment with both the high O2 concentration and toluene. These results indicated that O2-limited environments could prompt more CH4-derived carbon to be deposited into soils in the form of biomass C and organic C, thereby enhancing the contribution of CH4-derived carbon to soil community biomass and functionality of landfill cover soils (i.e. reduction of CO2 emission).
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Affiliation(s)
- Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA; US Geological Survey, Menlo Park, CA, 94025, USA
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Donglei Wu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Liang-Tong Zhan
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | | | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Alaska, 99775, USA
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Reis PCJ, Thottathil SD, Ruiz-González C, Prairie YT. Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates. Environ Microbiol 2019; 22:738-751. [PMID: 31769176 DOI: 10.1111/1462-2920.14877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/22/2019] [Indexed: 11/30/2022]
Abstract
Lake methane (CH4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha- and Gammaproteobacteria (Alpha- and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH4 oxidation rates. We found a clear niche separation of Alpha- and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH4 oxidation rates in lakes and that information on the MOB community can help predict CH4 oxidation rates and thus emissions from lakes.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Shoji D Thottathil
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), Barcelona, E-08003, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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Crevecoeur S, Ruiz-González C, Prairie YT, Del Giorgio PA. Large-scale biogeography and environmental regulation of methanotrophic bacteria across boreal inland waters. Mol Ecol 2019; 28:4181-4196. [PMID: 31479544 DOI: 10.1111/mec.15223] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 01/09/2023]
Abstract
Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here, we used high-throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic community composition and the environmental factors that influence their distribution and relative abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal landscape. Within one region, soil and soil water samples were additionally taken from the surrounding watersheds in order to cover the full terrestrial-aquatic continuum. The composition of methanotrophic communities across the boreal landscape showed only a modest degree of regional differentiation but a strong structuring along the hydrologic continuum from soil to lake communities, regardless of regions. This pattern along the hydrologic continuum was mostly explained by a clear niche differentiation between type I and type II methanotrophs along environmental gradients in pH, and methane concentrations. Our results suggest very different roles of type I and type II methanotrophs within inland waters, the latter likely having a terrestrial source and reflecting passive transport and dilution along the aquatic networks, but this is an unresolved issue that requires further investigation.
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Affiliation(s)
- Sophie Crevecoeur
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
| | - Paul A Del Giorgio
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Université du Québec à Montréal, Montréal, QC, Canada
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34
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Yamamoto K, Hackley KC, Kelly WR, Panno SV, Sekiguchi Y, Sanford RA, Liu WT, Kamagata Y, Tamaki H. Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Sci Rep 2019; 9:13484. [PMID: 31530884 PMCID: PMC6748922 DOI: 10.1038/s41598-019-49996-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/04/2019] [Indexed: 01/24/2023] Open
Abstract
Natural microbial communities consist of a limited number of abundant species and an extraordinarily diverse population of rare species referred to as the rare biosphere. Recent studies have revealed that the rare biosphere is not merely an inactive dormant population but may play substantial functional roles in the ecosystem. However, structure, activity and community assembly processes of the rare biosphere are poorly understood. In this study, we evaluated the present and living microbial community structures including rare populations in an aquifer ecosystem, the Mahomet Aquifer, USA, by both 16S rDNA and rRNA amplicon deep sequencing. The 13 groundwater samples formed three distinct groups based on the “entire” community structure, and the same grouping was obtained when focusing on the “rare” subcommunities (<0.1% of total abundance), while the “abundant” subcommunities (>1.0%) gave a different grouping. In the correlation analyses, the observed grouping pattern is associated with several geochemical factors, and structures of not only the entire community but also the rare subcommunity are correlated with geochemical profiles in the aquifer ecosystem. Our findings first indicate that the living rare biosphere in the aquifer system has the metabolic potential to adapt to local geochemical factors which dictate the community assembly processes.
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Affiliation(s)
- Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Walton R Kelly
- Groundwater Science Section, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign (UIUC), Champaign, IL, USA
| | - Samuel V Panno
- Illinois State Geological Survey, Prairie Research Institute, UIUC, Champaign, IL, USA
| | - Yuji Sekiguchi
- Biomedical Research Institute, AIST, Tsukuba, Ibaraki, Japan
| | | | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, UIUC, Urbana, IL, USA
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan. .,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan. .,Department of Civil and Environmental Engineering, UIUC, Urbana, IL, USA. .,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan.
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35
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Feng Y, Chen R, Stegen JC, Guo Z, Zhang J, Li Z, Lin X. Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions. Mol Ecol 2018; 27:5238-5251. [DOI: 10.1111/mec.14914] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/03/2018] [Accepted: 10/09/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - James C. Stegen
- Earth and Biological Sciences Directorate Ecosystem Sciences Team Pacific Northwest National Laboratory Richland Washington
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
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van Kruistum H, Bodelier PLE, Ho A, Meima-Franke M, Veraart AJ. Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study. Front Microbiol 2018; 9:1714. [PMID: 30108568 PMCID: PMC6080070 DOI: 10.3389/fmicb.2018.01714] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/09/2018] [Indexed: 11/21/2022] Open
Abstract
Although soil microbes are responsible for important ecosystem functions, and soils are under increasing environmental pressure, little is known about their resistance and resilience to multiple stressors. Here, we test resistance and recovery of soil methane-oxidizing communities to two different, repeated, perturbations: soil drying, ammonium addition and their combination. In replicated soil microcosms we measured methane oxidation before and after perturbations, while monitoring microbial abundance and community composition using quantitative PCR assays for the bacterial 16S rRNA and pmoA gene, and sequencing of the bacterial 16S rRNA gene. Although microbial community composition changed after soil drying, methane oxidation rates recovered, even after four desiccation events. Moreover, microcosms subjected to soil drying recovered significantly better from ammonium addition compared to microcosms not subjected to soil drying. Our results show the flexibility of microbial communities, even if abundances of dominant populations drop, ecosystem functions can recover. In addition, a history of stress may induce changes in community composition and functioning, which may in turn affect its future tolerance to different stressors.
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Affiliation(s)
- Henri van Kruistum
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Paul L E Bodelier
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Adrian Ho
- Institut für Mikrobiologie, Leibniz Universität Hannover, Hanover, Germany
| | - Marion Meima-Franke
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Annelies J Veraart
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Department Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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38
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Bakker MG, Looft T, Alt DP, Delate K, Cambardella CA. Bulk soil bacterial community structure and function respond to long-term organic and conventional agricultural management. Can J Microbiol 2018; 64:901-914. [PMID: 30058369 DOI: 10.1139/cjm-2018-0134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Understanding how soil microbiomes respond to management is essential to maximizing soil health. We contrasted microbiomes in bulk soil under long-term organic and conventional management in a grain production setting. Management category significantly impacted the relative abundances of 17% of the most abundant taxa. Both conventional and organic management favored particular taxa, but these effects were not reflected in summary richness and diversity indices. Management systems also lead to differences in soil edaphic properties, including pH and nutrient status; this may have been the mechanism by which change in the prokaryote community was enacted. Community change between years of sampling was less pronounced, with only 6 taxa differentially abundant among years. Management category also impacted the abundance of functional genes related to the production and consumption of greenhouse gases. Particulate methane monooxygenase genes were more frequent in soil under organic management, while soluble methane monooxygenase genes were more frequent in soil under conventional management in 1 of 2 years. Nitrous oxide reductase genes were significantly less abundant in soils under second-year alfalfa than in soils under corn. This work highlights the ability of agricultural management to enact broad rearrangements to the structure of bulk soil bacterial communities.
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Affiliation(s)
- Matthew G Bakker
- a National Laboratory for Agriculture and the Environment, USDA ARS, 1015 N University Boulevard, Ames, IA 50011, USA
| | - Torey Looft
- b National Animal Disease Center, USDA ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - David P Alt
- b National Animal Disease Center, USDA ARS, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Kathleen Delate
- c Departments of Agronomy & Horticulture, Iowa State University, 106 Horticulture Hall, Ames, IA 50011, USA
| | - Cynthia A Cambardella
- a National Laboratory for Agriculture and the Environment, USDA ARS, 1015 N University Boulevard, Ames, IA 50011, USA
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39
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Diversity of key genes for carbon and nitrogen fixation in soils from the Sør Rondane Mountains, East Antarctica. Polar Biol 2018. [DOI: 10.1007/s00300-018-2353-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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40
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He R, Su Y, Ma RC, Zhuang S. Characterization of toluene metabolism by methanotroph and its effect on methane oxidation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16816-16824. [PMID: 29616477 DOI: 10.1007/s11356-018-1863-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Methanotrophs not only oxidize CH4, but also can oxidize a relatively broad range of other substrates, including trichloroethylene, alkanes, alkenes, and aromatic compounds. In this study, Methylosinus sporium was used as a model organism to characterize toluene metabolism by methanotrophs. Reverse transcription quantitative PCR analysis showed that toluene enhanced the mmoX expression of M. sporium. When the toluene concentration was below 2000 mg m-3, the kinetics of toluene metabolism by M. sporium conformed to the Michaelis-Menten equation (Vmax = 0.238 g gdry weight-1 h-1, K m = 545.2 mg m-3). The use of a solid-phase extraction technique followed by a gas chromatography-mass spectrometry analysis and molecular docking calculation showed that toluene was likely to primarily bind the di-iron center structural region of soluble methane monooxygenase (sMMO) hydroxylase and then be oxidized to o-cresol. Although M. sporium oxidized toluene, it did not incorporate toluene into its biomass. The coexistence of toluene and CH4 could influence CH4 oxidation, the growth of methanotrophs, and the distribution of CH4-derived carbon, which were related to the ratio of the toluene concentration to biomass. These results would be helpful to understand the metabolism of CH4 and non-methane volatile organic compounds in the environment.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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41
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Variation in Soil Methane Fluxes and Comparison between Two Forests in China. FORESTS 2018. [DOI: 10.3390/f9040204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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May T, Polag D, Keppler F, Greule M, Müller L, König H. Methane oxidation in industrial biogas plants—Insights in a novel methanotrophic environment evidenced by pmoA gene analyses and stable isotope labelling studies. J Biotechnol 2018; 270:77-84. [DOI: 10.1016/j.jbiotec.2018.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 02/05/2023]
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43
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology 2018; 99:714-723. [PMID: 29323701 DOI: 10.1002/ecy.2138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 11/11/2022]
Abstract
Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,University of Zurich Research Priority Program Global Change and Biodiversity, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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Crenothrix are major methane consumers in stratified lakes. ISME JOURNAL 2017; 11:2124-2140. [PMID: 28585934 PMCID: PMC5563964 DOI: 10.1038/ismej.2017.77] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 04/13/2017] [Accepted: 04/21/2017] [Indexed: 01/29/2023]
Abstract
Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth’s natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an ‘unusual’ methane monooxygenase (MMO), which was only distantly related to ‘classical’ MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N2O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.
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45
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Narrowe AB, Angle JC, Daly RA, Stefanik KC, Wrighton KC, Miller CS. High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. Environ Microbiol 2017; 19:2192-2209. [DOI: 10.1111/1462-2920.13703] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/09/2017] [Accepted: 02/14/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Adrienne B. Narrowe
- Department of Integrative Biology; University of Colorado Denver; Denver CO USA
| | - Jordan C. Angle
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Rebecca A. Daly
- Department of Microbiology; The Ohio State University; Columbus OH USA
| | - Kay C. Stefanik
- School of Environment and Natural Resources; The Ohio State University; Columbus OH USA
| | - Kelly C. Wrighton
- Department of Microbiology; The Ohio State University; Columbus OH USA
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Shang Y, Sikorski J, Bonkowski M, Fiore-Donno AM, Kandeler E, Marhan S, Boeddinghaus RS, Solly EF, Schrumpf M, Schöning I, Wubet T, Buscot F, Overmann J. Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS One 2017; 12:e0173765. [PMID: 28288199 PMCID: PMC5348048 DOI: 10.1371/journal.pone.0173765] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 02/27/2017] [Indexed: 12/05/2022] Open
Abstract
Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients.
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Affiliation(s)
- Yu Shang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124, Braunschweig, Deutschland
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124, Braunschweig, Deutschland
- German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Deutschland
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, D-50674 Köln, Deutschland
| | - Anna-Maria Fiore-Donno
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Straße 47b, D-50674 Köln, Deutschland
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Section (310b), University of Hohenheim, Emil-Wolff-Straße. 27, D-70593 Stuttgart, Deutschland
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Section (310b), University of Hohenheim, Emil-Wolff-Straße. 27, D-70593 Stuttgart, Deutschland
| | - Runa S. Boeddinghaus
- Institute of Soil Science and Land Evaluation, Soil Biology Section (310b), University of Hohenheim, Emil-Wolff-Straße. 27, D-70593 Stuttgart, Deutschland
| | - Emily F. Solly
- Max-Planck-Institut für Biogeochemie, Hans-Knöll-Straße 10, D-07745 Jena, Deutschland
| | - Marion Schrumpf
- Max-Planck-Institut für Biogeochemie, Hans-Knöll-Straße 10, D-07745 Jena, Deutschland
| | - Ingo Schöning
- Max-Planck-Institut für Biogeochemie, Hans-Knöll-Straße 10, D-07745 Jena, Deutschland
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, D-06120, Halle/Saale, Deutschland
- German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Deutschland
| | - Francois Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Theodor-Lieser-Straße 4, D-06120, Halle/Saale, Deutschland
- German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Deutschland
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124, Braunschweig, Deutschland
- German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Deutschland
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Meyer KM, Klein AM, Rodrigues JLM, Nüsslein K, Tringe SG, Mirza BS, Tiedje JM, Bohannan BJM. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Mol Ecol 2017; 26:1547-1556. [PMID: 28100018 DOI: 10.1111/mec.14011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/14/2016] [Accepted: 01/03/2017] [Indexed: 11/29/2022]
Abstract
Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.
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Affiliation(s)
- Kyle M Meyer
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR, USA
| | - Ann M Klein
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR, USA
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Susannah G Tringe
- United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Babur S Mirza
- Utah Water Research Laboratory, Utah State University, Logan, UT, USA
| | - James M Tiedje
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR, USA
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Where less may be more: how the rare biosphere pulls ecosystems strings. ISME JOURNAL 2017; 11:853-862. [PMID: 28072420 PMCID: PMC5364357 DOI: 10.1038/ismej.2016.174] [Citation(s) in RCA: 567] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/06/2016] [Accepted: 11/12/2016] [Indexed: 02/05/2023]
Abstract
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.
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Pandit PS, Ranade DR, Dhakephalkar PK, Rahalkar MC. A pmoA-based study reveals dominance of yet uncultured Type I methanotrophs in rhizospheres of an organically fertilized rice field in India. 3 Biotech 2016; 6:135. [PMID: 28330207 PMCID: PMC4910840 DOI: 10.1007/s13205-016-0453-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/03/2016] [Indexed: 11/28/2022] Open
Abstract
Rice fields are one of the important sources of anthropogenic methane. Methanotrophs can oxidize up to 30 % of the produced methane and thus have a pivotal environmental role in methane mitigation. India occupies the largest region under rice cultivation; however, most of the studies done on methanotrophic communities have focused on the Northern region. We studied methanotrophic community of a flooded, organically fertilized rice field using pmoA clone library approach. Organic rice fields impose a more serious threat as they produce more methane. pmoA gene is the main functional gene which is primarily used for taxonomical analysis of methanotrophs. Our results showed that the pmoA clone libraries from two growth stages of rice were dominated by pmoA sequences which were very distant from cultivated Type Ia methanotrophic genera (80–82 % nucleotide similarity) indicative of the presence of a putatively novel genus. We designated this group of clones as ‘rice field clones’ as this also includes many pmoA sequences originating from other rice fields. Thus, our current knowledge of methanotroph diversity from Indian rice fields has been expanded revealing that a substantial portion of methanotrophic diversity is unexplored.
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Affiliation(s)
- Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
| | - Dilip R Ranade
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India
- Microbial Culture Collection, NCCS, Sai-Trinity Building, Pashan, Pune, Maharashtra, 411021, India
| | | | - Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, Maharashtra, 411004, India.
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50
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Wei XM, He R, Chen M, Su Y, Ma RC. Conversion of methane-derived carbon and microbial community in enrichment cultures in response to O2 availability. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7517-7528. [PMID: 26728286 DOI: 10.1007/s11356-015-6017-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
Methanotrophs not only play an important role in mitigating CH4 emissions from the environment, but also provide a large quantity of CH4-derived carbon to their habitats. In this study, the distribution of CH4-derived carbon and microbial community was investigated in a consortium enriched at three O2 tensions, i.e., the initial O2 concentrations of 2.5 % (LO-2), 5 % (LO-1), and 21 % (v/v) (HO). The results showed that compared with the O2-limiting environments (2.5 and 5 %), more CH4-derived carbon was converted into CO2 and biomass under the O2 sufficient condition (21 %). Besides biomass and CO2, a high conversion efficiency of CH4-derived carbon to dissolved organic carbon was detected in the cultures, especially in LO-2. Quantitative PCR and Miseq sequencing both showed that the abundance of methanotroph increased with the increasing O2 concentrations. Type II methanotroph Methylocystis dominated in the enrichment cultures, accounting for 54.8, 48.1, and 36.9 % of the total bacterial 16S rRNA gene sequencing reads in HO, LO-1, and LO-2, respectively. Methylotrophs, mainly including Methylophilus, Methylovorus, Hyphomicrobium, and Methylobacillus, were also abundant in the cultures. Compared with the O2 sufficient condition (21 %), higher microbial biodiversity (i.e., higher Simpson and lower Shannon indexes) was detected in LO-2 enriched at the initial O2 concentration of 2.5 %. These findings indicated that compared with the O2 sufficient condition, more CH4-derived carbon was exuded into the environments and promoted the growth of non-methanotrophic microbes in O2-limiting environments.
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Affiliation(s)
- Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Min Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
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