1
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Venetz J, Żygadłowska OM, Dotsios N, Wallenius AJ, van Helmond NAGM, Lenstra WK, Klomp R, Slomp CP, Jetten MSM, Veraart AJ. Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin. FEMS Microbiol Ecol 2024; 100:fiae007. [PMID: 38281061 PMCID: PMC10939384 DOI: 10.1093/femsec/fiae007] [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: 10/30/2023] [Revised: 12/08/2023] [Accepted: 01/25/2024] [Indexed: 01/29/2024] Open
Abstract
In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Nicky Dotsios
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Niels A G M van Helmond
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Robin Klomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3508 TA Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, 6525 AJ Nijmegen, The Netherlands
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2
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Guo W, He R, Zhao Y, Li D. Imbalanced metabolism induced NH 4+ accumulation and its effect on the central metabolism of Methylomonas sp. ZR1. Int Microbiol 2024; 27:49-66. [PMID: 38038804 DOI: 10.1007/s10123-023-00457-8] [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: 08/15/2022] [Revised: 07/23/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023]
Abstract
Nitrogen and carbon are the two most essential nutrient elements, and their metabolism is tightly coupled in single carbon metabolic microorganisms. However, the nitrogen metabolism and the nitrogen/carbon (N/C) metabolic balance in single-carbon metabolism is poorly studied. In this study, the nitrogen metabolism pattern of the fast growing methanotrophs Methylomonas sp. ZR1 grown in methane and methanol was studied. Effect study of different nitrogen sources on the cell growth of ZR1 indicates that nitrate salts are the best nitrogen source supporting the growth of ZR1 using methane and methanol as carbon source. However, its metabolic intermediate ammonium was found to accumulate with high N/C ratio in the medium and consequently inhibit the growth of ZR1. Studies of carbon and nitrogen metabolic kinetic under different N/C ratio conditions indicate that the accumulation of NH4+ is caused by the imbalanced nitrogen and carbon metabolism in ZR1. Feeding carbon skeleton α-ketoglutaric acid could effectively relieve the inhibition effect of NH4+ on the growth of ZR1, which further confirms this assumption. qPCR analysis of the expression level of the central metabolic key enzyme gene indicates that the nitrogen metabolic intermediate ammonium has strong regulation effect on the central nitrogen and carbon metabolism in ZR1. qPCR-combined genomic analysis confirms that a third ammonium assimilation pathway glycine synthesis system is operated in ZR1 to balance the nitrogen and carbon metabolism. Based on the qPCR result, it was also found that ZR1 employs two strategies to relieve ammonium stress in the presence of ammonium: assimilating excess ammonium or cutting off the nitrogen reduction reactions according to the available C1 substrate. Validating the connections between single-carbon and nitrogen metabolism and studying the accumulation and assimilation mechanism of ammonium will contribute to understand how nitrogen regulates cellular growth in single-carbon metabolic microorganisms.
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Affiliation(s)
- Wei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Ronglin He
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Yujie Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, 32 West 7Th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
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3
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Hartman WH, Bueno de Mesquita CP, Theroux SM, Morgan-Lang C, Baldocchi DD, Tringe SG. Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient. mSystems 2024; 9:e0093623. [PMID: 38170982 PMCID: PMC10804969 DOI: 10.1128/msystems.00936-23] [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: 09/11/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.
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Affiliation(s)
| | | | | | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dennis D. Baldocchi
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Susannah G. Tringe
- DOE Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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4
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Brown AM, Bass AM, Skiba U, MacDonald JM, Pickard AE. Urban landscapes and legacy industry provide hotspots for riverine greenhouse gases: A source-to-sea study of the River Clyde. WATER RESEARCH 2023; 236:119969. [PMID: 37099862 DOI: 10.1016/j.watres.2023.119969] [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: 12/11/2022] [Revised: 04/01/2023] [Accepted: 04/09/2023] [Indexed: 06/19/2023]
Abstract
There is growing global concern that greenhouse gas (GHG) emissions from water bodies are increasing because of interactions between nutrient levels and climate warming. This paper investigates key land-cover, seasonal and hydrological controls of GHGs by comparison of the semi-natural, agricultural and urban environments in a detailed source-to-sea study of the River Clyde, Scotland. Riverine GHG concentrations were consistently oversaturated with respect to the atmosphere. High riverine concentrations of methane (CH4) were primarily associated with point source inflows from urban wastewater treatment, abandoned coal mines and lakes, with CH4-C concentrations between 0.1 - 44 µg l-1. Concentrations of carbon dioxide (CO2) and nitrous oxide (N2O) were mainly driven by nitrogen concentrations, dominated by diffuse agricultural inputs in the upper catchment and supplemented by point source inputs from urban wastewater in the lower urban catchment, with CO2-C concentrations between 0.1 - 2.6 mg l-1 and N2O-N concentrations between 0.3 - 3.4 µg l-1. A significant and disproportionate increase in all GHGs occurred in the lower urban riverine environment in the summer, compared to the semi-natural environment, where GHG concentrations were higher in winter. This increase and change in GHG seasonal patterns points to anthropogenic impacts on microbial communities. The loss of total dissolved carbon, to the estuary is approximately 48.4 ± 3.6 Gg C yr-1, with the annual inorganic carbon export approximately double that of organic carbon and four times that of CO2, with CH4 accounting for 0.03%, with the anthropogenic impact of disused coal mines accelerating DIC loss. The annual loss of total dissolved nitrogen to the estuary is approximately 4.03 ± 0.38 Gg N yr-1 of which N2O represents 0.06%. This study improves our understanding of riverine GHG generation and dynamics which can contribute to our knowledge of their release to the atmosphere. It identifies where action could support reductions in aquatic GHG generation and emission.
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Affiliation(s)
- Alison M Brown
- UK Centre for Ecology & Hydrology (Edinburgh), Bush Estate, Penicuik, Midlothian, EH26 0QB, UK; University of Glasgow, College of Science and Engineering, School of Geographical and Earth Sciences, University Avenue, Glasgow, G12 8QQ, UK.
| | - Adrian M Bass
- University of Glasgow, College of Science and Engineering, School of Geographical and Earth Sciences, University Avenue, Glasgow, G12 8QQ, UK
| | - Ute Skiba
- UK Centre for Ecology & Hydrology (Edinburgh), Bush Estate, Penicuik, Midlothian, EH26 0QB, UK
| | - John M MacDonald
- University of Glasgow, College of Science and Engineering, School of Geographical and Earth Sciences, University Avenue, Glasgow, G12 8QQ, UK
| | - Amy E Pickard
- UK Centre for Ecology & Hydrology (Edinburgh), Bush Estate, Penicuik, Midlothian, EH26 0QB, UK
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5
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Lee J, Yun J, Yang Y, Jung JY, Lee YK, Yuan J, Ding W, Freeman C, Kang H. Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2647-2659. [PMID: 36719133 DOI: 10.1021/acs.est.2c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, BangorLL57 2UW, U.K
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
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6
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Liu X, Wang H, Wang W, Cheng X, Wang Y, Li Q, Li L, Ma L, Lu X, Tuovinen OH. Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave. Front Microbiol 2023; 14:1115449. [PMID: 36846803 PMCID: PMC9947541 DOI: 10.3389/fmicb.2023.1115449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.
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Affiliation(s)
- Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China,*Correspondence: Hongmei Wang, ;
| | - Weiqi Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Qing Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, United States
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Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH 4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition. mSystems 2022; 7:e0040322. [PMID: 36154142 PMCID: PMC9600857 DOI: 10.1128/msystems.00403-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.
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Rani V, Prasanna R, Kaushik R. Prospecting the significance of methane-utilizing bacteria in agriculture. World J Microbiol Biotechnol 2022; 38:176. [PMID: 35922575 DOI: 10.1007/s11274-022-03331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.
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Affiliation(s)
- Vijaya Rani
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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9
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Kambara H, Shinno T, Matsuura N, Matsushita S, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. Environmental Factors Affecting the Community of Methane-oxidizing Bacteria. Microbes Environ 2022; 37. [PMID: 35342121 PMCID: PMC8958294 DOI: 10.1264/jsme2.me21074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000 mg N L–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH4+ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.
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Affiliation(s)
- Hiromi Kambara
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | - Takahiro Shinno
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | | | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
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10
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Brown AM, Bass AM, Pickard AE. Anthropogenic-estuarine interactions cause disproportionate greenhouse gas production: A review of the evidence base. MARINE POLLUTION BULLETIN 2022; 174:113240. [PMID: 35090288 DOI: 10.1016/j.marpolbul.2021.113240] [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: 07/30/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Biologically productive regions such as estuaries and coastal areas, even though they only cover a small percentage of the world's oceans, contribute significantly to methane and nitrous oxide emissions. This paper synthesises greenhouse gas data measured in UK estuary studies, highlighting that urban wastewater loading is significantly correlated with both methane (P < 0.001) and nitrous oxide (P < 0.005) concentrations. It demonstrates that specific estuary typologies render them more sensitive to anthropogenic influences on greenhouse gas production, particularly estuaries that experience low oxygen levels due to reduced mixing and stratification or high sediment oxygen demand. Significantly, we find that estuaries with high urban wastewater loading may be hidden sources of greenhouse gases globally. Synthesising available information, a conceptual model for greenhouse gas concentrations in estuaries with different morphologies and mixing regimes is presented. Applications of this model should help identification of estuaries susceptible to anthropogenic impacts and potential hotspots for greenhouse gas emissions.
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Affiliation(s)
- Alison M Brown
- UK Centre for Ecology & Hydrology (Edinburgh), Bush Estate, Penicuik, Midlothian EH26 0QB, United Kingdom.
| | - Adrian M Bass
- University of Glasgow, College of Science and Engineering, School of Geographical and Earth Sciences, University Avenue, Glasgow, G12 8QQ, United Kingdom.
| | - Amy E Pickard
- UK Centre for Ecology & Hydrology (Edinburgh), Bush Estate, Penicuik, Midlothian EH26 0QB, United Kingdom.
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11
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Chen J, Feng M, Cui Y, Liu G. The impacts of nitrogen addition on upland soil methane uptake: A global meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148863. [PMID: 34247074 DOI: 10.1016/j.scitotenv.2021.148863] [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: 03/31/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Elevated nitrogen (N) addition from anthropogenic activities has great impacts on soil methane (CH4) uptake, which could interrupt the existing global CH4 balance and cause feedbacks to climate and biogeochemical processes. Previous studies have come to inconsistent conclusions on both the quantification of the response of CH4 uptake to N addition and understanding of its underlying mechanisms, probably due to the lack of experimental data. Here, we conduct a broad meta-analysis of 90 papers to quantify the responses of CH4 uptake to N addition in upland soil. The results show that N addition has a significant negative impact on soil CH4 uptake (-19.25%), which is termed the N inhibition effect. Soil pH is identified as the dominant factor, with the other factors affecting the CH4 uptake through the alteration of soil pH. The N inhibition effect is observed to be large and significant in forest and grassland, but small and insignificant in farmland, because of the distinct composition of their methanotrophic communities. A threshold of the N addition level is identified at about 68 kg N ha-1 year-1, which indicates the lowest N inhibition effect. Furthermore, the convex relationship between response ratio of CH4 uptake (negative) and N addition duration indicates that a medium level of N addition duration has the largest N inhibition effect, and longer or shorter durations will both reduce the effect. Our analysis of the N inhibition effect implies that controlling the N addition level could effectively reduce the CH4 concentration in the atmosphere and thus relieve global warming.
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Affiliation(s)
- Jianyu Chen
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Maoyuan Feng
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China.
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
| | - Gang Liu
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing 100871, PR China
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12
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Dong D, Li J, Ying S, Wu J, Han X, Teng Y, Zhou M, Ren Y, Jiang P. Mitigation of methane emission in a rice paddy field amended with biochar-based slow-release fertilizer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148460. [PMID: 34147789 DOI: 10.1016/j.scitotenv.2021.148460] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/15/2021] [Accepted: 06/10/2021] [Indexed: 06/12/2023]
Abstract
Despite improving soil quality and reducing nitrogen (N) loss in paddy soil, replacing chemical fertilizer with organic fertilizer would significantly accelerate greenhouse gas emission in terms of methane (CH4). The application of slow-release fertilizer has been proposed an effective approach to control CH4 emissions, in addition to reducing N loss. Yet, the understanding of CH4 emissions from paddy fields with the additions of different fertilizers is still less known. Therefore, the effects of different fertilizer treatments, including chemical fertilizer treatment (CF), mixed chemical and organic fertilizer treatment (OF), biochar-based slow-release fertilizer treatment (SF), and no fertilizer control treatment (CK) on CH4 emissions and methanogenic community structure in paddy soils were investigated through a field experiment. Results showed that slow-release fertilizer addition significantly decreased CH4 emissions by 33.4%, during the whole rice growing season compared to those in OF. The cumulative CH4 emissions were in a significantly positive relation to soil NH4+-N. Slow-release fertilizer amendment decreased the relative abundances of Methanosarcina and Methanoregula and increased the relative abundances of hydrogenotrophic Methanocella and Rice Cluster I. Reduced CH4 emissions with slow-release fertilizer amendment might be mainly attributed to the different forms of N in the fertilizer and available potassium (K) in the paddy soil. Our findings produce novel insights into the application of slow-release fertilizer in controlling CH4 emissions from rice fields.
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Affiliation(s)
- Da Dong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Jiong Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Shanshan Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Jiasen Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, Zurich 8092, Switzerland
| | - Yuanxin Teng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Miaorong Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yi Ren
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Peikun Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, China; College of Environmental and Resource Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, China.
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Rani V, Bhatia A, Kaushik R. Inoculation of plant growth promoting-methane utilizing bacteria in different N-fertilizer regime influences methane emission and crop growth of flooded paddy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145826. [PMID: 33631576 DOI: 10.1016/j.scitotenv.2021.145826] [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: 11/27/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4) emission in rice fields is greatly influenced by the type and quantity of nitrogenous fertilizer used. The net methane emission from paddy fields is also influenced by the activity of methane utilizing bacteria, which inhabit the flooded paddy ecosystem. Efficient methane utilizing and plant growth promoting bacteria Methylobacterium oryzae MNL7 and Paenibacillus polymyxa MaAL70, respectively were co-inoculated along with different nitrogenous fertilizer combinations in flooded paddy to assess their impact on cumulative methane emission and crop growth promotion. Co-inoculation significantly influenced the plant growth parameters of paddy, resulting in an increase in grain yield by 14.04, 11.08, and 12.38% in treatments receiving Urea, Di-ammonium Phosphate (DAP) + Urea, or farm yard manure (FYM), over their respective un-inoculated plots. Significant improvement in the rice grain nutrient quality in term of crude protein, Fe and Zn content was observed as a result of bacterial co-inoculation in FYM fertilized plots as compared to Urea and DAP+ Urea fertilized plots. Significantly higher cumulative methane emission of 63.39 kg ha-1 was observed in uninoculated plots fertilized with FYM treatment as compared to Urea (33.83 kg ha-1) and DAP+Urea (31.66 kg ha-1) treatments. Bacterial co-inoculation significantly reduced the cumulative methane emission by 12.03, 11.47 and 6.92% in Urea, DAP+Urea, and FYM fertilized plots over their respective uninoculated treatments. Among the different fertilizer treatments, bacterial co-inoculation with urea application performed significantly better in reducing cumulative methane emission. These findings suggest that methane utilizing bacteria which also possess plant growth promoting trait can be explored for developing a novel biofertilizer for flooded paddies, as they can aid in managing both the overall methane emission and enhancing crop yield.
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Affiliation(s)
- Vijaya Rani
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Arti Bhatia
- Center for Environemtal Sciences and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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Cordova-Gonzalez A, Birgel D, Kappler A, Peckmann J. Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum. Extremophiles 2021; 25:285-299. [PMID: 33866428 PMCID: PMC8102298 DOI: 10.1007/s00792-021-01228-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/01/2021] [Indexed: 11/30/2022]
Abstract
The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient availability. Aerobic methanotrophs synthesize a variety of lipids important for cell functions. However, culture-based experiments studying the influence of environmental parameters on lipid production by aerobic methanotrophs are scarce. Such information is crucial to interpret lipid patterns of methanotrophic bacteria in the environment. In this study, the alkaliphilic strain Methylotuvimicrobium alcaliphilum was cultivated under different salinities and different nitrate concentrations to assess the effect of changing conditions on the inventory of pentacyclic triterpenoids. The results indicate that hopanoid abundance is enhanced at lower salinity and higher nitrate concentration. The production of most pentacyclic triterpenoids was favored at low salinity, especially for aminotriol. Interestingly, 3-methyl-aminotetrol and tetrahymanol were favored at higher salinity. Bacteriohopanepolyols (BHPs), particularly aminotriol and 3-methyl-aminotriol, increased considerably at higher nitrate concentrations. Four novel N-containing BHPs—aminodiol, 3-methyl-aminodiol, and isomers of aminotriol and 3-methyl-aminotriol—were identified. This study highlights the significance of environmental factors for bacterial lipid production and documents the need for cultivation studies under variable conditions to utilize the full potential of the biomarker concept.
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Affiliation(s)
- Alexmar Cordova-Gonzalez
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
| | - Daniel Birgel
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany.
| | - Andreas Kappler
- Geomikrobiologie, Zentrum für Angewandte Geowissenschaften, Universität Tübingen, Tübingen, Germany
| | - Jörn Peckmann
- Institut für Geologie, Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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15
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Xu P, Zhou W, Jiang M, Khan I, Shaaban M, Jiang Y, Hu R. Nitrogen fertilizer application in the rice-growing season can stimulate methane emissions during the subsequent flooded fallow period. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140632. [PMID: 32688003 DOI: 10.1016/j.scitotenv.2020.140632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Winter-flooded rice paddy field (FR), characterized by water conserved in the field during the fallow period, is a typical cropping system in southwest China, leading to considerable methane (CH4) emissions. The effect of nitrogen (N) fertilization on CH4 emissions during rice-growing seasons is well studied in FR, further studies covering N fertilizer applied in the rice-growing seasons affects CH4 emissions during the subsequent fallow period is needed. Therefore, a field experiment was conducted in an FR of Sichuan province, China, with conventional N fertilized (CN) and N unfertilized (NN) treatments. The cumulative CH4 emission from CN treatment during the rice-growing season and the subsequent fallow period was 389 ± 29.4 and 158 ± 31.2 kg C ha-1, which were increased by 29.5% and 395% in comparison with the NN treatment, indicting N applied during the rice growing-season significantly facilitated CH4 emission during the subsequent fallow period. During the rice-growing season, higher CH4 emission from CN treatment could be attributed to elevated soil dissolved organic carbon (DOC) content that might have provided sufficient substrates for CH4 production. During the fallow period, as compared to NN treatment, higher CH4 emissions from CN treatment could be explained by greater linear regression slopes between CH4 fluxes, soil temperature and DOC to dissolved inorganic N (DIN) (DOC/DIN) ratio. Moreover, the structural equation model (SEM) described that the soil temperature exhibited the most significant effects on CH4 emissions for both treatments during the rice-growing season and subsequent fallow period. These findings are a major step forward to showing that N fertilizer applied in the rice-growing season could also affect CH4 emission during the subsequent fallow period, accompanying other soil parameters controlling CH4 emission.
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Affiliation(s)
- Peng Xu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhou
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengdie Jiang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Imran Khan
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Shaaban
- Department of Soil Science, Faculty of Agricultural Science and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Yanbin Jiang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ronggui Hu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of the Yangtze River), Ministry of Agriculture, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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16
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Islam SFU, Sander BO, Quilty JR, de Neergaard A, van Groenigen JW, Jensen LS. Mitigation of greenhouse gas emissions and reduced irrigation water use in rice production through water-saving irrigation scheduling, reduced tillage and fertiliser application strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:140215. [PMID: 32758960 DOI: 10.1016/j.scitotenv.2020.140215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Rice production systems are the largest anthropogenic wetlands on earth and feed more than half of the world's population. However, they are also a major source of global anthropogenic greenhouse gas (GHG) emissions. Several agronomic strategies have been proposed to improve water-use efficiency and reduce GHG emissions. The aim of this study was to evaluate the impact of water-saving irrigation (alternate wetting and drying (AWD) vs. soil water potential (SWP)), contrasting land establishment (puddling vs. reduced tillage) and fertiliser application methods (broadcast vs. liquid fertilisation) on water-use efficiency, GHG emissions and rice yield. The experiment was laid out in a randomised complete block design with eight treatments (all combinations of the three factors) and four replicates. AWD combined with broadcasting fertilisation was superior to SWP in terms of maintaining yield. However, seasonal nitrous oxide (N2O) emissions were significantly reduced by 64% and 66% in the Broadcast-SWP and Liquid fertiliser-SWP treatments, respectively, compared to corresponding treatments in AWD. The SWP also significantly reduced seasonal methane (CH4) emissions by 34 and 30% in the broadcast and liquid fertilisation treatments, respectively. Area-scaled GWPs were reduced by 48% and 54% in Broadcast-SWP and Liquid fertiliser-SWP treatments respectively compared to the corresponding treatments in AWD. Compared to AWD, the broadcast and liquid fertilisation in SWP irrigation treatments reduced yield-scaled GWPs by 46% and 37%, respectively. In terms of suitability, based on yield-scaled GWPs, the treatments can be ordered as follows: Broadcast-SWP < Broadcast-AWD = Liquid fertiliser-SWP < Liquid fertiliser-AWD. Growing-season water use was 15% lower in the SWP treatments compared with the water-saving AWD. Reduced tillage reduced additional water use during land preparation. The conclusions of this study are that improved water management and timely coordination of N fertiliser with crop demand can reduce water use, N loss via N2O emissions, and CH4 emissions.
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Affiliation(s)
- Syed Faiz-Ul Islam
- Soil Biology Group, Wageningen University, Droevendaalsesteeg 3, PO Box 47, 6700 AA Wageningen, the Netherlands; Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark; International Rice Research Institute (IRRI), Los Baños, the Philippines.
| | - Bjoern Ole Sander
- International Rice Research Institute (IRRI), Los Baños, the Philippines
| | - James R Quilty
- International Rice Research Institute (IRRI), Los Baños, the Philippines; Australian Center for International Agricultural Research (ACIAR), Canberra, ACT 2601, Australia
| | - Andreas de Neergaard
- Faculty of Social Sciences, University of Copenhagen, Øster Farimagsgade 5, Copenhagen K, Denmark
| | - Jan Willem van Groenigen
- Soil Biology Group, Wageningen University, Droevendaalsesteeg 3, PO Box 47, 6700 AA Wageningen, the Netherlands
| | - Lars Stoumann Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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Invited Review: Methane sources, quantification, and mitigation in grazing beef systems. APPLIED ANIMAL SCIENCE 2020. [DOI: 10.15232/aas.2019-01951] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Zhou XQ, Hao YY, Gu B, Feng J, Liu YR, Huang Q. Microbial Communities Associated with Methylmercury Degradation in Paddy Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:7952-7960. [PMID: 32437137 DOI: 10.1021/acs.est.0c00181] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioaccumulation of the neurotoxin methylmercury (MeHg) in rice has raised worldwide concerns because of its risks to human health. Certain microorganisms are able to degrade MeHg in pure cultures, but the roles and diversities of the microbial communities in MeHg degradation in rice paddy soils are unknown. Using a series of microcosms, we investigated MeHg degradation in paddy soils from Hunan, Guizhou, and Hubei provinces, representing three major rice production regions in China, and further characterized one of the soils from the Hunan Province for microbial communities associated with MeHg degradation. Microbial demethylation was observed in all three soils, demonstrated by significantly more MeHg degraded in the unsterilized soils than in the sterilized controls. More demethylation occurred in water-saturated soils than in unsaturated soils, but the addition of molybdate and bromoethanesulfonic acid as the respective inhibitors of sulfate reducing bacteria and methanogens showed insignificant effects on MeHg degradation. However, the addition of Cu enhanced MeHg degradation and the enrichment of Xanthomonadaceae in the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses of the Hunan soil consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing MeHg degradation in the paddy soil, and they were confirmed by combined analyses of the co-occurrence network, random forest modeling, and linear discriminant analysis of the effect size. Our results shed additional light onto the roles of microbial communities in MeHg degradation in paddy soils and its subsequent bioaccumulation in rice grains.
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Affiliation(s)
- Xin-Quan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yun-Yun Hao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jiao Feng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
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van Grinsven S, Sinninghe Damsté JS, Harrison J, Villanueva L. Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake. Front Microbiol 2020; 11:715. [PMID: 32477281 PMCID: PMC7240106 DOI: 10.3389/fmicb.2020.00715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are of major importance in limiting methane emissions from lakes. They are known to preferably inhabit the oxycline of stratified water columns, often assumed due to an intolerance to atmospheric oxygen concentrations, but little is known on the response of methanotrophs to different oxygen concentrations as well as their preference for different electron acceptors. In this study, we enriched a methanotroph of the Methylobacter genus from the oxycline and the anoxic water column of a stratified lake, which was also present in the oxic water column in the winter. We tested the response of this Methylobacter-dominated enrichment culture to different electron acceptors, i.e., oxygen, nitrate, sulfate, and humic substances, and found that, in contrast to earlier results with water column incubations, oxygen was the preferred electron acceptor, leading to methane oxidation rates of 45–72 pmol cell−1 day−1. Despite the general assumption of methanotrophs preferring microaerobic conditions, methane oxidation was most efficient under high oxygen concentrations (>600 μM). Low (<30 μM) oxygen concentrations still supported methane oxidation, but no methane oxidation was observed with trace oxygen concentrations (<9 μM) or under anoxic conditions. Remarkably, the presence of nitrate stimulated methane oxidation rates under oxic conditions, raising the methane oxidation rates by 50% when compared to oxic incubations with ammonium. Under anoxic conditions, no net methane consumption was observed; however, methanotroph abundances were two to three times higher in incubations with nitrate and sulfate compared to anoxic incubations with ammonium as the nitrogen source. Metagenomic sequencing revealed the absence of a complete denitrification pathway in the dominant methanotroph Methylobacter, but the most abundant methylotroph Methylotenera seemed capable of denitrification, which can possibly play a role in the enhanced methane oxidation rates under nitrate-rich conditions.
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Affiliation(s)
- Sigrid van Grinsven
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - John Harrison
- School of the Environment, Washington State University Vancouver, Vancouver, WA, United States
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Utrecht, Netherlands
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Rodríguez Y, Firmino PIM, Arnáiz E, Lebrero R, Muñoz R. Elucidating the influence of environmental factors on biogas-based polyhydroxybutyrate production by Methylocystis hirsuta CSC1. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135136. [PMID: 31862586 DOI: 10.1016/j.scitotenv.2019.135136] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
The valorization of biogas as a feedstock for the generation of added-value bioproducts will play a key role on the sustainability of anaerobic digestion. The present work assessed the influence of key environmental parameters (O2:CH4 ratio, temperature and nitrogen source) on the growth and polyhydroxybutyrate (PHB) synthesis under nitrogen limiting conditions of the type II methanotroph Methylocystis hirsuta CSC1 using biogas as a feedstock. The O2:CH4 ratios tested (1:1, 1.5:1 and 2:1) did not affect significantly M. hirsuta CSC1 growth yields (~5 g TSS mol-1 CH4), although lower CH4 removal rates were reached under O2-limiting conditions (ratio 1:1). The highest PHB content (45 wt%) was achieved at a ratio 2:1 and was threefold higher than those obtained at lower ratios (~15 wt%). The increase in temperature from 15 to 25 °C resulted in increases in the growth yield (from 5 to 6 g TSS mol-1 CH4) and PHB content (from 32 to 40 wt%). Conversely, the lowest PHB content (30 wt%) was reached at 37 °C, together with a negligible growth under nutrient sufficient conditions. The nitrogen source also played a key role on both M. hirsuta CSC1 growth and PHB synthesis. Thus, ammonium resulted in the highest growth yield (7 g TSS mol-1 CH4), although the maximum PHB content was achieved when biomass was previously grown in nitrate as the nitrogen source (41 wt%). Nitrite exerted an inhibitory effect on M. hirsuta CSC1 growth.
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Affiliation(s)
- Yadira Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Paulo Igor Milen Firmino
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain; Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Esther Arnáiz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain.
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21
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Zhang L, Yuan F, Bai J, Duan H, Gu X, Hou L, Huang Y, Yang M, He JS, Zhang Z, Yu L, Song C, Lipson DA, Zona D, Oechel W, Janssens IA, Xu X. Phosphorus alleviation of nitrogen-suppressed methane sink in global grasslands. Ecol Lett 2020; 23:821-830. [PMID: 32100414 DOI: 10.1111/ele.13480] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 12/01/2022]
Abstract
Grassland ecosystems account for more than 10% of the global CH4 sink in soils. A 4-year field experiment found that addition of P alone did not affect CH4 uptake and experimental addition of N alone significantly suppressed CH4 uptake, whereas concurrent N and P additions suppressed CH4 uptake to a lesser degree. A meta-analysis including 382 data points in global grasslands corroborated these findings. Global extrapolation with an empirical modelling approach estimated that contemporary N addition suppresses CH4 sink in global grassland by 11.4% and concurrent N and P deposition alleviates this suppression to 5.8%. The P alleviation of N-suppressed CH4 sink is primarily attributed to substrate competition, defined as the competition between ammonium and CH4 for the methane mono-oxygenase enzyme. The N and P impacts on CH4 uptake indicate that projected increases in N and P depositions might substantially affect CH4 uptake and alter the global CH4 cycle.
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Affiliation(s)
- Lihua Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.,Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.,Biology Department, San Diego State University, San Diego, CA, 92182, USA.,State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Fenghui Yuan
- Biology Department, San Diego State University, San Diego, CA, 92182, USA.,Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Junhong Bai
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Hongtao Duan
- Key Laboratory of Watershed Geographic Sciences, Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xueying Gu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Longyu Hou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yao Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingan Yang
- Division of Epidemiology and Biostatistics, San Diego State University, San Diego, CA, 92182, USA
| | - Jin-Sheng He
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Zhenhua Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Lijun Yu
- LAPC, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Changchun Song
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - David A Lipson
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Donatella Zona
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Walter Oechel
- Biology Department, San Diego State University, San Diego, CA, 92182, USA
| | - Ivan A Janssens
- Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Xiaofeng Xu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.,Biology Department, San Diego State University, San Diego, CA, 92182, USA
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22
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Bian R, Shi W, Duan Y, Chai X. Effect of soil types and ammonia concentrations on the contribution of ammonia-oxidizing bacteria to CH 4 oxidation. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2019; 37:698-705. [PMID: 31023154 DOI: 10.1177/0734242x19843988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Irrigation of stabilized landfill leachate to landfill cover soil is a cost-effective operation for leachate treatment. The contribution of ammonia-oxidizing bacteria (AOB) in the cover soil to CH4 oxidation, however, is unclear, because AOB and methane-oxidizing bacteria (MOB) can co-oxidize CH4 and NH4+-N. Thus, the contribution of AOB and the inhibitory effect of NH4+-N to CH4 oxidation were determined by using an acetylene pretreatment discrimination method. The results showed that the contributions of AOB to CH4 oxidation varied with the soil type and the concentration of NH4+-N addition. The relative contribution of AOB to CH4 oxidation for compost without NH4+-N addition was the highest (65.0%), and was 2.5 and 3.4 times higher than the corresponding values for aged refuse and landfill cover soil, respectively. The inhibitory effect of NH4+-N was enhanced by increasing the concentration of NH4+-N addition for all the soil samples. At equal NH4+-N addition concentrations, the inhibitory effect was always the lowest for the compost sample. The abundances of particulate methane monooxygenase (pmoA) and ammonia monooxygenase (amoA) genes were key factors influencing the CH4 oxidation rate and contribution of AOB to CH4 oxidation. The higher abundance of pmoA and lower abundance of amoA in landfill cover soil could explain the higher CH4 oxidation rate and lower contribution of AOB to CH4 oxidation in this soil type. Meanwhile, the higher contribution of AOB to CH4 oxidation for compost could be attributed to the higher abundance of the amoA gene and lower abundance of pmoA.
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Affiliation(s)
- Rongxing Bian
- 1 State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, China
| | - Wei Shi
- 2 Xi'an Solid Waste Administration, China
| | | | - Xiaoli Chai
- 1 State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, China
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23
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Peng Y, Wang G, Li F, Yang G, Fang K, Liu L, Qin S, Zhang D, Zhou G, Fang H, Liu X, Liu C, Yang Y. Unimodal Response of Soil Methane Consumption to Increasing Nitrogen Additions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4150-4160. [PMID: 30892031 DOI: 10.1021/acs.est.8b04561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nitrogen (N) status has a great impact on methane (CH4) consumption by soils. Modeling studies predicting soil CH4 consumption assume a linear relationship between CH4 uptake and N addition rate. Here, we present evidence that a nonlinear relationship may better characterize changes in soil CH4 uptake with increasing N additions. By conducting a field experiment with eight N-input levels in a Tibetan alpine steppe, we observed a unimodal relationship; CH4 uptake increased at low to medium N levels but declined at high N levels. Environmental and microbial properties jointly determined this response pattern. The generality of the unimodal trend was further validated by two independent analyses: (i) we examined soil CH4 uptake across at least five N-input levels in upland ecosystems across China. A unimodal CH4 uptake-N addition rate relationship was observed in 3 out of 4 cases; and (ii) we performed a meta-analysis to explore the N-induced changes in soil CH4 uptake with increasing N additions across global upland ecosystems. Results showed that the changes in CH4 uptake exhibited a quadratic correlation with N addition rate. Overall, we suggest that the unimodal relationship should be considered in biogeochemistry models for accurately predicting soil CH4 consumption under global N enrichment.
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Affiliation(s)
- Yunfeng Peng
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
| | - Guanqin Wang
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Kai Fang
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Li Liu
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology , Chinese Academy of Sciences , Xining 810008 , P. R. China
- Key Laboratory of Tibetan Medicine Research , Chinese Academy of Sciences , Xining 810008 , P. R. China
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research , Chinese Academy of Sciences , Beijing 100101 , P. R. China
| | - Xuejun Liu
- College of Resources and Environmental Sciences , China Agricultural University , Beijing 100193 , P. R. China
| | - Chunyan Liu
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics , Chinese Academy of Sciences , Beijing 100029 , P. R. China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change , Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , P. R. China
- University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
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24
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López JC, Porca E, Collins G, Clifford E, Quijano G, Muñoz R. Ammonium influences kinetics and structure of methanotrophic consortia. WASTE MANAGEMENT (NEW YORK, N.Y.) 2019; 89:345-353. [PMID: 31079748 DOI: 10.1016/j.wasman.2019.04.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
The literature is conflicted on the influence of ammonium on the kinetics and microbial ecology of methanotrophy. In this study, methanotrophic cultures were enriched, under ammonium concentrations ranging from 0 to 200 mM, from an inoculum comprising leachate and top-cover soil from a landfill. Specific CH4 biodegradation rates were highest (7.8 × 10-4 ± 6.0 × 10-5 gCH4 gX-1 h-1) in cultures enriched at 4 mM NH4+, which were mainly dominated by type II methanotrophs belonging to Methylocystis spp. Lower specific CH4 oxidation rates (average values of 1.8-3.6 × 10-4 gCH4 gX-1 h-1) were achieved by cultures enriched at higher NH4+ concentrations (20 and 80 mM), and had higher affinity for CH4 compared to 4 mM enrichments. These lower affinities were attributed to lower diversity dominated by type I methanotrophs, of the Methylosarcina, Methylobacter and Methylomicrobium genera, encountered with increasing concentrations of NH4+. The study indicates that CH4 oxidation biotechnologies applied at low NH4+ concentrations can support efficient abatement of CH4 and high diversity of methanotrophic consortia, whilst enriching type II methanotrophs.
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Affiliation(s)
- Juan C López
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain
| | - Estefanía Porca
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Gavin Collins
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Eoghan Clifford
- Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; College of Engineering and Informatics, National University of Ireland Galway, University Road, Galway H91 F677, Ireland
| | - Guillermo Quijano
- Laboratory for Research on Advanced Processes for Water Treatment, Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Institute of Sustainable Proceses, University of Valladolid, Spain.
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25
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Plain C, Ndiaye FK, Bonnaud P, Ranger J, Epron D. Impact of vegetation on the methane budget of a temperate forest. THE NEW PHYTOLOGIST 2019; 221:1447-1456. [PMID: 30267569 DOI: 10.1111/nph.15452] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/19/2018] [Indexed: 06/08/2023]
Abstract
Upland forest soils are known to be the main biological sink for methane, but studies have shown that net methane uptake of a forest ecosystem can be reduced when methane emissions by vegetation are considered. We estimated the methane budget of a young oak plantation by considering tree stems but also the understorey vegetation. Automated chambers connected to a laser-based gas analyser, on tree stems, bare soil and soil covered with understorey vegetation, recorded CH4 fluxes for 7 months at 3 h intervals. Tree stem emissions were low and equated to only 0.1% of the soil sink. Conversely, the presence of understorey vegetation increased soil methane uptake. This plant-driven enhancement of CH4 uptake occurred when the soil was consuming methane. At the stand level, the methane budget shifted from -1.4 ± 0.4 kg C ha-1 when we upscaled data obtained only on bare soil, to -2.9 ± 0.6 kg C ha-1 when we considered soil area that was covered with understorey vegetation. These results indicate that aerenchymatous plant species, which are known to reduce the methane sink in wetlands, actually increase soil methane uptake two-fold in an upland forest by enhancing methane and oxygen transport and/or by promoting growth of methanotrophic populations.
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Affiliation(s)
- Caroline Plain
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, F-54000, Nancy, France
| | - Fatou-Kiné Ndiaye
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, F-54000, Nancy, France
| | | | | | - Daniel Epron
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, F-54000, Nancy, France
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26
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Levy-Booth DJ, Giesbrecht IJW, Kellogg CTE, Heger TJ, D'Amore DV, Keeling PJ, Hallam SJ, Mohn WW. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO 2, and CH 4 fluxes in temperate rainforest soil. ISME JOURNAL 2018; 13:950-963. [PMID: 30538276 PMCID: PMC6461783 DOI: 10.1038/s41396-018-0334-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 11/10/2022]
Abstract
The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate-soil feedbacks in the PCTR.
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Affiliation(s)
- David J Levy-Booth
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada
| | - Ian J W Giesbrecht
- Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Colleen T E Kellogg
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Tula Foundation, Heriot Bay, BC, Canada
| | - Thierry J Heger
- The University of Applied Sciences Western Switzerland, CHANGINS, Delémont, Switzerland
| | - David V D'Amore
- U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station, Juneau, Alaska, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J Hallam
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
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27
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La H, Hettiaratchi JPA, Achari G, Dunfield PF. Biofiltration of methane. BIORESOURCE TECHNOLOGY 2018; 268:759-772. [PMID: 30064899 DOI: 10.1016/j.biortech.2018.07.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/06/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
The on-going annual increase in global methane (CH4) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH4 emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH4 concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH4 biofiltration studies that have been performed in the last decades.
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Affiliation(s)
- Helen La
- Department of Civil Engineering, Center for Environmental Engineering Research and Education (CEERE), University of Calgary, 2500 University Drive, NW, Calgary, Alberta T2N 1N4 Canada
| | - J Patrick A Hettiaratchi
- Department of Civil Engineering, Center for Environmental Engineering Research and Education (CEERE), University of Calgary, 2500 University Drive, NW, Calgary, Alberta T2N 1N4 Canada
| | - Gopal Achari
- Department of Civil Engineering, Center for Environmental Engineering Research and Education (CEERE), University of Calgary, 2500 University Drive, NW, Calgary, Alberta T2N 1N4 Canada.
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Drive, NW, Calgary, Alberta T2N 1N4 Canada
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28
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Mustapha NA, Hu A, Yu CP, Sharuddin SS, Ramli N, Shirai Y, Maeda T. Seeking key microorganisms for enhancing methane production in anaerobic digestion of waste sewage sludge. Appl Microbiol Biotechnol 2018; 102:5323-5334. [DOI: 10.1007/s00253-018-9003-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 11/24/2022]
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29
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Garg S, Clomburg JM, Gonzalez R. A modular approach for high-flux lactic acid production from methane in an industrial medium using engineered Methylomicrobium buryatense 5GB1. J Ind Microbiol Biotechnol 2018; 45:379-391. [PMID: 29675615 DOI: 10.1007/s10295-018-2035-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/01/2022]
Abstract
Convergence of market drivers such as abundant availability of inexpensive natural gas and increasing awareness of its global warming effects have created new opportunities for the development of small-scale gas-to-liquid (GTL) conversion technologies that can efficiently utilize methane, the primary component of natural gas. Leveraging the unique ability of methanotrophs that use methane as carbon and energy source, biological GTL platforms can be envisioned that are readily deployable at remote petroleum drilling sites where large chemical GTL infrastructure is uneconomical to set-up. Methylomicrobium buryatense, an obligate methanotroph, has gained traction as a potential industrial methanotrophic host because of availability of genetic tools and recent advances in its metabolic engineering. However, progress is impeded by low strain performance and lack of an industrial medium. In this study, we first established a small-scale cultivation platform using Hungate tubes for growth of M. buryatense at medium-to-high-throughput that also enabled 2X faster growth compared to that obtained in traditional glass serum bottles. Then, employing a synthetic biology approach we engineered M. buryatense with varying promoter (inducible and constitutive) and ribosome-binding site combinations, and obtained a strain capable of producing L-lactate from methane at a flux 14-fold higher than previously reported. Finally, we demonstrated L-lactate production in an industrial medium by replacing nitrate with less-expensive ammonium as the nitrogen source. Under these conditions, L-lactate was synthesized at a flux approximately 50-fold higher than that reported previously in a bioreactor system while achieving a titer of 0.6 g/L. These findings position M. buryatense closer to becoming an industrial host strain of choice, and pave new avenues for accelerating methane-to-chemical conversion using synthetic biology.
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Affiliation(s)
- Shivani Garg
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA
| | - James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street MS-667, Houston, TX, 77005, USA. .,Department of Bioengineering, Rice University, Houston, 77005, USA.
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30
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Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities. mSystems 2018; 3:mSystems00214-17. [PMID: 29404427 PMCID: PMC5790874 DOI: 10.1128/msystems.00214-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/04/2018] [Indexed: 01/21/2023] Open
Abstract
Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities. Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.
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31
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He R, Ma RC, Yao XZ, Wei XM. Response of methanotrophic activity to extracellular polymeric substance production and its influencing factors. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 69:289-297. [PMID: 28803765 DOI: 10.1016/j.wasman.2017.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/25/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
The accumulation of extracellular polymeric substance (EPS) is speculated to be related with the decrease of CH4 oxidation rate after a peak in long-term laboratory landfill covers and biofilters. However, few data have been reported about EPS production of methanotrophs and its feedback effects on methanotrophic activity. In this study, Methylosinus sporium was used asa model methanotroph to investigate EPS production and its influencing factors during CH4 oxidation. The results showed that methanotrophs could secret EPS into the habits during CH4 oxidation and had a negative feedback effect on CH4 oxidation. The EPS amount fitted well with the CH4 oxidation activity with the exponential model. The environmental factors such as pH, temperature, CH4, O2, NO3--N and NH4+-N could affect the EPS production of methanotrophs. When pH, temperature, CH4, O2 and N concentrations (including NO3--N and NH4+-N) were 6.5-7.5, 30-40°C, 10-15%, 10% and 20-140mgL-1, respectively, the high cell growth rate and CH4 oxidation activity of Methylosinus sporium occurred in the media with the low EPS production, which was beneficial to sustainable and efficient CH4 oxidation. In practice, O2-limited condition such as the O2 concentration of 10% might be a good way to control EPS production and enhance CH4 oxidation to mitigate CH4 emission from landfills.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xing-Zhi Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Meng Wei
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
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Duan YF, Reinsch S, Ambus P, Elsgaard L, Petersen SO. Activity of Type I Methanotrophs Dominates under High Methane Concentration: Methanotrophic Activity in Slurry Surface Crusts as Influenced by Methane, Oxygen, and Inorganic Nitrogen. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:767-775. [PMID: 28783780 DOI: 10.2134/jeq2017.02.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Livestock slurry is a major source of atmospheric methane (CH), but surface crusts harboring methane-oxidizing bacteria (MOB) could mediate against CH emissions. This study examined conditions for CH oxidation by in situ measurements of oxygen (O) and nitrous oxide (NO), as a proxy for inorganic N transformations, in intact crusts using microsensors. This was combined with laboratory incubations of crust material to investigate the effects of O, CH, and inorganic N on CH oxidation, using CH to trace C incorporation into lipids of MOB. Oxygen penetration into the crust was 2 to 14 mm, confining the potential for aerobic CH oxidation to a shallow layer. Nitrous oxide accumulated within or below the zone of O depletion. With 10 ppmv CH there was no O limitation on CH oxidation at O concentrations as low as 2%, whereas CH oxidation at 10 ppmv CH was reduced at ≤5% O. As hypothesized, CH oxidation was in general inhibited by inorganic N, especially NO, and there was an interaction between N inhibition and O limitation at 10 ppmv CH, as indicated by consistently stronger inhibition of CH oxidation by NH and NO at 3% compared with 20% O. Recovery of C in phospholipid fatty acids suggested that both Type I and Type II MOB were active, with Type I dominating high-concentration CH oxidation. Given the structural heterogeneity of crusts, CH oxidation activity likely varies spatially as constrained by the combined effects of CH, O, and inorganic N availability in microsites.
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Li S, Song L, Gao X, Jin Y, Liu S, Shen Q, Zou J. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System. Front Microbiol 2017; 8:409. [PMID: 28373862 PMCID: PMC5357657 DOI: 10.3389/fmicb.2017.00409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.
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Affiliation(s)
- Shuqing Li
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lina Song
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Xiang Gao
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Yaguo Jin
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Shuwei Liu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
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de Godoi SG, Neufeld ÂDH, Ibarr MA, Ferreto DOC, Bayer C, Lorentz LH, Vieira FCB. The conversion of grassland to acacia forest as an effective option for net reduction in greenhouse gas emissions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 169:91-102. [PMID: 26731308 DOI: 10.1016/j.jenvman.2015.11.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/17/2015] [Accepted: 11/28/2015] [Indexed: 06/05/2023]
Abstract
This study aimed to evaluate the effect of forestation with leguminous Acacia mearnsii De Wild in native grasslands on the soil greenhouse (GHG) fluxes and their main driving factors. The experiment was conducted in the Brazilian Pampa over the period of one year in a six-year-old Acacia plantation, evaluating four treatments: Acacia (AM), Acacia with litter periodically removed (A-l), Acacia after harvest (AH) and native grassland (NG) (reference treatment). Air samples were obtained by the static chamber method, and gas concentrations were evaluated by gas chromatography. Soil and climate factors were monitored. The accumulated fluxes of methane (CH4) and nitrous oxide (N2O) were statistically similar between the soils in the AM and NG treatments, which tended to oxidize CH4 (-1445 and -1752 g C-CH4 ha(-1) yr(-1), respectively) and had low emission of N2O (242 and 316 g N-N2O ha(-1) yr(-1)), most likely influenced by the low water-filled pore space and the low content of mineral N in the soil. However, the soil in the AH treatment presented higher emissions of both gases, totaling 1889 g C-CH4 ha(-1) yr(-1) and 1250 g N-N2O ha(-1) yr(-1). Afforestation neither significantly affected the total organic C stocks nor their lability, keeping the C management index for the forested area similar to that in the NG treatment. The conversion from grassland to Acacia forest represents an effective option for mitigating the net reduction in greenhouse gas emissions, which is basically determined by C accumulation in biomass and wood products.
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Affiliation(s)
- Stefânia Guedes de Godoi
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil
| | - Ângela Denise Hubert Neufeld
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil
| | - Mariana Alves Ibarr
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil
| | - Décio Oscar Cardoso Ferreto
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil
| | - Cimélio Bayer
- Departamento de Solos, Universidade Federal do Rio Grande do Sul, P.O. Box 15100, 91540-000, Porto Alegre, RS, Brazil
| | - Leandro Homrich Lorentz
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil
| | - Frederico Costa Beber Vieira
- Universidade Federal do Pampa - Campus São Gabriel, Avenida Antônio Trilha, 1847, Centro, 97300-000, São Gabriel, RS, Brazil.
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Gagliano AL, Tagliavia M, D'Alessandro W, Franzetti A, Parello F, Quatrini P. So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites. GEOBIOLOGY 2016; 14:150-162. [PMID: 26560641 DOI: 10.1111/gbi.12167] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/01/2015] [Indexed: 06/05/2023]
Abstract
This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.
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Affiliation(s)
- A L Gagliano
- Istituto Nazionale di Geofisica e Vulcanologia (INGV) - Sezione di Palermo, Palermo, Italy
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy
| | - M Tagliavia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
- Institute for Coastal Marine Environment (CNR-IAMC) U.O.S. of Capo Granitola, Campobello di Mazara, Italy
| | - W D'Alessandro
- Istituto Nazionale di Geofisica e Vulcanologia (INGV) - Sezione di Palermo, Palermo, Italy
| | - A Franzetti
- Department of Earth and Environmental Sciences, University of Milano- Bicocca, Milano, Italy
| | - F Parello
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy
| | - P Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
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Maris SC, Teira-Esmatges MR, Arbonés A, Rufat J. Effect of irrigation, nitrogen application, and a nitrification inhibitor on nitrous oxide, carbon dioxide and methane emissions from an olive (Olea europaea L.) orchard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 538:966-978. [PMID: 26367066 DOI: 10.1016/j.scitotenv.2015.08.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/10/2015] [Accepted: 08/10/2015] [Indexed: 06/05/2023]
Abstract
Drip irrigation combined with nitrogen (N) fertigation is applied in order to save water and improve nutrient efficiency. Nitrification inhibitors reduce greenhouse gas emissions. A field study was conducted to compare the emissions of nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) associated with the application of N fertiliser through fertigation (0 and 50kgNha(-1)), and 50kgNha(-1)+nitrification inhibitor in a high tree density Arbequina olive orchard. Spanish Arbequina is the most suited variety for super intensive olive groves. This system allows reducing production costs and increases crop yield. Moreover its oil has excellent sensorial features. Subsurface drip irrigation markedly reduced N2O and N2O+N2 emissions compared with surface drip irrigation. Fertiliser application significantly increased N2O+N2, but not N2O emissions. Denitrification was the main source of N2O. The N2O losses (calculated as emission factor) ranging from -0.03 to 0.14% of the N applied, were lower than the IPCC (2007) values. The N2O+N2 losses were the largest, equivalent to 1.80% of the N applied, from the 50kgNha(-1)+drip irrigation treatment which resulted in water filled pore space >60% most of the time (high moisture). Nitrogen fertilisation significantly reduced CO2 emissions in 2011, but only for the subsurface drip irrigation strategies in 2012. The olive orchard acted as a net CH4 sink for all the treatments. Applying a nitrification inhibitor (DMPP), the cumulative N2O and N2O+N2 emissions were significantly reduced with respect to the control. The DMPP also inhibited CO2 emissions and significantly increased CH4 oxidation. Considering global warming potential, greenhouse gas intensity, cumulative N2O emissions and oil production, it can be concluded that applying DMPP with 50kgNha(-1)+drip irrigation treatment was the best option combining productivity with keeping greenhouse gas emissions under control.
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Affiliation(s)
- S C Maris
- University of Lleida, Environment and Soil Science Department, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain.
| | - M R Teira-Esmatges
- University of Lleida, Environment and Soil Science Department, Av. Alcalde Rovira Roure 191, E-25198 Lleida, Spain
| | - A Arbonés
- Programa Ús Eficient de l'Aigua, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Parc Científic i Tecnològic Agroalimentari de Lleida (PCiTAL). Parc de Gardeny, Edifici Fruitcentre, E-2503 Lleida, Spain
| | - J Rufat
- Programa Ús Eficient de l'Aigua, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Parc Científic i Tecnològic Agroalimentari de Lleida (PCiTAL). Parc de Gardeny, Edifici Fruitcentre, E-2503 Lleida, Spain
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37
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Maanoja ST, Rintala JA. Methane oxidation potential of boreal landfill cover materials: The governing factors and enhancement by nutrient manipulation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 46:399-407. [PMID: 26298483 DOI: 10.1016/j.wasman.2015.08.011] [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: 02/20/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 06/04/2023]
Abstract
Methanotrophs inhabiting landfill covers are in a crucial role in mitigating CH4 emissions, but the characteristics of the cover material or ambient temperature do not always enable the maximal CH4 oxidation potential (MOP). This study aimed at identifying the factors governing MOPs of different materials used for constructing biocovers and other cover structures. We also tested whether the activity of methanotrophs could be enhanced at cold temperature (4 and 12°C) by improving the nutrient content (NO3(-), PO4(3-), trace elements) of the cover material. Compost samples from biocovers designed to support CH4 oxidation were exhibiting the highest MOPs (4.16 μmol CH4 g dw(-1) h(-1)), but also the soil samples collected from other cover structures were oxidising CH4 (0.41 μmol CH4 g dw(-1) h(-1)). The best predictors for the MOPs were the NO3(-) content and activity of heterotrophic bacteria at 72.8%, which were higher in the compost samples than in the soil samples. The depletion of NO3(-) from the landfill cover material limiting the activity of methanotrophs could not be confirmed by the nutrient manipulation assay at 4°C as the addition of nitrogen decreased the MOPs from 0.090 μmol CH4 g dw(-1) h(-1) to <0.085 μmol CH4 g dw(-1) h(-1). At 12°C, all nutrient additions reduced the MOPs. The inhibition was believed to result from high ionic concentration caused by nutrient addition. At 4°C, the addition of trace elements increased the MOPs (>0.096 μmol CH4 g dw(-1)h(-1)) suggesting that this was attributable to stimulation of the enzymatic activity of the psychrotolerant methanotrophs.
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Affiliation(s)
- Susanna T Maanoja
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland.
| | - Jukka A Rintala
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FIN-33101 Tampere, Finland.
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Kits KD, Campbell DJ, Rosana AR, Stein LY. Diverse electron sources support denitrification under hypoxia in the obligate methanotroph Methylomicrobium album strain BG8. Front Microbiol 2015; 6:1072. [PMID: 26500622 PMCID: PMC4594100 DOI: 10.3389/fmicb.2015.01072] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/18/2015] [Indexed: 11/30/2022] Open
Abstract
Aerobic methane-oxidizing bacteria (MOB) are a diverse group of microorganisms that are ubiquitous in natural environments. Along with anaerobic MOB and archaea, aerobic methanotrophs are critical for attenuating emission of methane to the atmosphere. Clearly, nitrogen availability in the form of ammonium and nitrite have strong effects on methanotrophic activity and their natural community structures. Previous findings show that nitrite amendment inhibits the activity of some cultivated methanotrophs; however, the physiological pathways that allow some strains to transform nitrite, expression of gene inventories, as well as the electron sources that support this activity remain largely uncharacterized. Here we show that Methylomicrobium album strain BG8 utilizes methane, methanol, formaldehyde, formate, ethane, ethanol, and ammonia to support denitrification activity under hypoxia only in the presence of nitrite. We also demonstrate that transcript abundance of putative denitrification genes, nirS and one of two norB genes, increased in response to nitrite. Furthermore, we found that transcript abundance of pxmA, encoding the alpha subunit of a putative copper-containing monooxygenase, increased in response to both nitrite and hypoxia. Our results suggest that expression of denitrification genes, found widely within genomes of aerobic methanotrophs, allow the coupling of substrate oxidation to the reduction of nitrogen oxide terminal electron acceptors under oxygen limitation. The present study expands current knowledge of the metabolic flexibility of methanotrophs by revealing that a diverse array of electron donors support nitrite reduction to nitrous oxide under hypoxia.
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Affiliation(s)
- K Dimitri Kits
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Dustin J Campbell
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Albert R Rosana
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, Faculty of Science, University of Alberta Edmonton, AB, Canada
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Myung J, Wang Z, Yuan T, Zhang P, Van Nostrand JD, Zhou J, Criddle CS. Production of Nitrous Oxide from Nitrite in Stable Type II Methanotrophic Enrichments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10969-10975. [PMID: 26301949 DOI: 10.1021/acs.est.5b03385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The coupled aerobic-anoxic nitrous decomposition operation is a new process for wastewater treatment that removes nitrogen from wastewater and recovers energy from the nitrogen in three steps: (1) NH4(+) oxidation to NO2(-), (2) NO2(-) reduction to N2O, and (3) N2O conversion to N2 with energy production. Here, we demonstrate that type II methanotrophic enrichments can mediate step two by coupling oxidation of poly(3-hydroxybutyrate) (P3HB) to NO2(-) reduction. Enrichments grown with NH4(+) and NO2(-) were subject to alternating 48-h aerobic and anoxic periods, in which CH4 and NO2(-) were added together in a "coupled" mode of operation or separately in a "decoupled mode". Community structure was stable in both modes and dominated by Methylocystis. In the coupled mode, production of P3HB and N2O was low. In the decoupled mode, significant P3HB was produced, and oxidation of P3HB drove reduction of NO2(-) to N2O with ∼ 70% conversion for >30 cycles (120 d). In batch tests of wasted cells from the decoupled mode, N2O production rates increased at low O2 or high NO2(-) levels. The results are significant for the development of engineered processes that remove nitrogen from wastewater and for understanding of conditions that favor environmental production of N2O.
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Affiliation(s)
- Jaewook Myung
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Zhiyue Wang
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Ping Zhang
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University , Stanford, California 94305, United States
- Woods Institute for the Environment, Stanford, California 94305, United States
- William and Cloy Codiga Resource Recovery Center, Stanford, California 94305, United States
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Tellez-Rio A, García-Marco S, Navas M, López-Solanilla E, Tenorio JL, Vallejo A. N2O and CH4 emissions from a fallow-wheat rotation with low N input in conservation and conventional tillage under a Mediterranean agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 508:85-94. [PMID: 25459752 DOI: 10.1016/j.scitotenv.2014.11.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/13/2014] [Accepted: 11/11/2014] [Indexed: 06/04/2023]
Abstract
Conservation agriculture that includes no tillage (NT) or minimum tillage (MT) and crop rotation is an effective practice to increase soil organic matter in Mediterranean semiarid agrosystems. But the impact of these agricultural practices on greenhouse gases (GHGs), such as nitrous oxide (N2O) and methane (CH4), is variable depending mainly on soil structure and short/long-term tillage. The main objective of this study was to assess the long-term effect of three tillage systems (NT, MT and conventional tillage (CT)) and land-covers (fallow/wheat) on the emissions of N2O and CH4 in a low N input agricultural system during one year. This was achieved by measuring crop yields, soil mineral N and dissolved organic C contents, and fluxes of N2O and CH4. Total cumulative N2O emissions were not significantly different (P>0.05) among the tillage systems or between fallow and wheat. The only difference was produced in spring, when N2O emissions were significantly higher (P<0.05) in fallow than in wheat subplots, and NT reduced N2O emissions (P<0.05) compared with MT and CT. Taking into account the water filled pore space (WFPS), both nitrification and denitrification could have occurred during the experimental period. Denitrification capacity in March was similar in all tillage systems, in spite of the higher DOC content maintained in the topsoil of NT. This could be due to the similar denitrifier densities, targeted by nirK copy numbers at that time. Cumulative CH4 fluxes resulted in small net uptake for all treatments, and no significant differences were found among tillage systems or between fallow and wheat land-covers. These results suggest that under a coarse-textured soil in low N agricultural systems, the impact of tillage on GHG is very low and that the fallow cycle within a crop rotation is not a useful strategy to reduce GHG emissions.
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Affiliation(s)
- Angela Tellez-Rio
- E.T.S.I. Agrónomos, Technical University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain.
| | - Sonia García-Marco
- E.T.S.I. Agrónomos, Technical University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Mariela Navas
- E.T.S.I. Agrónomos, Technical University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain; Centro de Biotecnología y Genómica de Plantas UPM-INIA. Dpto Biotecnología. E.T.S.I. Agrónomos. Technical University of Madrid. Campus Montegancedo, UPM. Autovía M-40, Salida 38N, 36S. 28223 Pozuelo de Alarcón. Madrid, Spain
| | - Emilia López-Solanilla
- E.T.S.I. Agrónomos, Technical University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain; Centro de Biotecnología y Genómica de Plantas UPM-INIA. Dpto Biotecnología. E.T.S.I. Agrónomos. Technical University of Madrid. Campus Montegancedo, UPM. Autovía M-40, Salida 38N, 36S. 28223 Pozuelo de Alarcón. Madrid, Spain
| | - Jose Luis Tenorio
- Dpto. de Medio Ambiente, INIA. Ctra. de La Coruña km. 7.5, 28040 Madrid, Spain
| | - Antonio Vallejo
- E.T.S.I. Agrónomos, Technical University of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Dam B, Dam S, Kim Y, Liesack W. Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. Environ Microbiol 2014; 16:3115-27. [PMID: 24373058 DOI: 10.1111/1462-2920.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/14/2013] [Indexed: 11/30/2022]
Abstract
Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.
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Affiliation(s)
- Bomba Dam
- Max Planck Institute for Terrestrial Microbiology, D-35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35043, Marburg, Germany
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Sanz-Cobena A, García-Marco S, Quemada M, Gabriel JL, Almendros P, Vallejo A. Do cover crops enhance N₂O, CO₂ or CH₄ emissions from soil in Mediterranean arable systems? THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 466-467:164-174. [PMID: 23906854 DOI: 10.1016/j.scitotenv.2013.07.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 07/02/2013] [Accepted: 07/05/2013] [Indexed: 06/02/2023]
Abstract
This study evaluates the effect of planting three cover crops (CCs) (barley, Hordeum vulgare L.; vetch, Vicia villosa L.; rape, Brassica napus L.) on the direct emission of N₂O, CO₂ and CH₄ in the intercrop period and the impact of incorporating these CCs on the emission of greenhouse gas (GHG) from the forthcoming irrigated maize (Zea mays L.) crop. Vetch and barley were the CCs with the highest N₂O and CO₂ losses (75 and 47% increase compared with the control, respectively) in the fallow period. In all cases, fluxes of N₂O were increased through N fertilization and the incorporation of barley and rape residues (40 and 17% increase, respectively). The combination of a high C:N ratio with the addition of an external source of mineral N increased the fluxes of N₂O compared with -Ba and -Rp. The direct emissions of N₂O were lower than expected for a fertilized crop (0.10% emission factor, EF) compared with other studies and the IPCC EF. These results are believed to be associated with a decreased NO₃(-) pool due to highly denitrifying conditions and increased drainage. The fluxes of CO₂ were in the range of other fertilized crops (i.e., 1118.71-1736.52 kg CO₂-Cha(-1)). The incorporation of CC residues enhanced soil respiration in the range of 21-28% for barley and rape although no significant differences between treatments were detected. Negative CH₄ fluxes were measured and displayed an overall sink effect for all incorporated CC (mean values of -0.12 and -0.10 kg CH₄-Cha(-1) for plots with and without incorporated CCs, respectively).
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Affiliation(s)
- A Sanz-Cobena
- Technical University of Madrid, School of Agriculture, Avd. Complutense s/n, 28040 Madrid, Spain.
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Aronson EL, Allison SD, Helliker BR. Environmental impacts on the diversity of methane-cycling microbes and their resultant function. Front Microbiol 2013; 4:225. [PMID: 23966984 PMCID: PMC3743065 DOI: 10.3389/fmicb.2013.00225] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 07/25/2013] [Indexed: 11/29/2022] Open
Abstract
Methane is an important anthropogenic greenhouse gas that is produced and consumed in soils by microorganisms responding to micro-environmental conditions. Current estimates show that soil consumption accounts for 5–15% of methane removed from the atmosphere on an annual basis. Recent variability in atmospheric methane concentrations has called into question the reliability of estimates of methane consumption and calls for novel approaches in order to predict future atmospheric methane trends. This review synthesizes the environmental and climatic factors influencing the consumption of methane from the atmosphere by non-wetland, terrestrial soil microorganisms. In particular, we focus on published efforts to connect community composition and diversity of methane-cycling microbial communities to observed rates of methane flux. We find abundant evidence for direct connections between shifts in the methane-cycling microbial community, due to climate and environmental changes, and observed methane flux levels. These responses vary by ecosystem and associated vegetation type. This information will be useful in process-based models of ecosystem methane flux responses to shifts in environmental and climatic parameters.
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Affiliation(s)
- Emma L Aronson
- Department of Plant Pathology and Microbiology, University of California Riverside, CA, USA ; Department of Ecology and Evolutionary Biology, University of California Irvine, CA, USA
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Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia. DIVERSITY 2013. [DOI: 10.3390/d5030541] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Duan YF, Elsgaard L, Petersen SO. Inhibition of methane oxidation in a slurry surface crust by inorganic nitrogen: an incubation study. JOURNAL OF ENVIRONMENTAL QUALITY 2013; 42:507-515. [PMID: 23673843 DOI: 10.2134/jeq2012.0230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Livestock slurry is an important source of methane (CH). However, depending on the dry matter content of the slurry, a floating crust may form where methane-oxidizing bacteria (MOB) and CH oxidation activity have been found, suggesting that surface crusts may reduce CH emissions from slurry. However, it is not known how MOB in this environment interact with inorganic nitrogen (N). We studied inhibitory effects of ammonium (NH), nitrate (NO), and nitrite (NO) on potential CH oxidation in a cattle slurry surface crust. At headspace concentrations of 100 and 10,000 ppmv, CH oxidation was assayed at salt concentrations up to 500 mM. First-order rate constants were used to evaluate the strength of inhibition. Nitrite was the most potent inhibitor, reducing methanotrophic activity by up to 70% at only 1 mM NO. Methane-oxidizing bacteria were least sensitive to NO, tolerating up to 30 mM NO at 100 ppmv CH and 50 mM NO at 10,000 ppmv CH without any decline in activity. The inhibition by NH increased progressively, and no range of tolerance was observed. Methane concentrations of 10,000 ppmv resulted in 50- to 100-fold higher specific CH uptake rates than 100 ppmv CH but did not change the inhibition patterns of N salts. In slurry surface crusts, MOB maintained activity at higher concentrations of NH and NO than reported for MOB in soils and sediments, possibly showing adaptation to high N concentrations in the slurry environment. Yet it appears that the effectiveness of surface crusts as CH sinks will depend on inorganic N concentrations.
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Lee SH, Li C, Heber AJ. The effect of nitrate on ethylene biofiltration. JOURNAL OF HAZARDOUS MATERIALS 2012; 241-242:331-339. [PMID: 23063558 DOI: 10.1016/j.jhazmat.2012.09.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 09/16/2012] [Accepted: 09/20/2012] [Indexed: 06/01/2023]
Abstract
This study investigated the effects of filter media types and nitrate (NO(3)(-)) concentrations in nutrient solutions on C(2)H(4) biofiltration. A new nutrient solution with zero NO(3)(-) concentration was supplied to two perlite-bed biotrickling filters, two perlite-bed biofilters, and two GAC (Granular Activated Carbon)-bed biofilters, while the other with 2 g L(-1) of NO(3)(-) was used for the other two GAC biofilters. All reactors underwent a total test duration of over 175 days with an EBRT (Empty Bed Residence Time) of 30 s, inlet gas flow rate of 7 L min(-1), and inlet C(2)H(4) concentrations of 20-30 mg m(-3). NO(3)(-) concentration and media type significantly affected the C(2)H(4) removal efficiencies in all types of biofiltration. The perlite media with no NO(3)(-) achieved C(2)H(4) removal efficiencies 10-50% higher than the others. A NO(3)(-) concentration as high as 2 g L(-1) in the original nutrient solution may act as an inhibitor that suppresses the growth or activity of C(2)H(4) degraders. In addition, the perlite media resulted in higher C(2)H(4) removal efficiencies than GAC media, because the hydrophilic surface of the perlite leads to a higher moisture content and thus to favorable microbial growth.
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Affiliation(s)
- Sang-Hun Lee
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University St., West Lafayette, 47907-2093 IN, USA.
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Abstract
Organic crusts on liquid manure storage tanks harbor ammonia- and nitrite-resistant methane oxidizers and may significantly reduce methane emissions. Methane oxidation potential (0.6 mol CH(4) m(-2) day(-1)) peaked during fall and winter, after 4 months of crust development. Consequences for methane mitigation potential of crusts are discussed.
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Banger K, Tian H, Lu C. Do nitrogen fertilizers stimulate or inhibit methane emissions from rice fields? GLOBAL CHANGE BIOLOGY 2012; 18:3259-3267. [PMID: 28741830 DOI: 10.1111/j.1365-2486.2012.02762.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 06/04/2012] [Indexed: 05/22/2023]
Abstract
In rice cultivation, there are controversial reports on net impacts of nitrogen (N) fertilizers on methane (CH 4 ) emissions. Nitrogen fertilizers increase crop growth as well as alter CH 4 producing (Methanogens) and consuming (Methanotrophs) microbes, and thereby produce complex effects on CH 4 emissions. Objectives of this study were to determine net impact of N fertilizers on CH 4 emissions and to identify their underlying mechanisms in the rice soils. Database was obtained from 33 published papers that contained CH 4 emissions observations from N fertilizer (28-406 kg N ha-1 ) treatment and its control. Results have indicated that N fertilizers increased CH 4 emissions in 98 of 155 data pairs in rice soils. Response of CH 4 emissions per kg N fertilizer was significantly (P < 0.05) greater at < 140 kg N ha-1 than > 140 kg N ha-1 indicating that substrate switch from CH 4 to ammonia by Methanotrophs may not be a dominant mechanism for increased CH 4 emissions. On the contrary, decreased CH 4 emission in intermittent drainage by N fertilizers has suggested the stimulation of Methanotrophs in rice soils. Effects of N fertilizer stimulated Methanotrophs in reducing CH 4 emissions were modified by the continuous flood irrigation due to limitation of oxygen to Methanotrophs. Greater response of CH 4 emissions per kg N fertilizer in urea than ammonia sulfate probably indicated the interference of sulfate in the CH 4 production process. Overall, response of CH 4 emissions to N fertilizers was correlated with N-induced crop yield (r = +0.39; P < 0.01), probably due to increased carbon substrates for Methanogens. Using CH 4 emission observations, this meta-analysis has identified dominant microbial processes that control net effects of N fertilizers on CH 4 emissions in rice soils. Finally, we have provided a conceptual model that included microbial processes and controlling factors to predict effects of N fertilizers on CH 4 emissions in rice soils.
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Affiliation(s)
- Kamaljit Banger
- Ecosystem Dynamics and Global Ecology (EDGE) Laboratory, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
- International Center for Climate and Global Change Research, Auburn University, Auburn, AL, 36849, USA
| | - Hanqin Tian
- Ecosystem Dynamics and Global Ecology (EDGE) Laboratory, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
- International Center for Climate and Global Change Research, Auburn University, Auburn, AL, 36849, USA
| | - Chaoqun Lu
- Ecosystem Dynamics and Global Ecology (EDGE) Laboratory, School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
- International Center for Climate and Global Change Research, Auburn University, Auburn, AL, 36849, USA
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Aronson EL, Vann DR, Helliker BR. Methane flux response to nitrogen amendment in an upland pine forest soil and riparian zone. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/2012jg001962] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Alam MS, Jia Z. Inhibition of methane oxidation by nitrogenous fertilizers in a paddy soil. Front Microbiol 2012; 3:246. [PMID: 22783249 PMCID: PMC3389332 DOI: 10.3389/fmicb.2012.00246] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 06/18/2012] [Indexed: 11/22/2022] Open
Abstract
Nitrogenous fertilizers are generally thought to have an important role in regulating methane oxidation. In this study, the effect of ammonium on methane oxidation activity was investigated in a paddy soil using urea at concentrations of 0, 50, 100, 200, and 400 μg N per gram dry weight soil (N/g.d.w.s) and ammonium sulfate at concentrations of 0, 50, and 200 μg N/g.d.w.s. The results of this study demonstrate that urea concentrations of 200 μg N/g.d.w.s. and above significantly inhibit methane oxidation activity, whereas no statistically significant difference was observed in methane oxidation activity among soil microcosms with urea concentrations of less than 200 μg N/g.d.w.s after incubation for 27 days. Similar results were obtained in a sense that methane oxidation activity was inhibited only when the ammonium sulfate concentration was 200 μg N/g.d.w.s in soil microcosms in this study. Phylogenetic analysis of pmoA genes showed that nitrogen fertilization resulted in apparent changes in the community composition of methane-oxidizing bacteria (MOB). Type I MOB displayed an increased abundance in soil microcosms amended with nitrogenous fertilizers, whereas type II MOB dominated the native soil. Furthermore, although no statistically significant relationship was observed between pmoA gene and amoA gene abundances, methane oxidation activity was significantly negatively correlated with nitrification activity in the presence of urea or ammonium sulfate. Our results indicate that the methane oxidation activity in paddy soils might be inhibited when the concentration of ammonium fertilizers is high and that the interactions between ammonia and methane oxidizers need to be further investigated.
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Affiliation(s)
- M. Saiful Alam
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese, Academy of Sciences, Nanjing, Jiangsu ProvinceP.R. China
- Graduate School of Chinese Academy of SciencesBeijing, P.R. China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese, Academy of Sciences, Nanjing, Jiangsu ProvinceP.R. China
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