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Yao X, Hu B. Methane-dependent denitrification by Methylomirabilis: an indirect nitrous oxide sink? Trends Microbiol 2024:S0966-842X(24)00179-3. [PMID: 39127550 DOI: 10.1016/j.tim.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]
Abstract
Methane-dependent complete denitrification primarily involves nitrate reduction to nitrite by ANME-2d archaea and nitrite reduction to dinitrogen by Methylomirabilis bacteria. 'Candidatus Methylomirabilis sinica' integrates the divisional labor. Physiological traits of this bacterium potentially enable the simultaneous reduction of N2O and CH4 emissions. This forum article explores these traits and possible microbial mechanisms for co-reduction, providing guidance for greenhouse gas management strategies.
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Affiliation(s)
- Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, 310058 Hangzhou, China; College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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2
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Qiu Z, Yu H, Zhu C, Shen W. NosZ I carrying microorganisms determine N 2O emissions from the subtropical paddy field under elevated CO 2 and strongly CO 2-responsive cultivar. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173255. [PMID: 38761936 DOI: 10.1016/j.scitotenv.2024.173255] [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: 12/14/2023] [Revised: 03/22/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Elevated CO2 (eCO2) decreases N2O emissions from subtropical paddy fields, but the underlying mechanisms remain to be investigated. Herein, the response of key microbial nitrogen cycling genes to eCO2 (ambient air +200 μmol CO2 mol-1) in four rice cultivars, including two weakly CO2-responsive (W27, H5) and two strongly CO2-responsive cultivars (Y1540, L1988), was investigated. Except for nosZ I, eCO2 did not significantly alter the abundance of the other genes. NosZ I was a crucial factor governing N2O emissions, especially under eCO2 and a strongly responsive cultivar. eCO2 affected the nosZ I gene abundance (p < 0.05), for instance, the nosZ I gene abundance of cultivar W27 increased from 1.53 × 107 to 2.86 × 107 copies g-1 dw soil (p < 0.05). In the nosZ I microbial community, the known taxa were mainly Pseudomonadota (phylum) (19.74-31.72 %) and Alphaproteobacteria (class) (0.56-13.12 %). In the nosZ I community assembly process, eCO2 enhanced the role of stochasticity, increasing from 35 % to 85 % (p < 0.05), thereby inducing diffusion limitations of weakly responsive cultivars to dominate (67 %). Taken together, the increase in nosZ I gene abundance is a potential reason for the alleviation of N2O emissions from subtropical paddy fields under eCO2.
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Affiliation(s)
- Zijian Qiu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Haiyang Yu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315800, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Weishou Shen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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3
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Zeng Y, Tan C, Zhang L, You L, Zheng W, Chen H, Peng H, Wu C, Liang Y. Long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174839. [PMID: 39025147 DOI: 10.1016/j.scitotenv.2024.174839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/11/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
The discovery of complete ammonia oxidizers (comammox) has dramatically altered our perception of nitrogen (N) biogeochemistry. However, their functional importance vs. the canonical ammonia oxidizers (i.e., ammonia oxidizing-archaea (AOA) and bacteria (AOB)) in agroecosystems is still poorly understood. Accordingly, a new assay using acetylene, 3,4-dimethylpyrazole phosphate (DMPP), and 1-octyne was adopted to assess the ammonia (NH3) oxidation and nitrous oxide (N2O) production activity of these functional guilds in a subtropical Inceptisol under long-term different fertilization regimes. These regimes include CK (no fertilizer control), synthetic fertilizer only (NPK), organic manure only (M) and organic manure plus synthetic fertilizer (MNPK). AOA dominated NH3 oxidation in the M treatment, while AOB dominated both NH3 oxidation and N2O production in all treatments except M. Comammox always played a minor role in both NH3 oxidation and N2O production across all treatments. Both M and MNPK treatments significantly increased the activity and growth of comammox. Compared to NPK, comammox exhibited increases of 270 % and 326 % in the NH3 oxidation rates, and increases of 1472 % and 563 % in the N2O production rates in M and MNPK, respectively. Random forest model revealed that copper (Cu), comammox abundance, and dissolved organic nitrogen (DON) were the most important predictors for the NH3 oxidation rates of comammox. Redundancy analyses (RDA) showed that fertilizer treatments significantly altered the community composition of NH3 oxidizers, and pH was the overarching parameter underpinning the community shift of the NH3 oxidizers. Overall, this study provides evidence that comammox play a minor yet unneglectable role in the nitrification of agroecosystems, and the long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol.
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Affiliation(s)
- Yu Zeng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Che Tan
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Zhang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lelin You
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Wanning Zheng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Chen
- Zhejiang Key Laboratory of Recycling and Eco-treatment of Waste Biomass, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Hongyun Peng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chunyan Wu
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yongchao Liang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Xie M, Lv M, Zhao Z, Li L, Jiang H, Yu Y, Zhang X, Liu P, Chen J. New insights of bacterial and eukaryotic phenotypes on the plastics collected from the typical natural habitat of the endangered crocodile lizard. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116541. [PMID: 38848637 DOI: 10.1016/j.ecoenv.2024.116541] [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: 02/14/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
Although accumulating evidence indicates that endangered animals suffer from plastic pollution, this has been largely overlooked. Here, we explored the bacteria and eukaryotes living in the plastics gathered from the natural habitat of the highly endangered crocodile lizard. The results demonstrated that the bacterial and eukaryotic communities on plastics formed a unique ecosystem that exhibited lower diversity than those in the surrounding water and soil. However, microbes displayed a more complex and stable network on plastic than that in water or soil, implying unique mechanisms of stabilization. These mechanisms enhanced their resilience and contributed to the provision of stable ecological services. Eukaryotes formed a simpler and smaller network than bacteria, indicating different survival strategies. The bacteria residing on the plastics played a significant role in carbon transformation and sequestration, which likely impacted carbon cycling in the habitat. Furthermore, microbial exchange between plastics and the crocodile lizard was observed, suggesting that plastisphere serves as a mobile gene bank for the exchange of information, including potentially harmful substances. Overall, microbes on plastic appear to significantly impact the crocodile lizard and its natural habitat via various pathways. These results provided novel insights into risks evaluation of plastic pollution and valuable guidance for government efforts in plastic pollutant control in nature reserves.
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Affiliation(s)
- Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Mei Lv
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Zhiwen Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Haiying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Yepin Yu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Xiujuan Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Ping Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China.
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Lidstrom ME. Direct Methane Removal from Air by Aerobic Methanotrophs. Cold Spring Harb Perspect Biol 2024; 16:a041671. [PMID: 37923397 PMCID: PMC11216182 DOI: 10.1101/cshperspect.a041671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
The rapid pace of climate change has created great urgency for short-term mitigation strategies. Appropriately, the long-term target for intervening in global warming is CO2, but experts suggest that methane should be a key short-term target. Methane has a warming impact 34 times greater than CO2 on a 100-year timescale, and 86 times greater on a 20-year timescale, and its short half-life in the atmosphere provides the opportunity for near-term positive climate impacts. One approach to removing methane is the use of bacteria for which methane is their sole carbon and energy source (methanotrophs). Such bacteria convert methane to CO2 and biomass, a potentially value-added product and co-benefit. If air above emissions sites with elevated methane is targeted, technology harnessing the aerobic methanotrophs has the potential to become economically viable and environmentally sound. This article discusses challenges and opportunities for using aerobic methanotrophs for methane removal from air, including the avoidance of increased N2O emissions.
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Affiliation(s)
- Mary E Lidstrom
- Department of Chemical Engineering, Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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Zhou Z, Shi X, Bhople P, Jiang J, Chater CCC, Yang S, Perez-Moreno J, Yu F, Liu D. Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120895. [PMID: 38626487 DOI: 10.1016/j.jenvman.2024.120895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 04/18/2024]
Abstract
Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.
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Affiliation(s)
- Ziyan Zhou
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Parag Bhople
- Crops, Environment, And Land Use Department, Environment Research Centre, Teagasc, Johnstown Castle, Wexford, Y35TC98, Ireland
| | - Jishao Jiang
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Caspar C C Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Plants, Photosynthesis, and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Shimei Yang
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jesus Perez-Moreno
- Colegio de Postgraduados, Campus Montecillo, Edafologia, Texcoco, 56230, Mexico
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - Dong Liu
- The Germplasm Bank of Wild Species & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Xiang F, Han L, Jiang S, Xu X, Zhang Z. Black soldier fly larvae mitigate greenhouse gas emissions from domestic biodegradable waste by recycling carbon and nitrogen and reconstructing microbial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33347-33359. [PMID: 38676863 DOI: 10.1007/s11356-024-33308-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
Black soldier fly larvae have been proven to reduce greenhouse gas emissions in the treatment of organic waste. However, the microbial mechanisms involved have not been fully understood. The current study mainly examined the dynamic changes of carbon and nitrogen, greenhouse gas emissions, the succession of microbial community structure, and changes in functional gene abundance in organic waste under larvae treatment and non-aeration composting. Thirty percent carbon and 55% nitrogen in the organic waste supplied were stored in larvae biomass. Compared to the non-aeration composting, the larvae bioreactor reduced the proportion of carbon and nitrogen converted into greenhouse gases (CO2, CH4, and N2O decreased by 62%, 87%, and 95%, respectively). 16S rRNA sequencing analysis indicated that the larvae bioreactor increased the relative abundance of Methanophaga, Marinobacter, and Campylobacter during the bioprocess, enhancing the consumption of CH4 and N2O. The metagenomic data showed that the intervention of larvae reduced the ratio of (nirK + nirS + nor)/nosZ in the residues, thereby reducing the emission of N2O. Larvae also increased the functional gene abundance of nirA, nirB, nirD, and nrfA in the residues, making nitrite more inclined to be reduced to ammonia instead of N2O. The larvae bioreactor mitigated greenhouse gas emissions by redistributing carbon and nitrogen and remodeling microbiomes during waste bioconversion, giving related enterprises a relative advantage in carbon trading.
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Affiliation(s)
- FangMing Xiang
- College of Environmental and Resource Sciences, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China
- JiaXing FuKang Biotechnology Company Limited, TongXiang Economic HiTech Zone, Building 1-19#, Development Ave 133, Tongxiang, 314515, People's Republic of China
| | - LuYing Han
- College of Environmental and Resource Sciences, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China
| | - ShuoYun Jiang
- College of Environmental and Resource Sciences, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, Hangzhou, 311121, People's Republic of China
| | - XinHua Xu
- College of Environmental and Resource Sciences, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China
| | - ZhiJian Zhang
- College of Environmental and Resource Sciences, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China.
- China Academy of West Region Development, Zhejiang University, YuHangTang Ave 866, Hangzhou, 310058, People's Republic of China.
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Chen KH, Feng J, Bodelier PLE, Yang Z, Huang Q, Delgado-Baquerizo M, Cai P, Tan W, Liu YR. Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields. Nat Commun 2024; 15:3471. [PMID: 38658559 PMCID: PMC11043409 DOI: 10.1038/s41467-024-47827-y] [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: 04/04/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13C-metagenome-assembled genomes and 13C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.
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Affiliation(s)
- Kang-Hua Chen
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiao Feng
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, The Netherlands
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, 41012, Spain
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
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Liu Z, Gu H, Yao Q, Jiao F, Hu X, Liu J, Jin J, Liu X, Wang G. Soil pH and carbon quality index regulate the biogeochemical cycle couplings of carbon, nitrogen and phosphorus in the profiles of Isohumosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171269. [PMID: 38423323 DOI: 10.1016/j.scitotenv.2024.171269] [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: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
Soil biogeochemical cycles are essential for regulating ecosystem functions and services. However, little knowledge has been revealed on microbe-driven biogeochemical processes and their coupling mechanisms in soil profiles. This study investigated the vertical distribution of soil functional composition and their contribution to carbon (C), nitrogen (N) and phosphorus (P) cycling in the humus horizons (A-horizons) and parent material horizons (C-horizons) in Udic and Ustic Isohumosols using shotgun sequencing. Results showed that the diversity and relative abundance of microbial functional genes was influenced by soil horizons and soil types. In A-horizons, the relative abundances of N mineralization and liable C decomposition genes were significantly greater, but the P cycle-related genes, recalcitrant C decomposition and denitrification genes were lower compared to C-horizons. While, Ustic Isohumosols had lower relative abundances of C decomposition genes but higher relative abundances of N mineralization and P cycling-related pathways compared to Udic Isohumosols. The network analysis revealed that C-horizons had more interactions and stronger stability of functional gene networks than in A-horizons. Importantly, our results provide new insights into the potential mechanisms for the coupling processes of soil biogeochemical cycles among C, N and P, which is mediated by specific microbial taxa. Soil pH and carbon quality index (CQI) were two sensitive indicators for regulating the relative abundances and the relationships of functional genes in biogeochemical cycles. This study contributes to a deeper understanding of the ecological functions of soil microorganisms, thus providing a theoretical basis for the exploration and utilization of soil microbial resources and the development of soil ecological control strategies.
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Affiliation(s)
- Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Yao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Feng Jiao
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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Xu X, Liu Y, Tang C, Yang Y, Yu L, Lesueur D, Herrmann L, Di H, Li Y, Li Q, Xu J. Microbial resistance and resilience to drought and rewetting modulate soil N 2O emissions with different fertilizers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170380. [PMID: 38281640 DOI: 10.1016/j.scitotenv.2024.170380] [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: 08/08/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
Future climate models indicate an enhanced severity of regional drought and frequent rewetting events, which may cause cascading impacts on soil nitrogen cycle and nitrous oxide (N2O) emissions, but the underlying microbial mechanism remains largely unknown. Here we report an incubation study that examined the impacts of soil moisture status and nitrification inhibitor (DCD) on the N2O-producers and N2O-reducers following the application of urea and composted swine manure in an acid soil. The soil moisture treatments included 100 % water-holding capacity (WHC) (wetting, 35.3 % gravimetric soil water content), 40 % WHC (drought, 7 % gravimetric soil water content), and 40 % to 100 % WHC (rewetting). The results showed that N2O emissions were significantly decreased under drought conditions and were significantly increased after rewetting. The resistance of ammonia-oxidizing bacteria and nosZII, which was inhibited by urea or manure application, modulated N2O emissions under drought conditions. The resilience of the functional guilds modulated their dominant role in N2O emissions with rewetting. Ammonia-oxidizing bacteria, nirS-type denitrifying bacteria and nosZI showed significant resilience in response to rewetting. Significant negative relationships were observed between N2O emissions and nosZII clade under wetting condition and between N2O emissions and nosZI clade after rewetting. Our results highlighted the importance of microbial resistance and resilience in modulating N2O emissions, which help to better understand the dominant way of N2O emissions, and consequently make efficient mitigation strategies under the global climate change.
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Affiliation(s)
- Xiaoya Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Yaowei Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Caixian Tang
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yihan Yang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lei Yu
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Didier Lesueur
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Eco&Sols, Hanoi, Viet Nam; Eco&Sols, Université de Montpellier (UMR), CIRAD, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut de Recherche pour le Développement (IRD), Montpellier SupAgro, 34060 Montpellier, France; Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Asia hub, Common Microbial Biotechnology Platform (CMBP), Hanoi, Viet Nam; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment-Deakin University, Melbourne, VIC 3125, Australia; Chinese Academy of Tropical Agricultural Sciences, Rubber Research Institute, Haikou, China
| | - Laetitia Herrmann
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Asia hub, Common Microbial Biotechnology Platform (CMBP), Hanoi, Viet Nam; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment-Deakin University, Melbourne, VIC 3125, Australia
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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11
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Zhong L, Li X, Sun Y, Xiao H, Tang Y, Wang R, Su X. Effects of microplastics on N 2O production and reduction potential in crop soils of northern China. CHEMOSPHERE 2024; 351:141256. [PMID: 38246503 DOI: 10.1016/j.chemosphere.2024.141256] [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: 08/22/2023] [Revised: 12/27/2023] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Microplastics (MPs) pollution are found to be increasing in vegetable soils and potentially affecting N2O production and their associated pathways; however, its specific effects remain unclear. Here, we selected two common MPs, PE and PP at four different concentration levels of 0, 0.5, 1.5 and 3%, and conducted several incubation experiments aiming to explore soil bacterial and fungal N2O production. Results showed that the bacteria were the main contributors for the production of N2O, regardless of the absence or presence of MPs; and its contribution was decreased with increasing concentrations of PE and PP. The nosZ clade I and II genes were positively correlated with N2O reduction rates, indicating a combined regulation on soil N2O reduction. PE significantly inhibited the bacterial nitrification and denitrification, but did not affect the total N2O production rates; while PP significantly reduced both the bacterial and fungal N2O production rates. The resistance of fungal N2O production to MPs pollution was stronger than that of the bacterial N2O production. It highlights that the MPs pollution could reduce the potential of N2O production and reduction, and thus disturb soil nitrogen cycling system; while the inhibition on N2O production via bacteria and fungi varies with different types of MPs. This study is conducive to an improved and more comprehensive understanding of the ecological impacts of MPs within the agroecosystem.
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Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China.
| | - Xinhao Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yuru Sun
- Beijing Construction Engineering Group Environmental Remediation Co., Ltd, National Engineering Laboratory for Site Remediation Technologies, Beijing, 100015, China
| | - Hui Xiao
- Institute of Agricultural Resources and Environment, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, 400715, China.
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12
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Stein LY. Agritech to Tame the Nitrogen Cycle. Cold Spring Harb Perspect Biol 2024; 16:a041668. [PMID: 37788889 PMCID: PMC10910340 DOI: 10.1101/cshperspect.a041668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While the Haber-Bosch process for N-fixation has enabled a steady food supply for half of humanity, substantial use of synthetic fertilizers has caused a radical unevenness in the global N-cycle. The resulting increases in nitrate production and greenhouse gas (GHG) emissions have contributed to eutrophication of both ground and surface waters, the growth of oxygen minimum zones in coastal regions, ozone depletion, and rising global temperatures. As stated by the Food and Agriculture Organization of the United Nations, agriculture releases ∼9.3 Gt CO2 equivalents per year, of which methane (CH4) and nitrous oxide (N2O) account for 5.3 Gt CO2 equivalents. N-pollution and slowing the runaway N-cycle requires a combined effort to replace chemical fertilizers with biological alternatives, which after a 10-yr span of usage could eliminate a minimum of 30% of ag-related GHG emissions (∼1.59 Gt), protect waterways from nitrate pollution, and protect soils from further deterioration. Agritech solutions include bringing biological fertilizers and biological nitrification inhibitors to the marketplace to reduce the microbial conversion of fertilizer nitrogen into GHGs and other toxic intermediates. Worldwide adoption of these plant-derived molecules will substantially elevate nitrogen use efficiency by crops while blocking the dominant source of N2O to the atmosphere and simultaneously protecting the biological CH4 sink. Additional agritech solutions to curtail N-pollution, soil erosion, and deterioration of freshwater supplies include soil-free aquaponics systems that utilize improved microbial inocula to enhance nitrogen use efficiency without GHG production. With adequate and timely investment and scale-up, microbe-based agritech solutions emphasizing N-cycling processes can dramatically reduce GHG emissions on short time lines.
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Affiliation(s)
- Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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13
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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14
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Yang X, Duan P, Liu Q, Wang K, Li D. Addition of cellulose and hemicellulose degrading microorganisms intensified nitrous oxide emission during composting. BIORESOURCE TECHNOLOGY 2024; 393:130100. [PMID: 38013032 DOI: 10.1016/j.biortech.2023.130100] [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: 08/10/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
This study aims to clarify the mechanisms underlying effects of inoculating cellulose and hemicellulose-degrading microorganisms on nitrous oxide (N2O) emissions during composting with silkworm excrement and mulberry branches. Inoculation with cellulose and hemicellulose-degrading microorganisms resulted in significant increases of total N2O emission by 10.4 ± 2.0 % (349.1 ± 6.2 mg N kg-1 dw) and 26.7 ± 2.1 % (400.6 ± 6.8 mg N kg-1 dw), respectively, compared to the control (316.3 ± 3.6 mg N kg-1 dw). The stimulation of N2O emission was attributed to the enhanced contribution of ammonia-oxidizing bacteria (AOB) and denitrifying bacteria to N2O production, as evidenced by the increased AOB amoA and denitrifying nirK gene abundances. Moreover, microbial inoculation stimulated N2O reduction to N2 owing to increased abundances of nosZⅠ and nosZⅠⅠ genes. These findings highlight the necessity to develop cost-effective and environmentally friendly strategies to reduce N2O emissions when cellulose and hemicellulose-degrading microorganisms are inoculated during composting.
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Affiliation(s)
- Xinyi Yang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China; Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Pengpeng Duan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China; Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Qiumei Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China; Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Kelin Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China; Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Dejun Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China; Institutional Center for Shared Technologies and Facilities of Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China.
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15
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Zhang F, Gu Z, Wang H, Wang R, Qing J, Xu X, Baoyin T, Zhong L, Rui Y, Li FY. Short term grazing increased growing-season N 2O production and decreased its reduction potential by reducing the abundance and expression of nosZ clade II gene in a semi-arid steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168361. [PMID: 37944603 DOI: 10.1016/j.scitotenv.2023.168361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 10/23/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023]
Abstract
Understanding nitrous oxide (N2O) production as well as reduction in response to grazing and mowing is essential for designing better management strategies to improve sustainability of grassland ecosystems. We evaluated how four years of grazing or mowing altered N2O production and reduction potential, gene abundance, and expression of microbial functional groups pertinent to N2O production in situ on a typical grassland in Inner Mongolia. In our study, we found that grazing dramatically raised soil ammonium (NH4+-N) and nitrate (NO3--N) concentrations, AOB gene abundance and potential of N2O production through nitrification (NN2O) and denitrification (DN2O) in summer, but lessened the expression of nosZ clade II gene in all seasons. Mowing had minor effect on soil inorganic nitrogen (N) concentrations. Mowing diminished the quantity of denitrification genes (narG and nosZ), expression of nosZ and nosZ clade II genes, and DN2O concentration. The expression and abundance of nosZ clade II gene were related to DN2. These results suggested that short-term grazing could enhance N2O production potential in peak growing season, while the reduction in abundance and expression of nosZ calde II gene might be an important contributor to the enhanced N2O production of semi-arid typical steppe grasslands.
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Affiliation(s)
- Feifan Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Zhibin Gu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Hongyue Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Ruying Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing 100101, China
| | - Taogetao Baoyin
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China.
| | - Yichao Rui
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology & Environment, Inner Mongolia University, Hohhot 010021, China
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16
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Yin Y, Kara-Murdoch F, Murdoch RW, Yan J, Chen G, Xie Y, Sun Y, Löffler FE. Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback. THE ISME JOURNAL 2024; 18:wrae027. [PMID: 38447133 PMCID: PMC10960958 DOI: 10.1093/ismejo/wrae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/08/2024]
Abstract
Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25 μM, followed by hydrogenotrophic (KI, 60-90 μM) and methylotrophic (KI, 110-130 μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.
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Affiliation(s)
- Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Fadime Kara-Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Yanchen Sun
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
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17
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Qiu L, Gou X, Kong Y, Tu F, Peng X, Xu L, Zhou S, Huang C, Chen Y, Liu L, Tu L. Nitrogen addition stimulates N 2O emissions via changes in denitrification community composition in a subtropical nitrogen-rich forest. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119274. [PMID: 37890399 DOI: 10.1016/j.jenvman.2023.119274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Microbially driven nitrification and denitrification play important roles in regulating soil N availability and N2O emissions. However, how the composition of nitrifying and denitrifying prokaryotic communities respond to long-term N additions and regulate soil N2O emissions in subtropical forests remains unclear. Seven years of field experiment which included three N treatments (+0, +50, +150 kg N ha-1 yr-1; CK, LN, HN) was conducted in a subtropical forest. Soil available nutrients, N2O emissions, net N mineralization, denitrification potential and enzyme activities, and the composition and diversity of nitrifying and denitrifying communities were measured. Soil N2O emissions from the LN and HN treatments increased by 42.37% and 243.32%, respectively, as compared to the CK. Nitrogen addition significantly inhibited nitrification (N mineralization) and significantly increased denitrification potentials and enzymes. Nitrification and denitrification abundances (except nirK) were significantly lower in the HN, than CK treatment and were not significantly correlated with N2O emissions. Nitrogen addition significantly increased nirK abundance while maintaining the positive effects of denitrification and N2O emissions to N deposition, challenging the conventional wisdom that long-term N addition reduces N2O emissions by inhibiting microbial growth. Structural equation modeling showed that the composition, diversity, and abundance of nirS- and nirK-type denitrifying prokaryotic communities had direct effects on N2O emissions. Mechanistic investigations have revealed that denitrifier keystone taxa transitioned from N2O-reducing (complete denitrification) to N2O-producing (incomplete denitrification) with increasing N addition, increasing structural complexity and diversity of the denitrifier co-occurrence network. These results significantly advance current understanding of the relationship between denitrifying community composition and N2O emissions, and highlight the importance of incorporating denitrifying community dynamics and soil environmental factors together in models to accurately predict key ecosystem processes under global change.
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Affiliation(s)
- Lingjun Qiu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xin Gou
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuemei Kong
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Fangyang Tu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xia Peng
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lin Xu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shixing Zhou
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Congde Huang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuqin Chen
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Li Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lihua Tu
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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18
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Wang X, Xiang B, Li J, Zhang M, Frostegard A, Bakken L, Zhang X. Using adaptive and aggressive N 2O-reducing bacteria to augment digestate fertilizer for mitigating N 2O emissions from agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166284. [PMID: 37586512 DOI: 10.1016/j.scitotenv.2023.166284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Nitrous oxide (N2O) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying N2O-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of N2O, ability to grow in organic waste, and ability to survive in farmland soil. In this study, we enriched such organisms by sequential anaerobic batch incubations with N2O and reciprocating inoculation between the sterilized substrates of anaerobic manure digestate and soils. 16S rDNA amplicon sequencing and metagenomics analysis showed that a cluster of bacteria containing nosZ genes encoding N2O-reductase, was enriched during the incubation process. Strains of several dominant members were then isolated and characterized, and three of them were found to harbor the nosZ gene but none of the other denitrifying genes, thus qualifying as NNRB. The selected isolates were tested for their capacities to reduce N2O emissions from three different typical Chinese farmland soils. The results indicated the significant mitigation effect of these isolates, even in very acidic red soil. In conclusion, this study demonstrated a strategy to engineer the soil microbiome with promising NNRB with high adaptability to livestock manure digestate as well as different agricultural soils, which would be suitable for developing novel fertilizer for farmland application to efficiently mitigate the N2O emissions from agricultural soils.
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Affiliation(s)
- Xinhui Wang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baoyu Xiang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Li
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Asa Frostegard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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19
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Xue Y, Chen H, Xiao P, Jin L, Logares R, Yang J. Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:769-782. [PMID: 37688478 PMCID: PMC10667671 DOI: 10.1111/1758-2229.13196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/17/2023] [Indexed: 09/11/2023]
Abstract
Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12-month high-frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre-mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll-a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi-nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.
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Affiliation(s)
- Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Huihuang Chen
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | - Peng Xiao
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Lei Jin
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
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20
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Quiton-Tapia S, Balboa S, Omil F, Garrido JM, Suarez S. How efficiently does a metabolically enhanced system with denitrifying anaerobic methane oxidizing microorganisms remove antibiotics? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122033. [PMID: 37348697 DOI: 10.1016/j.envpol.2023.122033] [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: 04/12/2023] [Revised: 05/26/2023] [Accepted: 06/10/2023] [Indexed: 06/24/2023]
Abstract
In this work, the novel N-damo (Nitrite dependent anaerobic methane oxidation) process was investigated at high biomass activities for its potential to remove simultaneously nitrite and methane, as well as selected antibiotics commonly found in sewage in trace amounts. For this purpose, two MBRs were operated at three high nitrite loading rates (NLRs), namely 76 ± 9.9, 161.5 ± 11.4 and 215.2 ± 24.2 mg N-NO⁻2 L-1 d-1, at long-term operation. The MBRs performance achieved a significantly high nitrite removal activity for an N-damo process (specific denitrifying activity of up to 540 mg N-NO⁻2 g-1 VSS d-1), even comparable to heterotrophic denitrification values. In this study, we have implemented a novel operational strategy that sets our work apart from previous studies with similar bioreactors. Specifically, we have introduced Cerium as a trace element in the feeding medium, which serves as a key differentiating factor. It allowed maintaining a stable reactor operation at high NLRs. Microbial community composition evidenced that both MBRs were dominated with N-damo bacteria (67-87% relative abundance in period III and I, respectively). However, a decrease in functional N-damo bacteria (Candidatus Methylomirabilis) abundance was observed during the increase in biomass activity and concentration, concomitantly with an increase of the other minor families (Hypomicrobiaceae and Xanthobacteraceae). Most of the selected antibiotics showed high biotransformation such as sulfamethoxazole, trimethoprim, cefalexin and azithromycin, whereas others such as roxithromycin and clarithromycin were only partially degraded (20-35%). On the contrary, ciprofloxacin showed almost no removal. Despite the metabolic enhancement, no apparent increase on the antibiotic removal was observed throughout the operation, suggesting that microbiological composition was of greater influence than its primary metabolic activity on the removal of antibiotics.
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Affiliation(s)
- Silvana Quiton-Tapia
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Sabela Balboa
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Francisco Omil
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Juan Manuel Garrido
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
| | - Sonia Suarez
- CRETUS Institute. Department of Chemical Engineering, School of Engineering, Universidade de Santiago de Compostela, Rúa Lope Gómez de Marzoa, E-15782, Santiago de Compostela, Spain.
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21
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Shang S, Song M, Wang C, Dou X, Wang J, Liu F, Zhu C, Wang S. Decrease of nitrogen cycle gene abundance and promotion of soil microbial-N saturation restrain increases in N 2O emissions in a temperate forest with long-term nitrogen addition. CHEMOSPHERE 2023; 338:139378. [PMID: 37419152 DOI: 10.1016/j.chemosphere.2023.139378] [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: 04/04/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Increases in soil available nitrogen (N) influence N-cycle gene abundances and emission of nitrous oxide (N2O), which is primarily due to N-induced soil acidification in forest. Moreover, the extent of microbial-N saturation could control microbial activity and N2O emission. The contributions of N-induced alterations of microbial-N saturation and N-cycle gene abundances to N2O emission have rarely been quantified. Here, the mechanism underlying N2O emission under N additions (three chemical forms of N, i.e., NO3--N, NH4+-N and NH4NO3-N, and each at two rates, 50 and 150 kg N ha-1 year-1, respectively) spanning 2011-2021 was investigated in a temperate forest in Beijing. Results showed N2O emissions increased at both low and high N rates of all the three forms compared with control during the whole experiment. However, N2O emissions were lower in high rate of NH4NO3-N and NH4+-N treatments than the corresponding low N rates in the recent three years. Effects of N on microbial-N saturation and abundances of N-cycle genes were dependent on the N rate and form as well as experimental time. Specifically, negative effects of N on N-cycle gene abundances and positive effects of N on microbial-N saturation were demonstrated in high N rate treatments, particularly with NH4+ addition during 2019-2021. Such effects were associated with soil acidification. A hump-backed trend between microbial-N saturation and N2O emissions was observed, suggesting N2O emissions decreased with increase of the microbial-N saturation. Furthermore, N-induced decreases in N-cycle gene abundances restrained N2O emissions. In particular, the nitrification process, dominated by ammonia-oxidize archaea, is critical to determination of N2O emissions in response to the N addition in the temperate forest. We confirmed N addition promoted soil microbial-N saturation and reduced N-cycle gene abundances, which restrained the continuous increase in N2O emissions. It is important for understanding the forest-N-microbe nexus under climate change.
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Affiliation(s)
- Shuaishuai Shang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Minghua Song
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, A11, Datun Road, Chaoyang District, Beijing, 100101, China
| | - Chunmei Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaomin Dou
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxin Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Fangfang Liu
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Chenying Zhu
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Shiqi Wang
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
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22
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Xue R, Zhang K, Liu X, Jiang B, Luo H, Li M, Mo Y, Liu C, Li L, Fan L, Chen W, Cheng L, Chen J, Chen F, Zhuang D, Qing J, Lin Y, Zhang X. Variations of methane fluxes and methane microbial community composition with soil depth in the riparian buffer zone of a sponge city park. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117823. [PMID: 37129967 DOI: 10.1016/j.jenvman.2023.117823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/10/2023] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Riparian buffers benefit both natural and man-made ecosystems by preventing soil erosion, retaining soil nutrients, and filtering pollutants. Nevertheless, the relationship between vertical methane fluxes, soil carbon, and methane microbial communities in riparian buffers remains unclear. This study examined vertical methane fluxes, soil carbon, and methane microbial communities in three different soil depths (0-5 cm, 5-10 cm, and 10-15 cm) within a riparian buffer of a Sponge City Park for one year. Structural equation model (SEM) results demonstrated that vertical methane fluxes varied with soil depths (λ = -0.37) and were primarily regulated by methanogenic community structure (λ = 0.78). Notably, mathematical regression results proposed that mcrA/pmoA ratio (R2 = 0.8) and methanogenic alpha diversity/methanotrophic alpha diversity ratio (R2 = 0.8) could serve as valid predictors of vertical variation in methane fluxes in the riparian buffer of urban river. These findings suggest that vertical variation of methane fluxes in riparian buffer soils is mainly influenced by carbon inputs and methane microbial abundance and community diversity. The study's results quantitatively the relationship between methane fluxes in riparian buffer soils and abiotic and biotic factors in the vertical direction, therefore contributing to the further development of mathematical models of soil methane emissions.
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Affiliation(s)
- Ru Xue
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China; Limnology, Department of Ecology and Genetics, Uppsala University, Uppsala, 75236, Sweden
| | - Ke Zhang
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China; Sichuan Higher Education Engineering Research Center for Disaster Prevention and Mitigation of Village Construction, Sichuan Agricultural University, Chengdu, 611830, China
| | - Xiaoling Liu
- Department of Information Engineering, Sichuan Water Conservancy Vocational College, Chengdu, 611231, China
| | - Bing Jiang
- Dujiangyan Campus, Sichuan Agricultural University, Chengdu, 611830, China
| | - Hongbing Luo
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China; Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China; Sichuan Higher Education Engineering Research Center for Disaster Prevention and Mitigation of Village Construction, Sichuan Agricultural University, Chengdu, 611830, China.
| | - Mei Li
- School of Urban and Rural Construction, Chengdu University, Chengdu, 610106, China
| | - You Mo
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China; Sichuan Higher Education Engineering Research Center for Disaster Prevention and Mitigation of Village Construction, Sichuan Agricultural University, Chengdu, 611830, China
| | - Cheng Liu
- Dujiangyan Campus, Sichuan Agricultural University, Chengdu, 611830, China
| | - Lin Li
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Liangqian Fan
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Wei Chen
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Lin Cheng
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Jia Chen
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Fenghui Chen
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Daiwei Zhuang
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Jing Qing
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Yuanmao Lin
- Department of Municipal Engineering, College of Civil Engineering, Sichuan Agricultural University, Chengdu, 611830, China
| | - Xiaohong Zhang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China
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23
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Quitón-Tapia S, Trueba-Santiso A, Garrido JM, Suárez S, Omil F. Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics. BIORESOURCE TECHNOLOGY 2023:129476. [PMID: 37429551 DOI: 10.1016/j.biortech.2023.129476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to achieve carbon-neutral wastewater treatment solutions, aligned with the sustainable development goals. Here, the enzymatic activities in a membrane bioreactor highly enriched in N-damo bacteria operated at high nitrogen removal rates were investigated. Metaproteomic analyses, with a special focus on metalloenzymes, revealed the complete enzymatic route of N-damo including their unique nitric oxide dismutases. The relative protein abundance evidenced that "Ca. Methylomirabilis lanthanidiphila" was the predominant N-damo species, attributed to the induction of its lanthanide-binding methanol dehydrogenase in the presence of cerium. Metaproteomics also disclosed the activity of the accompanying taxa in denitrification, methylotrophy and methanotrophy. The most abundant functional metalloenzymes from this community require copper, iron, and cerium as cofactors which was correlated with the metal consumptions in the bioreactor. This study highlights the usefulness of metaproteomics for evaluating the enzymatic activities in engineering systems to optimize microbial management.
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Affiliation(s)
- Silvana Quitón-Tapia
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Alba Trueba-Santiso
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain.
| | - Juan M Garrido
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Sonia Suárez
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
| | - Francisco Omil
- CRETUS, Department of Chemical Engineering, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Galicia, Spain
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24
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Guo P, Wang Q, Ni L, Xu S, Zheng D, Wang Y, Cai F, Cui M, Zheng Z, Gao X, Zhang D. Improved simultaneous nitrification-denitrification in fixed-bed baffled bioreactors treating mariculture wastewater: Performance and microbial community behaviors. BIORESOURCE TECHNOLOGY 2023:129468. [PMID: 37429548 DOI: 10.1016/j.biortech.2023.129468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
As mariculture develops, wastewater treatment becomes crucial. In this study, fixed-bed baffled reactors (FBRs) packed with carbon fiber (CFBR) or polyurethane (PFBR) as biofilm carriers were used for mariculture wastewater treatment. Under salinity shocks between 0.10 and 30.00 g/L, the reactors showed efficient and stable nitrogen removal capacities, and the maximum NH4+-N removal rates were 107.31 and 105.42 mg/(L·d) for CFBR and PFBR, respectively, with an initial NH4+-N concentration of 120.00 mg/L. Further, in the independent aerobic chambers of the FBRs for nitrogen removal, taxa enrichment varied depending on the biofilm carrier, and the assembly process was more deterministic in CFBR than in PFBR. Two distinct clusters representing the spatial distribution of the adhering and deposited sludge in CFBR and the front and rear compartments in PFBR were noted. Furthermore, microbial interactions were more numerous and stable in CFBR. These findings improve the application prospects of FBRs in mariculture wastewater treatment.
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Affiliation(s)
- Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Qiong Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Lingfang Ni
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Silong Xu
- School of Chemistry, and Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, Xi'an Jiaotong University, Xi'an 710049, China
| | - Daoqiong Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Fang Cai
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mingyu Cui
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Zhiwei Zheng
- Shanghai Yuming Technology Co., Ltd., Shanghai 201802, China
| | - Xiuqing Gao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; College of Biology and Pharmacy, Three Gorges University, Yichang 443002, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China.
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25
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Pan B, Liu S, Wang Y, Li D, Li M. FT-ICR-MS combined with fluorescent spectroscopy reveals the driving mechanism of the spatial variation in molecular composition of DOM in 22 plateau lakes. ENVIRONMENTAL RESEARCH 2023:116272. [PMID: 37276978 DOI: 10.1016/j.envres.2023.116272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 06/07/2023]
Abstract
Dissolved organic matter (DOM) is the largest carbon pool and directly affects the biogeochemistry in lakes. In the current study, fourier transform ion cyclotron mass spectrometry (FT-ICR-MS) combined with fluorescent spectroscopy was used to assess the molecular composition and driving mechanism of DOM in 22 plateau lakes in Mongolia Plateau Lakes Region (MLR), Qinghai Plateau Lakes Region (QLR) and Tibet Plateau Lakes Region (TLR) of China. The limnic dissolved organic carbon (DOC) content ranged from 3.93 to 280.8 mg L-1 and the values in MLR and TLR were significantly higher than that in QLR. The content of lignin was the highest in each lake and showed a gradually decreasing trend from MLR to TLR. Random forest model and structural equation model implied that altitude played an important role in lignin degradation while the contents of total nitrogen (TN) and chlorophyll a (Chl-a) have a great influence on the increase of DOM Shannon index. Our results also suggested that the inspissation of DOC and the promoted endogenous DOM production caused by the inspissation of nutrient resulted in a positive relationship between limnic DOC content and limnic factors such as salinity, alkalinity and nutrient concentration. From MLR to QLR and TLR, the molecular weight and the number of double bonds gradually decreased but the humification index (HIX) also decreased. In addition, from the MLR to the TLR, the proportion of lignin gradually decreased, while the proportion of lipid gradually increased. Both above results suggested that photodegradation was dominated in lakes of TLR, while microbial degradation was dominated in lakes of MLR.
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Affiliation(s)
- Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, 710048, Shaanxi, PR China
| | - Siwan Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yeyong Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Dianbao Li
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, 710048, Shaanxi, PR China
| | - Ming Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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26
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Zhu Y, Xu Y, Xu J, Meidl P, He Y. Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131548. [PMID: 37141779 DOI: 10.1016/j.jhazmat.2023.131548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/06/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023]
Abstract
PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H2S and CH4 emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.
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Affiliation(s)
- Yanjie Zhu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China; College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peter Meidl
- Institute of Biology, Freie Universität Berlin, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China.
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27
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Khairunisa BH, Loganathan U, Ogejo JA, Mukhopadhyay B. Nitrogen transformation processes catalyzed by manure microbiomes in earthen pit and concrete storages on commercial dairy farms. ENVIRONMENTAL MICROBIOME 2023; 18:32. [PMID: 37041573 PMCID: PMC10091836 DOI: 10.1186/s40793-023-00483-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Storing manure is an essential aspect of nutrient management on dairy farms. It presents the opportunity to use manure efficiently as a fertilizer in crop and pasture production. Typically, the manure storages are constructed as earthen, concrete, or steel-based structures. However, storing manure can potentially emit aerial pollutants to the atmosphere, including nitrogen and greenhouse gases, through microbial and physicochemical processes. We have characterized the composition of the microbiome in two manure storage structures, a clay-lined earthen pit and an aboveground concrete storage tank, on commercial dairy farms, to discern the nitrogen transformation processes, and thereby, inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2, and 2.1-2.75 m below the surface) of the storages, identifying a set of Amplicon Sequence Variant (ASVs) and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to gaseous N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. The nitrate-transformation linked ASVs were more prevalent at the near-surface locations and all depths of the inlet. Anammox bacteria and archaeal or bacterial autotrophic nitrifiers were not detected in either storage. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N2O, and methane.
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Affiliation(s)
- Bela Haifa Khairunisa
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Usha Loganathan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jactone A Ogejo
- Department of Biological System Engineering, Blacksburg, VA, 24061, USA.
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, 24061, USA.
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24061, USA.
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Xie L, Liu D, Chen Z, Niu Y, Meng L, Ding W. Non-native Brachiaria humidicola with biological nitrification inhibition capacity stimulates in situ grassland N2O emissions. Front Microbiol 2023; 14:1127179. [PMID: 37007459 PMCID: PMC10064092 DOI: 10.3389/fmicb.2023.1127179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/27/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionBrachiaria humidicola, a tropical grass, could release root exudates with biological nitrification inhibition (BNI) capacity and reduce soil nitrous oxide (N2O) emissions from grasslands. However, evidence of the reduction effect in situ in tropical grasslands in China is lacking.MethodsTo evaluate the potential effects of B. humidicola on soil N2O emissions, a 2-year (2015–2017) field experiment was established in a Latosol and included eight treatments, consisting of two pastures, non-native B. humidicola and a native grass, Eremochloa ophiuroide, with four nitrogen (N) application rates. The annual urea application rates were 0, 150, 300, and 450 kg N ha−1.ResultsThe average 2-year E. ophiuroides biomass with and without N fertilization were 9.07–11.45 and 7.34 t ha−1, respectively, and corresponding values for B. humidicola increased to 31.97–39.07 and 29.54 t ha−1, respectively. The N-use efficiencies under E. ophiuroide and B. humidicola cultivation were 9.3–12.0 and 35.5–39.4%, respectively. Annual N2O emissions in the E. ophiuroides and B. humidicola fields were 1.37 and 2.83 kg N2O-N ha−1, respectively, under no N fertilization, and 1.54–3.46 and 4.30–7.19 kg N2O-N ha−1, respectively, under N fertilization.DiscussionsAccording to the results, B. humidicola cultivation increased soil N2O emissions, especially under N fertilization. This is because B. humidicola exhibited the more effective stimulation effect on N2O production via denitrification primarily due to increased soil organic carbon and exudates than the inhibition effect on N2O production via autotrophic nitrification. Annual yield-scaled N2O emissions in the B. humidicola treatment were 93.02–183.12 mg N2O-N kg−1 biomass, which were significantly lower than those in the E. ophiuroides treatment. Overall, our results suggest that cultivation of the non-native grass, B. humidicola with BNI capacity, increased soil N2O emissions, while decreasing yield-scaled N2O emissions, when compared with native grass cultivation.
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Affiliation(s)
- Lu Xie
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Deyan Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuhui Niu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Lei Meng
- College of Tropical Crops, Hainan University, Haikou, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Weixin Ding,
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Liu B, Gao J, Xue M, Lu B, Ye C, Liu J, Yang J, Qian J, Xu X, Wang W, Tao Y, Ao W. High exogenous humus inhibits greenhouse gas emissions from steppe lakes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 319:120946. [PMID: 36574810 DOI: 10.1016/j.envpol.2022.120946] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Although freshwater lakes are considered to be an important source of greenhouse gas (GHG) emissions, the potential driving mechanisms of such emissions are not well understood, especially in steppe lakes. In this study, the GHG emission characteristics in Hulun Lake Basin, including Hulun Lake, Beier Lake, Wulannuoer Lake, and their surrounding watersheds were investigated. The average methane (CH4) and nitrous oxide (N2O) emission fluxes released from rivers were 67.84 ± 20.53 and 0.11 ± 0.04 μg m-2·min-1, which were larger than those of lakes, with values of 28.60 ± 13.02 and 0.06 ± 0.02 μg m-2·min-1, respectively. Conversely, the average carbon dioxide (CO2) emission flux from lakes (1816.58 ± 498.98 μg m-2·min-1) was higher than that of rivers of (1795.41 ± 670.49 μg m-2·min-1). The water in Hulun Lake Basin was rich in organic matter and had a high chemical oxygen demand (COD). Three-dimensional fluorescence combined with a parallel factor analysis (3D-EEM-PARAFAC) demonstrated that the organic matter was composed of four humus types (from Component 1 (C1) to Component 4 (C4)), of which, C1 and C4 were terrestrial humus. The fluorescence index (FI) and humification index (HIX) indicated that the organic matter in the water was mainly imported from exogenous humus. The GHG emission fluxes were negatively correlated with these four components, indicating that GHG emissions were mainly affected by the organic matter source and components, and humus was the most important factor that inhibited GHG emissions in steppe lakes. However, the GHG emission flux was relatively high in some areas of the lake, especially in areas with high nutrient levels or where algal blooms occurred, as evidenced by the significantly positive correlations with total nitrogen (TN), total phosphorous (TP), and chlorophyll-a (chl-a) (p < 0.01). The algae-derived organic matter simulated the decomposition of refractory humus, thus, promoting GHG emissions. These findings are crucial for accurately evaluating the GHG emission fluxes, understanding the carbon cycle, and proposing future management strategies for steppe lakes.
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Affiliation(s)
- Bo Liu
- School of Geographical Science, Nantong University, Nantong, 226019, China; State of Environmental Protection Scientific Observation and Research Station for Ecological Environment of Hulun Lake Wetland, Hulunbuir, 021008, China
| | - Jin Gao
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
| | - Mengyong Xue
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Binfu Lu
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Chenghui Ye
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Jiangmin Liu
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Jiasen Yang
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
| | - Jiale Qian
- School of Geographical Science, Nantong University, Nantong, 226019, China
| | - Xiaoguang Xu
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
| | - Wenlin Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, 210042, China; State of Environmental Protection Scientific Observation and Research Station for Ecological Environment of Hulun Lake Wetland, Hulunbuir, 021008, China.
| | - Yulong Tao
- Hulunbuir Academy of Inland Lakes in Northern Cold and Arid Areas, Hulunbuir, 021008, China; State of Environmental Protection Scientific Observation and Research Station for Ecological Environment of Hulun Lake Wetland, Hulunbuir, 021008, China
| | - Wen Ao
- Hulunbuir Academy of Inland Lakes in Northern Cold and Arid Areas, Hulunbuir, 021008, China; State of Environmental Protection Scientific Observation and Research Station for Ecological Environment of Hulun Lake Wetland, Hulunbuir, 021008, China
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Xing CY, Li H, Li Q, Lu LH, Li Z. Shifts in composition and function of bacterial communities reveal the effect of small barriers on nitrous oxide and methane accumulation in fragmented rivers. Front Microbiol 2023; 14:1110025. [PMID: 36896435 PMCID: PMC9990636 DOI: 10.3389/fmicb.2023.1110025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Rivers are often blocked by barriers to form different habitats, but it is not clear whether this change will affect the accumulation of N2O and CH4 in rivers. Here, low barriers (less than 2 m, LB) increased N2O concentration by 1.13 times and CH4 decreased by 0.118 times, while high barriers (higher than 2 m, less than 5 m high, HB) increased N2O concentration by 1.19 times and CH4 by 2.76 times. Co-occurrence network analysis indicated LB and HB can promote the enrichment of Cyanobium and Chloroflexi, further limiting complete denitrification and increasing N2O accumulation. The LB promotes methanotrophs (Methylocystis, Methylophilus, and Methylotenera) to compete with denitrifiers (Pseudomonas) in water, and reduce CH4 accumulation. While the HB can promote the methanotrophs to compete with nitrifiers (Nitrosospira) in sediment, thus reducing the consumption of CH4. LB and HB reduce river velocity, increase water depth, and reduce dissolved oxygen (DO), leading to enrichment of nirS-type denitrifiers and the increase of N2O concentration in water. Moreover, the HB reduces DO concentration and pmoA gene abundance in water, which can increase the accumulation of CH4. In light of the changes in the microbial community and variation in N2O and CH4 accumulation, the impact of fragmented rivers on global greenhouse gas emissions merits further study.
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Affiliation(s)
- Chong-Yang Xing
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institutes of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
| | - Hang Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institutes of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
| | - Qi Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institutes of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
| | - Lun-Hui Lu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institutes of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
| | - Zhe Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institutes of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
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Aryal B, Gurung R, Camargo AF, Fongaro G, Treichel H, Mainali B, Angove MJ, Ngo HH, Guo W, Puadel SR. Nitrous oxide emission in altered nitrogen cycle and implications for climate change. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120272. [PMID: 36167167 DOI: 10.1016/j.envpol.2022.120272] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/28/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N2O) emissions, which are accelerating at an unprecedented rate. N2O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N2O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N2O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N2O generation. The authors also estimate the N2O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N2O-N yr-1 in 2050. In order to minimize and tackle the N2O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.
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Affiliation(s)
- Babita Aryal
- Naaya Aayam Multidisciplinary Institute, NAMI, University of Northampton, Jorpati, Kathmandu, Nepal
| | - Roshni Gurung
- Naaya Aayam Multidisciplinary Institute, NAMI, University of Northampton, Jorpati, Kathmandu, Nepal
| | - Aline F Camargo
- Federal University of Santa Catarina, Post-graduation Program in Biotechnology and Biosciences, Florianopólis, Brazil; Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul, Erechim, Brazil
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, 88040-900, Florianópolis, SC, Brazil
| | - Helen Treichel
- Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul, Erechim, Brazil
| | - Bandita Mainali
- School of Engineering and Mathematical Sciences, La Trobe University, Bendigo, VIC, 3550, Australia; School of Engineering, Macquarie University, Sydney, Australia
| | - Michael J Angove
- Department of Pharmacy and Biomedical Science, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bendigo, VIC-3550, Australia
| | - Huu Hao Ngo
- Faculty of Engineering, University of Technology Sydney (UTS), PO Box 123, Broadway, NSW, 2007, Australia
| | - Wenshan Guo
- Faculty of Engineering, University of Technology Sydney (UTS), PO Box 123, Broadway, NSW, 2007, Australia
| | - Shukra Raj Puadel
- Department of Civil Engineering, Pulchowk Campus, Institute of Engineering, Tribhuwan University, Pulchowk, Lalitpur, 44700, Nepal; Department of Environmental Engineering, College of Science and Technology, Korea University, Sejong, Republic of Korea.
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Huang D, Gao L, Cheng M, Yan M, Zhang G, Chen S, Du L, Wang G, Li R, Tao J, Zhou W, Yin L. Carbon and N conservation during composting: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156355. [PMID: 35654189 DOI: 10.1016/j.scitotenv.2022.156355] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Composting, as a conventional solid waste treatment method, plays an essential role in carbon and nitrogen conservation, thereby reducing the loss of nutrients and energy. However, some carbon- and nitrogen-containing gases are inevitably released during the process of composting due to the different operating conditions, resulting in carbon and nitrogen losses. To overcome this obstacle, many researchers have been trying to optimize the adjustment parameters and add some amendments (i.e., pHysical amendments, chemical amendments and microbial amendments) to reduce the losses and enhance carbon and nitrogen conservation. However, investigation regarding mechanisms for the conservation of carbon and nitrogen are limited. Therefore, this review summarizes the studies on physical amendments, chemical amendments and microbial amendments and proposes underlying mechanisms for the enhancement of carbon and nitrogen conservation: adsorption or conversion, and also evaluates their contribution to the mitigation of the greenhouse effect, providing a theoretical basis for subsequent composting-related researchers to better improve carbon and nitrogen conservation measures. This paper also suggests that: assessing the contribution of composting as a process to global greenhouse gas mitigation requires a complete life cycle evaluation of composting. The current lack of compost clinker impact on carbon and nitrogen sequestration capacity of the application site needs to be explored by more research workers.
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Affiliation(s)
- Danlian Huang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China.
| | - Lan Gao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Min Cheng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Ming Yan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Gaoxia Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Sha Chen
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Li Du
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Guangfu Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Ruijin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Jiaxi Tao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Wei Zhou
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
| | - Lingshi Yin
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China
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Zhang Y, Wu X, Chen C, Xu J, Dong F, Liu X, Li X, Zheng Y. Application of thifluzamide alters microbial network structure and affects methane cycle genes in rice-paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155769. [PMID: 35526624 DOI: 10.1016/j.scitotenv.2022.155769] [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: 12/24/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Thifluzamide is an effective agent for controlling rice sheath blight and has a long half-life in soil. However, the effects of thifluzamide on the abundance of microbes harboring methane-cycle genes and soil microbial community assembly patterns are not well known. Thus, we conducted a three-month indoor mesocosm experiment to ascertain the effects of thifluzamide (0.05, 0.5, and 5 mg kg-1 soil; 0.05 mg kg-1 soil being recommended) on bacterial and archaeal community structure and on the abundance of methanogen genes using two typical paddy soils: sandy soil from Hangzhou (HZ) and loam sandy soil from Jiansanjiang (JSJ). The effects of thifluzamide on soil microorganisms were related to soil type. In JSJ loam sandy soil, thifluzamide significantly increased bacterial α diversity after 7-30 d and archaeal α diversity at 30 and 60 d. In HZ sandy soil, however, α diversity did not change significantly. Network analysis showed that thifluzamide-treated soils possessed more complex networks with more total nodes and links, a higher average degree of connectivity, and more keystone species. Thifluzamide application increased the number of keystone species associated with methane production in both types of paddy soil. A relatively greater number of modules were significantly negatively correlated with mcrA abundance in the HZ T10 network, but more modules were positively correlated with mcrA abundance in the JSJ T100 network. The half-life of thifluzamide varied for the different doses, i.e., from 152.0 to 419.6 d. The results reveal that methane-cycle genes, soil microbiome assembly, and interactions among microbial species all change in response to thifluzamide stress.
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Affiliation(s)
- Ying Zhang
- College of Plant Protection, Hunan Agricultural University, Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Changsha 410128, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China; Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Xiaohu Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Caijun Chen
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Jun Xu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Fengshou Dong
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Xingang Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
| | - Xiaogang Li
- College of Plant Protection, Hunan Agricultural University, Southern Regional Collaborative Innovation Center for Grain and Oil Crops, Changsha 410128, China.
| | - Yongquan Zheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agricultural Product Quality and Safety, Ministry of Agriculture, Beijing, 100193, China
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions. NITROGEN 2022. [DOI: 10.3390/nitrogen3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.
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Müller C, Zhang L, Zipfel S, Topitsch A, Lutz M, Eckert J, Prasser B, Chami M, Lü W, Du J, Einsle O. Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature 2022; 608:626-631. [PMID: 35896743 DOI: 10.1038/s41586-022-05015-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N2O) from soils and industrial processes have increased considerably over the last decades1-3. As the final step of bacterial denitrification, N2O is reduced to chemically inert N2 (refs. 1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N2OR) (ref. 5). The assembly of its unique [4Cu:2S] active site cluster CuZ requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. 4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N2OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu+ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N2OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N2OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N2OR.
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Affiliation(s)
- Christoph Müller
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sara Zipfel
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Annika Topitsch
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marleen Lutz
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Johannes Eckert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Benedikt Prasser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Wei Lü
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Juan Du
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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Glaciers as microbial habitats: current knowledge and implication. J Microbiol 2022; 60:767-779. [DOI: 10.1007/s12275-022-2275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 10/16/2022]
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Venturini AM, Gontijo JB, Mandro JA, Paula FS, Yoshiura CA, da França AG, Tsai SM. Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils. Microb Genom 2022; 8. [PMID: 35894927 PMCID: PMC9455692 DOI: 10.1099/mgen.0.000853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jéssica A Mandro
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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38
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Stuchiner ER, von Fischer JC. Using isotope pool dilution to understand how organic carbon additions affect N 2 O consumption in diverse soils. GLOBAL CHANGE BIOLOGY 2022; 28:4163-4179. [PMID: 35377524 PMCID: PMC9321687 DOI: 10.1111/gcb.16190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 02/24/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Nitrous oxide (N2 O) is a formidable greenhouse gas with a warming potential ~300× greater than CO2 . However, its emissions to the atmosphere have gone largely unchecked because the microbial and environmental controls governing N2 O emissions have proven difficult to manage. The microbial process N2 O consumption is the only know biotic pathway to remove N2 O from soil pores and therefore reduce N2 O emissions. Consequently, manipulating soils to increase N2 O consumption by organic carbon (OC) additions has steadily gained interest. However, the response of N2 O emissions to different OC additions are inconsistent, and it is unclear if lower N2 O emissions are due to increased consumption, decreased production, or both. Simplified and systematic studies are needed to evaluate the efficacy of different OC additions on N2 O consumption. We aimed to manipulate N2 O consumption by amending soils with OC compounds (succinate, acetate, propionate) more directly available to denitrifiers. We hypothesized that N2 O consumption is OC-limited and predicted these denitrifier-targeted additions would lead to enhanced N2 O consumption and increased nosZ gene abundance. We incubated diverse soils in the laboratory and performed a 15 N2 O isotope pool dilution assay to disentangle microbial N2 O emissions from consumption using laser-based spectroscopy. We found that amending soils with OC increased gross N2 O consumption in six of eight soils tested. Furthermore, three of eight soils showed Increased N2 O Consumption and Decreased N2 O Emissions (ICDE), a phenomenon we introduce in this study as an N2 O management ideal. All three ICDE soils had low soil OC content, suggesting ICDE is a response to relaxed C-limitation wherein C additions promote soil anoxia, consequently stimulating the reduction of N2 O via denitrification. We suggest, generally, OC additions to low OC soils will reduce N2 O emissions via ICDE. Future studies should prioritize methodical assessment of different, specific, OC-additions to determine which additions show ICDE in different soils.
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Affiliation(s)
- Emily R. Stuchiner
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Joseph C. von Fischer
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
- Department of BiologyColorado State UniversityFort CollinsColoradoUSA
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Zhong L, Qing J, Liu M, Cai X, Li G, Li FY, Chen G, Xu X, Xue K, Wang Y. Fungi and Archaea Control Soil N 2O Production Potential in Chinese Grasslands Rather Than Bacteria. Front Microbiol 2022; 13:844663. [PMID: 35651488 PMCID: PMC9149426 DOI: 10.3389/fmicb.2022.844663] [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] [Received: 12/28/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.
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Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Min Liu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian Cai
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Gaoyuan Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Guanyi Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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40
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Bacterial Communities of Forest Soils along Different Elevations: Diversity, Structure, and Functional Composition with Potential Impacts on CO 2 Emission. Microorganisms 2022; 10:microorganisms10040766. [PMID: 35456816 PMCID: PMC9032212 DOI: 10.3390/microorganisms10040766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial communities at three sites at elevations of 1400 m, 1600 m, and 2200 m in a temperate forest. We showed that microbial taxonomic composition did not change with elevation (p = 0.311), though soil bacterial α-diversities did. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were abundant phyla in almost all soil samples, while Nitrospirae, closely associated with soil nitrogen cycling, was the fourth most abundant phylum in soils at 2200 m. Chemoheterotrophy and aerobic chemoheterotrophy were the two most abundant functions performed in soils at 1400 m and 1600 m, while nitrification (25.59% on average) and aerobic nitrite oxidation (19.38% on average) were higher in soils at 2200 m. Soil CO2 effluxes decreased (p < 0.050) with increasing elevation, while they were positively correlated (r = 0.55, p = 0.035) with the abundances of bacterial functional groups associated with carbon degradation. Moreover, bacterial functional composition, rather than taxonomic composition, was significantly associated with soil CO2 effluxes, suggesting a decoupling of taxonomy and function, with the latter being a better predictor of ecosystem functions. Annual temperature, annual precipitation, and pH shaped (p < 0.050) both bacterial taxonomic and functional communities. By establishing linkages between bacterial taxonomic communities, abundances of bacterial functional groups, and soil CO2 fluxes, we provide novel insights into how soil bacterial communities could serve as potential proxies of ecosystem functions.
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Lin Q, Wang S, Li Y, Riaz L, Yu F, Yang Q, Han S, Ma J. Effects and mechanisms of land-types conversion on greenhouse gas emissions in the Yellow River floodplain wetland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152406. [PMID: 34921878 DOI: 10.1016/j.scitotenv.2021.152406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/18/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The mechanism and extent of changes in greenhouse gas (GHG) emissions from seasonal river-floodplain wetlands subjected to land-type conversion are unknown. We monitored GHG fluxes and characterized soil microbial communities in four types of wetland (Riverside lower-beach wetland (RLW), Riverside higher-beach wetland (RHW), Cultivated wetland (CW), Mesophytic wetland (MW)) in the Yellow River flood land. Results revealed that land reclamation activities altered the distribution patterns of carbon (C) and nitrogen (N) in soil, as well as the structure and activities of microbial communities, leading to changes in the GHG emissions. Cumulative CO2 and N2O emissions were highest in CW, which were 2.10-10.71 times and 3.19-8.61 times greater than the other three wetlands, respectively, whereas cumulative CH4 emissions were highest in RLW (1850.192 mg·m-2). CW exhibited the highest 100-years-scale Global Warming Potential (GWP100-CO2-eq) (81.175 t CO2-eq·ha-1), which was 9.93, 3.12, and 2.11 times greater than RLW, RHW, and MW. Moreover, reclaiming riverside wetland as farmland will increase CO2 and N2O emission fluxes by 54.546-72.684 t·ha-1 and 2.615-2.988 kg·ha-1, respectively. 16S rRNA high throughput sequencing revealed that bacterial community composition changed significantly overtime and seasons. GHG fluxes showed a significant positive linear correlation with bacterial OTUs (y = 0.71x-319.4, R2 = 0.304) and Shannon index (y = 228.62x-796.6, R2 = 0.336). Structure equation models indicated that soil C, N and moisture content were the primary factors influencing bacterial community evolution, which had an impact on GHG fluxes. Actinomycetes were significantly affected by total carbon (TC) content, dissolved organic carbon (DOC), and C/N, while ammonia oxidizing and nitrifying bacteria were greatly influenced by NO3--N rather than TN and NH4+-N content. Opportunities exist to reduce GHG emissions and mitigate climate change by maintaining the original state of riverside wetland or restoring cultivated land to wetland in the Yellow River floodplain wetland.
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Affiliation(s)
- Qingwei Lin
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, 453007, PR China
| | - Shishi Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China
| | - Yingchen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, 453007, PR China
| | - Luqman Riaz
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China
| | - Fei Yu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, 453007, PR China.
| | - Qingxiang Yang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, 453007, PR China
| | - Shijie Han
- School of Life Sciences, Henan University, Kaifeng 475004, PR China
| | - Jianmin Ma
- College of Life Sciences, Henan Normal University, Xinxiang 453007, PR China; Puyang Field Scientific Observation and Research Station for Yellow River Wetland Ecosystem, Henan Province, PR China; Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, 453007, PR China.
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García-Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. GLOBAL CHANGE BIOLOGY 2022. [PMID: 34923712 DOI: 10.6084/m9.figshare.14370896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Feng Zhang
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Diego Abalos
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Pablo García-Palacios
- Departamento de Biología y Geología, Física y Química Inorgánica y Analítica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
| | - Jørgen Eivind Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
| | - Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
- iCLIMATE Interdisciplinary Centre for Climate Change, Aarhus University, Roskilde, Denmark
- Aarhus University Centre for Circular Bioeconomy, Aarhus University, Tjele, Denmark
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Zhang Y, Zhang F, Abalos D, Luo Y, Hui D, Hungate BA, García‐Palacios P, Kuzyakov Y, Olesen JE, Jørgensen U, Chen J. Stimulation of ammonia oxidizer and denitrifier abundances by nitrogen loading: Poor predictability for increased soil N 2 O emission. GLOBAL CHANGE BIOLOGY 2022; 28:2158-2168. [PMID: 34923712 PMCID: PMC9303726 DOI: 10.1111/gcb.16042] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/10/2021] [Indexed: 05/15/2023]
Abstract
Unprecedented nitrogen (N) inputs into terrestrial ecosystems have profoundly altered soil N cycling. Ammonia oxidizers and denitrifiers are the main producers of nitrous oxide (N2 O), but it remains unclear how ammonia oxidizer and denitrifier abundances will respond to N loading and whether their responses can predict N-induced changes in soil N2 O emission. By synthesizing 101 field studies worldwide, we showed that N loading significantly increased ammonia oxidizer abundance by 107% and denitrifier abundance by 45%. The increases in both ammonia oxidizer and denitrifier abundances were primarily explained by N loading form, and more specifically, organic N loading had stronger effects on their abundances than mineral N loading. Nitrogen loading increased soil N2 O emission by 261%, whereas there was no clear relationship between changes in soil N2 O emission and shifts in ammonia oxidizer and denitrifier abundances. Our field-based results challenge the laboratory-based hypothesis that increased ammonia oxidizer and denitrifier abundances by N loading would directly cause higher soil N2 O emission. Instead, key abiotic factors (mean annual precipitation, soil pH, soil C:N ratio, and ecosystem type) explained N-induced changes in soil N2 O emission. Altogether, these findings highlight the need for considering the roles of key abiotic factors in regulating soil N transformations under N loading to better understand the microbially mediated soil N2 O emission.
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Affiliation(s)
- Yong Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Feng Zhang
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Diego Abalos
- Department of AgroecologyAarhus UniversityTjeleDenmark
| | - Yiqi Luo
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Dafeng Hui
- Department of Biological SciencesTennessee State UniversityNashvilleTennesseeUSA
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society and Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Pablo García‐Palacios
- Departamento de Biología y GeologíaFísica y Química Inorgánica y AnalíticaEscuela Superior de Ciencias Experimentales y TecnologíaUniversidad Rey Juan CarlosMóstolesSpain
- Instituto de Ciencias AgrariasConsejo Superior de Investigaciones CientíficasMadridSpain
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate EcosystemsUniversity of GöttingenGöttingenGermany
- Agro‐Technological InstituteRUDN UniversityMoscowRussia
- Institute of Environmental SciencesKazan Federal UniversityKazanRussia
| | - Jørgen Eivind Olesen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Uffe Jørgensen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
| | - Ji Chen
- Department of AgroecologyAarhus UniversityTjeleDenmark
- iCLIMATE Interdisciplinary Centre for Climate ChangeAarhus UniversityRoskildeDenmark
- Aarhus University Centre for Circular BioeconomyAarhus UniversityTjeleDenmark
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Liu LY, Xie GJ, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Microbial methane emissions from the non-methanogenesis processes: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151362. [PMID: 34740653 DOI: 10.1016/j.scitotenv.2021.151362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
Methane, a potent greenhouse gas of global importance, has traditionally been considered as an end product of microbial methanogenesis of organic matter. Paradoxically, growing evidence has shown that some microbes, such as cyanobacteria, algae, fungi, purple non-sulfur bacteria, and cryptogamic covers, produce methane in oxygen-saturated aquatic and terrestrial ecosystems. The non-methanogenesis process could be an important potential contributor to methane emissions. This systematic review summarizes the knowledge of microorganisms involved in the non-methanogenesis process and the possible mechanisms of methane formation. Cyanobacteria-derived methane production may be attributed to either demethylation of methyl phosphonates or linked to light-driven primary productivity, while algae produce methane by utilizing methylated sulfur compounds as possible carbon precursors. In addition, fungi produce methane by utilizing methionine as a possible carbon precursor, and purple non-sulfur bacteria reduce carbon dioxide to methane by nitrogenase. The microbial methane distribution from the non-methanogenesis processes in aquatic and terrestrial environments and its environmental significance to global methane emissions, possible mechanisms of methane production in each open water, water-to-air methane fluxes, and the impact of climate change on microorganisms are also discussed. Finally, future perspectives are highlighted, such as establishing more in-situ experiments, quantifying methane flux through optimizing empirical models, distinguishing individual methane sources, and investigating nitrogenase-like enzyme systems to improve our understanding of microbial methane emission from the non-methanogenesis process.
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Affiliation(s)
- Lu-Yao Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Liang D, Robertson GP. Nitrification is a minor source of nitrous oxide (N 2 O) in an agricultural landscape and declines with increasing management intensity. GLOBAL CHANGE BIOLOGY 2021; 27:5599-5613. [PMID: 34383336 PMCID: PMC9291997 DOI: 10.1111/gcb.15833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 05/15/2023]
Abstract
The long-term contribution of nitrification to nitrous oxide (N2 O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2 O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2 O, we test the relative importance of nitrification-derived N2 O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2 O fluxes was 13%-17% in a conventionally fertilized annual cropping system, 27%-42% in a low-input cover-cropped annual cropping system, and 52%-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be <10% of these values because of low N2 O yields in cultured nitrifiers (typically 0.04%-8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2 O was produced by ammonia-oxidizing bacteria rather than archaea, who appeared responsible for no more than 30% of nitrification-derived N2 O production in all but one ecosystem. Although the proportion of nitrification-derived N2 O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2 O (higher Vmax ) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2 O in all ecosystems examined.
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Affiliation(s)
- Di Liang
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
| | - G. Philip Robertson
- Department of Plant, Soil and Microbial Sciences and Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- W. K. Kellogg Biological StationMichigan State UniversityHickory CornersMichiganUSA
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Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. mBio 2021; 12:e0170821. [PMID: 34544276 PMCID: PMC8546591 DOI: 10.1128/mbio.01708-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
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Li D, Li H, Chen D, Xue L, He H, Feng Y, Ji Y, Yang L, Chu Q. Clay-hydrochar composites mitigated CH 4 and N 2O emissions from paddy soil: A whole rice growth period investigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146532. [PMID: 33773345 DOI: 10.1016/j.scitotenv.2021.146532] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
With the favorable microporous structure and excellent adsorption capacity, clay-hydrochar composites (CHCs) serve as promising materials to mitigate greenhouse gas emissions (GHG) from the paddy fields. Three clays were co-pyrolyzed with hydrochar derived from poplar sawdust to obtain CHCs, which were applied to the paddy fields to investigate the effects on methane (CH4) and nitrous oxide (N2O) emissions. Three CHCs were labeled as bentonite-hydrochar composite (BTHC), montmorillonite-hydrochar composite (MTHC), and kaolinite-hydrochar composite (KTHC), respectively. The effects of these three CHCs on GHG emissions were determined by monitoring the dynamic CH4 and N2O emissions in the paddy soil column ecosystem during the rice-growing season. The results showed that compared with the control group, three CHCs significantly mitigated CH4 and N2O emissions by 21.4%-47.5% and 5.2%-36.8%, respectively. Furthermore, the fluorescent components result displayed CHCs increased humic-like content by 29.62%-59.72%. A structural equation model was used to assess the hypothesis mitigation mechanism, which exemplified that GHG emissions negatively correlated with pmoA and nosZ genes, possibly resulting in the CH4 and N2O mitigation. Among the three CHCs, the KTHC amendment mitigated the CH4 and N2O emissions by 47.5% and 36.8%, respectively, which was superior to BTHC and MTHC. Hence, it was recommended for application to the field. Overall, this study demonstrates the mitigating effects of CHCs on GHG emissions for the first time, and the reduced CH4 and N2O emissions could contribute to increased soil C and N retention for better agricultural nutrients management.
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Affiliation(s)
- Detian Li
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
| | - Huiting Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
| | - Danyan Chen
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
| | - Lihong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environment Science, Nanjing Agricultural University, Nanjing 210095, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China
| | - Huayong He
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China
| | - Yanfang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; College of Resources and Environment Science, Nanjing Agricultural University, Nanjing 210095, China; School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212001, China.
| | - Yang Ji
- College of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Linzhang Yang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Qingnan Chu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain and Key Laboratory for Crop and Animal Integrated Farming of Ministry of Agriculture and Rural Affairs, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Zhou J, Xing J. Haloalkaliphilic denitrifiers-dependent sulfate-reducing bacteria thrive in nitrate-enriched environments. WATER RESEARCH 2021; 201:117354. [PMID: 34157573 DOI: 10.1016/j.watres.2021.117354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/17/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
As bridge in global cycles of carbon, nitrogen, and sulfur, sulfate-reducing bacteria (SRB) play more and more important role under various environments, especially the saline-alkali environments with significant increase in area caused by human activities. Sulfate reduction can be inhibited by environmental nitrate. However, how SRB cope with environmental nitrate stress in these extreme environments still remain unclear. Here, after a long-term enrichment of sediment from saline-alkali Qinghai Lake of China using anaerobic filter reactors, nitrate was added to evaluate the response of SRB. With the increase in nitrate concentrations, the inhibition on sulfate reduction was gradually observed. Interestingly, extension of hydraulic retention time can relieve the inhibition caused by high nitrate concentration. Mass balance analysis showed that nitrate reduction is prior to sulfate reduction. Further metatranscriptomic analysis shows that, genes of nitrite reductase (periplasmic cytochrome c nitrite reductase gene) and energy metabolisms (lactate dehydrogenase, formate dehydrogenase, pyruvate:ferredoxin-oxidoreductase, and fumarate reductase genes) in SRB was down-regulated, challenging the long-held opinion that up-regulation of these genes can relieve the nitrate inhibition. Most importantly, the nitrate addition activated the denitrification pathway in denitrifying bacteria (DB) via significantly up-regulating the expression of the corresponding genes (nitrite reductase, nitric oxide reductase c subunit, nitric oxide reductase activation protein and nitrous oxide reductase genes), quickly reducing the environmental nitrate and relieving the nitrate inhibition on SRB. Our findings unravel that in response to environmental nitrate stress, haloalkaliphilic SRB show dependency on DB, and expand our knowledge of microbial relationship during sulfur and nitrogen cycles.
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Affiliation(s)
- Jiemin Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jianmin Xing
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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Shi W, Du M, Ye C, Zhang Q. Divergent effects of hydrological alteration and nutrient addition on greenhouse gas emissions in the water level fluctuation zone of the Three Gorges Reservoir, China. WATER RESEARCH 2021; 201:117308. [PMID: 34102598 DOI: 10.1016/j.watres.2021.117308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
Changes in global rainfall patterns and construction of artificial dams have led to widespread alteration of hydrological processes in riparian ecosystems. At the same time, many riparian ecosystems, such as those associated with the Yangtze, are being subjected to enhanced inputs of nitrogen (N) and phosphorus (P) due to intensified agricultural activity in surrounding uplands. Together, these environmental changes may alter the magnitude and direction of greenhouse gasses (GHGs) fluxes from riparian soils. We conducted an in situ experiment combined with quantitative PCR approach (qPCR) to elucidate the effects of hydrological alterations (continuous flooding (CF), periodic flooding (PF), and no flooding (NF)) and nutrient addition (N addition (urea, 100 kg N ha-1 y-1), P addition (P2O5, 20 kg ha-1y-1), N + P addition, and control (CK)) on three major GHGs including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes as well as the underlying mechanisms. Our results showed that hydrological alterations greatly affected GHGs emissions, possibly by altering soil moisture, soil organic C, and C:N ratios. The CF, with higher soil moisture and lower C:N ratio, increased CH4 emissions 13-fold and reduced CO2 and N2O emissions by 37.3% and 72.2% averaged over the growing seasons compared with no flooding. PF enhanced CH4 emissions 5.7-fold and decreased N2O emissions by 69.0% in comparison with no flooding. Nutrient additions had no significant effect on CO2 or CH4 flux, but P addition significantly lowered N2O flux. Interactions between hydrological alterations and nutrient additions were not detected for any GHGs. As a result, hydrological alterations and nutrient additions affected the global warming potential (GWP) of growing season GHG budgets on a 100-year time horizon, mainly by changing the CO2 emissions. CF reduced GWP from 597 to 439 g CO2-eq m-2, and N + P addition enhanced GWP from 489 to 625 g CO2-eq m-2. The qPCR analysis revealed that decreased CH4 oxidation potential may lead to the enrichment of CH4 emissions under the hydrological alterations, and reduced nitrification and denitrification potential contributed to the reduction of N2O fluxes under all the treatments. Our study indicates that continuous flooding could curb the contribution of riparian GHGs fluxes to global warming but that the combination of N and P additions may increase the greenhouse effect mainly by regulating the CO2 emissions of growing season in riparian ecosystem.
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Affiliation(s)
- Wenjun Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, PR China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China; The University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ming Du
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, PR China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Chen Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, PR China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China.
| | - Quanfa Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, PR China; Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, PR China.
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