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Shen L, He Y, Hu Q, Yang Y, Ren B, Yang W, Geng C, Jin J, Bai Y. Vertical distribution of Candidatus Methylomirabilis and Methanoperedens in agricultural soils. Appl Microbiol Biotechnol 2024; 108:47. [PMID: 38175239 DOI: 10.1007/s00253-023-12876-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 01/05/2024]
Abstract
Candidatus Methylomirabilis-related bacteria conduct anaerobic oxidation of methane (AOM) coupling with NO2- reduction, and Candidatus Methanoperedens-related archaea perform AOM coupling with reduction of diverse electron acceptors, including NO3-, Fe (III), Mn (IV) and SO42-. Application of nitrogen fertilization favors the growth of these methanotrophs in agricultural fields. Here, we explored the vertical variations in community structure and abundance of the two groups of methanotrophs in a nitrogen-rich vegetable field via using illumina MiSeq sequencing and quantitative PCR. The retrieved Methylomirabilis-related sequences had 91.12%-97.32% identity to the genomes of known Methylomirabilis species, and Methanoperedens-related sequences showed 85.49%-97.48% identity to the genomes of known Methanoperedens species which are capable of conducting AOM coupling with reduction of NO3- or Fe (III). The Methanoperedens-related archaeal diversity was significantly higher than Methylomirabilis-related bacteria, with totally 74 and 16 operational taxonomic units, respectively. In contrast, no significant difference in abundance between the bacteria (9.19 × 103-3.83 × 105 copies g-1 dry soil) and the archaea (1.55 × 104-3.24 × 105 copies g-1 dry soil) was observed. Furthermore, the abundance of both groups of methanotrophs exhibited a strong vertical variation, which peaked at 30-40 and 20-30 cm layers, respectively. Soil water content and pH were the key factors influencing Methylomirabilis-related bacterial diversity and abundance, respectively. For the Methanoperedens-related archaea, both soil pH and ammonium content contributed significantly to the changes of these archaeal diversity and abundance. Overall, we provide the first insights into the vertical distribution and regulation of Methylomirabilis-related bacteria and Methanoperedens-related archaea in vegetable soils. KEY POINTS: • The archaeal diversity was significantly higher than bacterial. • There was no significant difference in the abundance between bacteria and archaea. • The abundance of bacteria and archaea peaked at 30-40 and 20-30 cm, respectively.
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Affiliation(s)
- Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Yefan He
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Qinan Hu
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Caiyu Geng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jinghao Jin
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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2
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Zhang X, Wang R, Wang H, Xu Z, Feng C, Zhao F. CH 4 control and nitrogen removal from constructed wetlands by plant combination. CHEMOSPHERE 2024; 355:141898. [PMID: 38579951 DOI: 10.1016/j.chemosphere.2024.141898] [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: 12/07/2023] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Global warming trend is accelerating. This study proposes a green and economical methane (CH4) control strategy by plant combination in constructed wetlands (CWs). In this study, a single planting of Acorus calamus L. hybrid constructed wetland (HCW-A) and a mixed planting of Acorus calamus L. and Eichhornia crassipes (Mart.) Solms hybrid constructed wetland (HCW-EA) were constructed. The differences in nitrogen removal performance and CH4 emissions between HCW-A and HCW-EA were compared and analyzed. The findings indicated that HCW-EA demonstrated significant improvements over HCW-A, with NH4+-N and TN removal rates increasing by 21.61% and 16.38% respectively, and CH4 emissions decreased by 43.36%. The microbiological analysis results showed that plant combination promoted the enrichment of Proteobacteria, Alphaproteobacteria and Bacillus. More nitrifying bacteria carrying nxrA genes and denitrifying bacteria carrying nirK genes accelerated the nitrogen transformation process. In addition, the absolute abundance ratio of pmoA/mcrA increased, reducing the release of CH4.
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Affiliation(s)
- Xinwen Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, China
| | - Rongzhen Wang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, China
| | - Hongxiu Wang
- Inspur General Software Co., Ltd, Jinan, 250101, China
| | - Zhenghe Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, China.
| | - Chengye Feng
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, China
| | - Fangxing Zhao
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, China
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He T, Yin Q, Li X. Effects of Antibiotics on the DAMO Process and Microbes in Cattle Manure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:3883-3894. [PMID: 38347804 DOI: 10.1021/acs.est.3c07135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) can mitigate methane emissions; however, this process has not been studied in cattle manure, an important source of methane emissions in animal agriculture. The objective of this study was to investigate the occurrence of DAMO microbes in cattle manure and examine the impacts of veterinary antibiotics on the DAMO process in cattle manure. Results show that DAMO archaea and bacteria consistently occur at high concentrations in beef cattle manure. During the long-term operation of a sequencing batch reactor seeded with beef cattle manure, the DAMO activities intensified, and DAMO microbial biomass increased. Exposure to chlortetracycline at initial concentrations up to 5000 μg L-1 did not inhibit DAMO activities or affect the concentrations of the 16S rRNA gene and functional genes of DAMO microbes. In contrast, exposure to tylosin at initial concentrations of 50 and 500 μg L-1 increased the activities of the DAMO microbes. An initial concentration of 5000 μg L-1 TYL almost entirely halted DAMO activities and reduced the concentrations of DAMO microbes. These results show the occurrence of DAMO microbes in cattle manure and reveal that elevated concentrations of dissolved antibiotics could inhibit the DAMO process, potentially affecting net methane emissions from cattle manure.
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Affiliation(s)
- Ting He
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- Institute of Chemistry, Henan Academy of Sciences, Zheng Zhou 450002, Henan, P. R. China
| | - Qidong Yin
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Bai Y, Wang Y, Shen L, Shang B, Ji Y, Ren B, Yang W, Yang Y, Ma Z, Feng Z. Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169311. [PMID: 38103608 DOI: 10.1016/j.scitotenv.2023.169311] [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: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g-1 (dry soil) day-1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.
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Affiliation(s)
- Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yanping Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Bo Shang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yang Ji
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhiguo Ma
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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5
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Zhao Q, Lu Y. Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166049. [PMID: 37543312 DOI: 10.1016/j.scitotenv.2023.166049] [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: 05/19/2023] [Revised: 07/19/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.
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Affiliation(s)
- Qingzhou Zhao
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China
| | - Yahai Lu
- College of Urban and Environmental Science, Peking University, Beijing 100871, PR China.
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6
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Grégoire DS, George NA, Hug LA. Microbial methane cycling in a landfill on a decadal time scale. Nat Commun 2023; 14:7402. [PMID: 37973978 PMCID: PMC10654671 DOI: 10.1038/s41467-023-43129-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.
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Affiliation(s)
- Daniel S Grégoire
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
- Department of Chemistry, Carleton University, Ottawa, ON, K1S 5B6, Canada.
| | - Nikhil A George
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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7
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Cheng H, Yang Y, He Y, Zhan X, Liu Y, Hu Z, Huang H, Yao X, Yang W, Jin J, Ren B, Liu J, Hu Q, Jin Y, Shen L. Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river. CHEMOSPHERE 2023; 324:138295. [PMID: 36893867 DOI: 10.1016/j.chemosphere.2023.138295] [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: 12/06/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH4 cycle. This AOM process acts as a novel pathway for CH4 emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 105-2.47 × 107 copies g-1 (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH4 g-1 (dry weight) d-1, which could potentially reduce 10.3% of CH4 emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH4+ and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH4 emissions from riverine ecosystems.
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Affiliation(s)
- Haixiang Cheng
- College of Chemistry and Material Engineering, Quzhou University, Quzhou, 324000, China.
| | - Yuling Yang
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yefan He
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xugang Zhan
- Quzhou Bureau of Ecology and Environment, Quzhou, 324000, China
| | - Yan Liu
- Wuxi River Drinking Water Source Protection and Management Center, Quzhou, 324000, China
| | - Zhengfeng Hu
- Eco-environmental Science Research & Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | - Hechen Huang
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xiaochen Yao
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wangting Yang
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jinghao Jin
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Bingjie Ren
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jiaqi Liu
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Qinan Hu
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuhan Jin
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Lidong Shen
- Institue of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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8
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Yang WT, Shen LD, Bai YN. Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems. ENVIRONMENTAL RESEARCH 2023; 219:115174. [PMID: 36584837 DOI: 10.1016/j.envres.2022.115174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/07/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH4). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH4 emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH4 emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH4 sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH4 mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.
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Affiliation(s)
- Wang-Ting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Li-Dong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Ya-Nan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
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9
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Shen LD, Geng CY, Ren BJ, Jin JH, Huang HC, Liu X, Yang WT, Yang YL, Liu JQ, Tian MH. Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils. MICROBIAL ECOLOGY 2023; 85:441-453. [PMID: 35098330 DOI: 10.1007/s00248-022-01968-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 106 ~ 4.62 × 106 copies g-1 dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.
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Affiliation(s)
- Li-Dong Shen
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Cai-Yu Geng
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Bing-Jie Ren
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jing-Hao Jin
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - He-Chen Huang
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xin Liu
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wang-Ting Yang
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Mao-Hui Tian
- Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
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10
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Cheng H, Yang Y, Shen L, Liu Y, Zhan X, Hu Z, Huang H, Jin J, Ren B, He Y, Jin Y, Su Z. Spatial variations of activity and community structure of nitrite-dependent anaerobic methanotrophs in river sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158288. [PMID: 36030855 DOI: 10.1016/j.scitotenv.2022.158288] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Rivers are an important site for methane emissions and reactive nitrogen removal. The process of nitrite-dependent anaerobic methane oxidation (n-damo) links the global carbon cycle and the nitrogen cycle, but its role in methane mitigation and nitrogen removal in rivers is poorly known. In the present study, we investigated the activity, abundance, and community composition of n-damo bacteria in sediment of the upper, middle, and lower reaches of Wuxijiang River (Zhejiang Province, China). The 13CH4 stable isotope experiments showed that the methane oxidation activity of n-damo was 0.11-1.88 nmol CO2 g-1 (dry sediment) d-1, and the activity measured from the middle reaches was significantly higher than that from the remaining regions. It was estimated that 3.27 g CH4 m-2 year-1 and 8.72 g N m-2 year-1 could be consumed via n-damo. Quantitative PCR confirmed the presence of n-damo bacteria, and their 16S rRNA gene abundance varied between 5.45 × 105 and 5.86 × 106 copies g-1 dry sediment. Similarly, the abundance of n-damo bacteria was significantly higher in the middle reaches. High-throughput sequencing showed a high n-damo bacterial diversity, with totally 152 operational taxonomic units being detected at 97 % sequence similarity cut-off. In addition, the n-damo bacterial community composition also varied spatially. The inorganic nitrogen (NH4+, NO2-, NO3-) level was found to be the key environmental factor controlling the n-damo activity and bacterial community composition. Overall, our results showed the spatial variations and environmental regulation of the activity and community structure of n-damo bacteria in river sediment, which expanded our understanding of the quantitative importance of n-damo in both methane oxidation and reactive nitrogen removal in riverine systems.
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Affiliation(s)
- Haixiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou 324000, China
| | - Yuling Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Yan Liu
- Wuxi River Drinking Water Source Protection and Management Center, Quzhou 324000, China
| | - Xugang Zhan
- Quzhou Bureau of Ecology and Environment, Quzhou 324000, China
| | - Zhengfeng Hu
- Eco-environmental Science Research & Design Institute of Zhejiang Province, Hangzhou 310007, China
| | - Hechen Huang
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jinghao Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Bingjie Ren
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yefan He
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuhan Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhenfa Su
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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11
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Yang WT, Wang WQ, Shen LD, Bai YN, Liu X, Tian MH, Wang C, Feng YF, Liu Y, Yang YL, Liu JQ, Geng CY. Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156534. [PMID: 35679939 DOI: 10.1016/j.scitotenv.2022.156534] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo), catalyzed by bacteria closely related to Candidatus Methylomirabilis oxyfera, links the global carbon and nitrogen cycles. Currently, the contribution of n-damo in controlling methane emissions and nitrogen removal, and the key regulatory factors of this process in Chinese paddy fields are poorly known. Here, soil samples from 20 paddy fields located in different climate zones across China were collected to examine the n-damo activity and bacterial communities. The n-damo activity and bacterial abundance varied from 1.05 to 5.97 nmol CH4 g-1 (dry soil) d-1 and 2.59 × 105 to 2.50 × 107 copies g-1 dry soil, respectively. Based on the n-damo activity, it was estimated that approximately 0.91 Tg CH4 and 2.17 Tg N could be consumed annually via n-damo in Chinese paddy soils. The spatial variations in n-damo activity and community structure of n-damo bacteria were significantly (p < 0.05) affected by the soil ammonium content, labile organic carbon content and pH. Furthermore, significant differences in n-damo activity, bacterial abundance and community composition were observed among different climate zones. The n-damo activity was found to be positively correlated with the mean annual air temperature. Taken together, our results demonstrated the potential importance of n-damo in both methane consumption and nitrogen removal in Chinese paddy soils, and this process was regulated by local soil and climatic factors.
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Affiliation(s)
- Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Wei-Qi Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Ya-Nan Bai
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Chun Wang
- Key Laboratory of Humid Subtropical Eco-geographical Process, Ministry of Education, Fujian Normal University, Fuzhou 350007, China
| | - Yan-Fang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210044, China
| | - Yang Liu
- Information Center, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Cai-Yu Geng
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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12
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Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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13
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Yang Y, Shen L, Bai Y, Zhao X, Wang S, Liu J, Liu X, Tian M, Yang W, Jin J, Huang H, Wu H. Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils. Environ Microbiol 2022; 24:5005-5018. [PMID: 35799420 DOI: 10.1111/1462-2920.16102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH4 ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH4 emissions from paddy fields.
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Affiliation(s)
- Yuling Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Lidong Shen
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yanan Bai
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shuwei Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiaqi Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xin Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Maohui Tian
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Wangting Yang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Jinghao Jin
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Hechen Huang
- Jiangsu Key Laboratory of Agricultural Meteorology, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Hongsheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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14
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Lemaire ON, Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry 2022; 61:805-821. [PMID: 35500274 PMCID: PMC9118554 DOI: 10.1021/acs.biochem.2c00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Microbial anaerobic
oxidation of alkanes intrigues the scientific
community by way of its impact on the global carbon cycle, and its
biotechnological applications. Archaea are proposed to degrade short-
and long-chain alkanes to CO2 by reversing methanogenesis,
a theoretically reversible process. The pathway would start with alkane
activation, an endergonic step catalyzed by methyl-coenzyme M reductase
(MCR) homologues that would generate alkyl-thiols carried by coenzyme
M. While the methane-generating MCR found in methanogens has been
well characterized, the enzymatic activity of the putative alkane-fixing
counterparts has not been validated so far. Such an absence of biochemical
investigations contrasts with the current explosion of metagenomics
data, which draws new potential alkane-oxidizing pathways in various
archaeal phyla. Therefore, validating the physiological function of
these putative alkane-fixing machines and investigating how their
structures, catalytic mechanisms, and cofactors vary depending on
the targeted alkane have become urgent needs. The first structural
insights into the methane- and ethane-capturing MCRs highlighted unsuspected
differences and proposed some explanations for their substrate specificity.
This Perspective reviews the current physiological, biochemical, and
structural knowledge of alkyl-CoM reductases and offers fresh ideas
about the expected mechanistic and chemical differences among members
of this broad family. We conclude with the challenges of the investigation
of these particular enzymes, which might one day generate biofuels
for our modern society.
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Affiliation(s)
- Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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15
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He B, Cai C, McCubbin T, Muriel JC, Sonnenschein N, Hu S, Yuan Z, Marcellin E. A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility. Metabolites 2022; 12:metabo12040314. [PMID: 35448501 PMCID: PMC9024614 DOI: 10.3390/metabo12040314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/18/2022] [Accepted: 03/26/2022] [Indexed: 11/16/2022] Open
Abstract
Methane is an abundant low-carbon fuel that provides a valuable energy resource, but it is also a potent greenhouse gas. Therefore, anaerobic oxidation of methane (AOM) is an essential process with central features in controlling the carbon cycle. Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens) is a recently discovered methanotrophic archaeon capable of performing AOM via a reverse methanogenesis pathway utilizing nitrate as the terminal electron acceptor. Recently, reverse methanogenic pathways and energy metabolism among anaerobic methane-oxidizing archaea (ANME) have gained significant interest. However, the energetics and the mechanism for electron transport in nitrate-dependent AOM performed by M. nitroreducens is unclear. This paper presents a genome-scale metabolic model of M. nitroreducens, iMN22HE, which contains 813 reactions and 684 metabolites. The model describes its cellular metabolism and can quantitatively predict its growth phenotypes. The essentiality of the cytoplasmic heterodisulfide reductase HdrABC in the reverse methanogenesis pathway is examined by modeling the electron transfer direction and the specific energy-coupling mechanism. Furthermore, based on better understanding electron transport by modeling, a new energy transfer mechanism is suggested. The new mechanism involves reactions capable of driving the endergonic reactions in nitrate-dependent AOM, including the step reactions in reverse canonical methanogenesis and the novel electron-confurcating reaction HdrABC. The genome metabolic model not only provides an in silico tool for understanding the fundamental metabolism of ANME but also helps to better understand the reverse methanogenesis energetics and its thermodynamic feasibility.
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Affiliation(s)
- Bingqing He
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Chen Cai
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
| | - Jorge Carrasco Muriel
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (J.C.M.); (N.S.)
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (J.C.M.); (N.S.)
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, Formerly AWMC), The University of Queensland, Brisbane, QLD 4072, Australia; (C.C.); (S.H.); (Z.Y.)
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia; (B.H.); (T.M.)
- Correspondence:
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16
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Hester ER, Vaksmaa A, Valè G, Monaco S, Jetten MSM, Lüke C. Effect of water management on microbial diversity and composition in an Italian rice field system. FEMS Microbiol Ecol 2022; 98:6529233. [PMID: 35170720 PMCID: PMC8924702 DOI: 10.1093/femsec/fiac018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/26/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the ‘Alternate Wetting and Drying’ (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable.
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Affiliation(s)
- Eric R Hester
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Giampiero Valè
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy.,DiSIT-Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, Piazza San Eusebio 5, I-13100 Vercelli, Italy
| | - Stefano Monaco
- CREA - Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 13100, Vercelli, Italy
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
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17
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Hu J, Ke X, Wang B, Mei Y, Xiao N, Wan X, Liu G, Hu M, Zhao J. SSThe coexistence and diversity of Candidatus methylomirabilis oxyfera-like and anammox bacteria in sediments of an urban eutrophic lake. Int Microbiol 2022; 25:457-469. [DOI: 10.1007/s10123-021-00230-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022]
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18
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Tian MH, Shen LD, Liu X, Bai YN, Hu ZH, Jin JH, Feng YF, Liu Y, Yang WT, Yang YL, Liu JQ. Response of nitrite-dependent anaerobic methanotrophs to elevated atmospheric CO 2 concentration in paddy fields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149785. [PMID: 34467934 DOI: 10.1016/j.scitotenv.2021.149785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-damo) catalyzed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a new pathway for the regulation of methane emissions from paddy fields. Elevated atmospheric CO2 concentrations (e[CO2]) can indirectly affect the structure and function of microbial communities. However, the response of M. oxyfera-like bacteria to e[CO2] is currently unknown. Here, we investigated the effect of e[CO2] (ambient CO2 + 200 ppm) on community composition, abundance, and activity of M. oxyfera-like bacteria at different depths (0-5, 5-10, and 10-20 cm) in paddy fields across multiple rice growth stages (tillering, jointing, and flowering). High-throughput sequencing showed that e[CO2] had no significant effect on the community composition of M. oxyfera-like bacteria. However, quantitative PCR suggested that the 16S rRNA gene abundance of M. oxyfera-like bacteria increased significantly in soil under e[CO2], particularly at the tillering stage. Furthermore, 13CH4 tracer experiments showed potential n-damo activity of 0.31-8.91 nmol CO2 g-1 (dry soil) d-1. E[CO2] significantly stimulated n-damo activity, especially at the jointing and flowering stages. The n-damo activity and abundance of M. oxyfera-like bacteria increased by an average of 90.9% and 50.0%, respectively, under e[CO2]. Correlation analysis showed that the increase in soil dissolved organic carbon content caused by e[CO2] had significant effects on the activity and abundance of M. oxyfera-like bacteria. Overall, this study provides the first evidence for a positive response of M. oxyfera-like bacteria to e[CO2], which may help reduce methane emissions from paddy fields under future climate change conditions.
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Affiliation(s)
- Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Ya-Nan Bai
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zheng-Hua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Jing-Hao Jin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yan-Fang Feng
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing 210044, China
| | - Yang Liu
- Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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Shi LD, Wang Z, Liu T, Wu M, Lai CY, Rittmann BE, Guo J, Zhao HP. Making good use of methane to remove oxidized contaminants from wastewater. WATER RESEARCH 2021; 197:117082. [PMID: 33819663 DOI: 10.1016/j.watres.2021.117082] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/13/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Being an energetic fuel, methane is able to support microbial growth and drive the reduction of various electron acceptors. These acceptors include a broad range of oxidized contaminants (e.g., nitrate, nitrite, perchlorate, bromate, selenate, chromate, antimonate and vanadate) that are ubiquitously detected in water environments and pose threats to human and ecological health. Using methane as electron donor to biologically reduce these contaminants into nontoxic forms is a promising solution to remediate polluted water, considering that methane is a widely available and inexpensive electron donor. The understanding of methane-based biological reduction processes and the responsible microorganisms has grown in the past decade. This review summarizes the fundamentals of metabolic pathways and microorganisms mediating microbial methane oxidation. Experimental demonstrations of methane as an electron donor to remove oxidized contaminants are summarized, compared, and evaluated. Finally, the review identifies opportunities and unsolved questions that deserve future explorations for broadening understanding of methane oxidation and promoting its practical applications.
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Affiliation(s)
- Ling-Dong Shi
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Wang
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Liu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Mengxiong Wu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Chun-Yu Lai
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, Arizona 85287-5701, U.S.A
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Lab Water Pollution Control & Environment, Zhejiang University, Hangzhou, Zhejiang, China.
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Guerrero-Cruz S, Vaksmaa A, Horn MA, Niemann H, Pijuan M, Ho A. Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications. Front Microbiol 2021; 12:678057. [PMID: 34054786 PMCID: PMC8163242 DOI: 10.3389/fmicb.2021.678057] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.
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Affiliation(s)
- Simon Guerrero-Cruz
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
| | - Marcus A. Horn
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, ’t Horntje, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
- Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Universitat de Girona, Girona, Spain
| | - Adrian Ho
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Division of Applied Life Sciences, Gyeongsang National University, Jinju, South Korea
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21
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Kumar M, Yadav AN, Saxena R, Rai PK, Paul D, Tomar RS. Novel methanotrophic and methanogenic bacterial communities from diverse ecosystems and their impact on environment. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Ding J, Zeng RJ. Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143928. [PMID: 33316511 DOI: 10.1016/j.scitotenv.2020.143928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.
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Affiliation(s)
- Jing Ding
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China; Jiangsu Provincial Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, Jiangsu 215009, China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; CAS Key Laboratory for Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, China.
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23
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Shen LD, Tian MH, Cheng HX, Liu X, Yang YL, Liu JQ, Xu JB, Kong Y, Li JH, Liu Y. Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114623. [PMID: 33618455 DOI: 10.1016/j.envpol.2020.114623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 06/12/2023]
Abstract
Nitrite (NO2-)- and nitrate (NO3-)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO2-- and NO3--dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 107 to 2.8 × 108 copies g-1 dry sediment) than upstream sediments (2.4 × 107 to 3.5 × 107 copies g-1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 105 to 4.8 × 105 copies g-1 dry sediment). The 13CH4 tracer experiments suggested the occurrence of NO2-- and NO3--dependent AOM activities, and their rates were 4.7-14.1 and 0.8-2.6 nmol CO2 g-1 (dry sediment) d-1, respectively. Further, the rates of NO2--dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO3- concentration was the key factor affecting the spatial variations of abundance and activity of NO2--dependent anaerobic methanotrophs. Overall, our results showed different responses of NO2-- and NO3--dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hai-Xiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jiang-Bing Xu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yun Kong
- College of Resources and Environment, Yangtze University, Hubei, Wuhan, 430100, China
| | - Jian-Hui Li
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Yan Liu
- Wuxijiang National Wetland Park Service, Quzhou, 324000, China
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24
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Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering. Microorganisms 2020; 8:microorganisms8040550. [PMID: 32290343 PMCID: PMC7232337 DOI: 10.3390/microorganisms8040550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
Drained peatlands are significant sources of the greenhouse gas (GHG) carbon dioxide. Rewetting is a proven strategy used to protect carbon stocks; however, it can lead to increased emissions of the potent GHG methane. The response to rewetting of soil microbiomes as drivers of these processes is poorly understood, as are the biotic and abiotic factors that control community composition. We analyzed the pro- and eukaryotic microbiomes of three contrasting pairs of minerotrophic fens subject to decade-long drainage and subsequent long-term rewetting. Abiotic soil properties including moisture, dissolved organic matter, methane fluxes, and ecosystem respiration rates were also determined. The composition of the microbiomes was fen-type-specific, but all rewetted sites showed higher abundances of anaerobic taxa compared to drained sites. Based on multi-variate statistics and network analyses, we identified soil moisture as a major driver of community composition. Furthermore, salinity drove the separation between coastal and freshwater fen communities. Methanogens were more than 10-fold more abundant in rewetted than in drained sites, while their abundance was lowest in the coastal fen, likely due to competition with sulfate reducers. The microbiome compositions were reflected in methane fluxes from the sites. Our results shed light on the factors that structure fen microbiomes via environmental filtering.
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25
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Liu T, Guo J, Hu S, Yuan Z. Model-based investigation of membrane biofilm reactors coupling anammox with nitrite/nitrate-dependent anaerobic methane oxidation. ENVIRONMENT INTERNATIONAL 2020; 137:105501. [PMID: 32032775 DOI: 10.1016/j.envint.2020.105501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 05/28/2023]
Abstract
An innovative process coupling anaerobic ammonium oxidation (anammox) with nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) in membrane biofilm reactors (MBfRs) has been developed to achieve high-level nitrogen removal from both sidestream (i.e., anaerobic digestion liquor) and mainstream (i.e., domestic strength) wastewater. In this study, a 1D biofilm model embedding the n-DAMO and anammox reactions was developed to facilitate further understanding of the process and its optimization. The model was calibrated and validated using comprehensive data sets from two independent MBfRs, treating sidestream- and mainstream-strength wastewater, respectively. Modelling results revealed a unique biofilm stratification. While anammox bacteria dominated throughout the biofilm, n-DAMO archaea (coupling nitrate reduction with anaerobic methane oxidation) only occurred at the inner layer and n-DAMO bacteria (coupling nitrite reduction with anaerobic methane oxidation) spread more evenly with a slightly higher fraction in the outer layer. The established MBfRs were robust against dynamic influent flowrates and nitrite/ammonium ratios. Thicker biofilms were beneficial for not only the total nitrogen (TN) removal but also the system robustness. Additionally, a positive correlation between the nitrogen removal efficiency and the residual methane emission was observed, as a result of higher methane partial pressure required. However, there was a threshold of methane partial pressure, above which the residual methane increased but nitrogen removal efficiency was stable. Meanwhile, thicker biofilms were also favorable to achieve less residual methane emission. Simulation results also suggested the feasibility of methane-based MBfRs to polish mainstream anammox effluent to meet a stringent N discharge standard (e.g., TN < 5 mg/L).
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Affiliation(s)
- Tao Liu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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26
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He Z, Xu S, Zhao Y, Pan X. Methane emissions from aqueous sediments are influenced by complex interactions among microbes and environmental factors: A modeling study. WATER RESEARCH 2019; 166:115086. [PMID: 31536890 DOI: 10.1016/j.watres.2019.115086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 08/16/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Methane fluxes from aqueous sediments strongly influence global atmospheric methane. However, many questions still puzzle researchers; for example, why are some unstable sediments atmospheric methane sinks? In this study, a biofilm model originally developed for wastewater treatment was modified to simulate the microbial kinetics and substance conversions in aqueous surface sediments. The model was validated by the experimental data and could predict chemical profiles and microbial distributions in sediments. The model revealed complicated interactions between different microbial communities and environmental factors, including competition between aerobic methane-oxidizing bacteria, nitrite-dependent anaerobic methane-oxidizing bacteria, and anaerobic ammonia-oxidizing bacteria. The results of model simulations showed that the effects of environmental factors, especially dissolved oxygen and ammonia in overlying water, on methane fluxes are very complicated. Rapid environmental changes (which can be caused by tide, day-night alternation, or zoobenthic and human activity) and intensive competition between microbes greatly affected methane fluxes and resulted in alternation between atmospheric methane source and sink in unstable sediments. This study extends the application of a wastewater treatment model to ecological studies of microbial interactions in natural sediments and explains some problems that might be difficult to resolve by using experimental methods.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Shuyu Xu
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yuanhai Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China; Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
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27
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Xu S, Lu W, Mustafa M, Liu Y, Wang H. Presence of diverse nitrate‐dependent anaerobic methane oxidizing archaea in sewage sludge. J Appl Microbiol 2019; 128:775-783. [DOI: 10.1111/jam.14502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/29/2019] [Accepted: 10/23/2019] [Indexed: 01/03/2023]
Affiliation(s)
- S. Xu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse School of Environmental and Biological Engineering Nanjing University of Science and Technology Nanjing China
- School of Environment Tsinghua University Beijing China
| | - W. Lu
- School of Environment Tsinghua University Beijing China
| | - M.F. Mustafa
- Department of Environmental Design Health and Nutritional Sciences Research Complex Allama Iqbal Open University Islamabad Pakistan
| | - Y. Liu
- School of Environment Tsinghua University Beijing China
| | - H. Wang
- School of Environment Tsinghua University Beijing China
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28
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Luo JH, Wu M, Liu J, Qian G, Yuan Z, Guo J. Microbial chromate reduction coupled with anaerobic oxidation of methane in a membrane biofilm reactor. ENVIRONMENT INTERNATIONAL 2019; 130:104926. [PMID: 31228790 DOI: 10.1016/j.envint.2019.104926] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/02/2019] [Accepted: 06/12/2019] [Indexed: 06/09/2023]
Abstract
It has been reported that microbial reduction of sulfate, nitrite/nitrate and iron/manganese could be coupled with anaerobic oxidation of methane (AOM), which plays a significant role in controlling methane emission from anoxic niches. However, little is known about microbial chromate (Cr(VI)) reduction coupling with AOM. In this study, a microbial consortium was enriched via switching nitrate dosing to chromate feeding as the sole electron acceptor under anaerobic condition in a membrane biofilm reactor (MBfR), in which methane was continuously provided as the electron donor through bubble-less hollow fiber membranes. According to long-term reactor operation and chromium speciation analysis, soluble chromate could be reduced into Cr(III) compounds by using methane as electron donor. Fluorescence in situ hybridization and high-throughput 16S rRNA gene amplicon profiling further indicated that after feeding chromate Candidatus 'Methanoperedens' (a known nitrate-dependent anaerobic methane oxidation archaeon) became sole anaerobic methanotroph in the biofilm, potentially responsible for the chromate bio-reduction driven by methane. Two potential pathways of the microbial AOM-coupled chromate reduction were proposed: (i) Candidatus 'Methanoperedens' independently utilizes chromate as electron acceptor to form Cr(III) compounds, or (ii) Candidatus 'Methanoperedens' oxidizes methane to generate intermediates or electrons, which will be utilized to reduce chromate to Cr(III) compounds by unknown chromate reducers synergistically. Our findings suggest a possible link between the biogeochemical chromium and methane cycles.
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Affiliation(s)
- Jing-Huan Luo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland 4072, Australia; School of Environmental and Chemical Engineering, Shanghai University, 333 Nanchen Road, Shanghai 200444, PR China
| | - Mengxiong Wu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianyong Liu
- School of Environmental and Chemical Engineering, Shanghai University, 333 Nanchen Road, Shanghai 200444, PR China
| | - Guangren Qian
- School of Environmental and Chemical Engineering, Shanghai University, 333 Nanchen Road, Shanghai 200444, PR China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland 4072, Australia.
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29
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Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Karin Stultiens
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | | | - Wouter Versantvoort
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | | | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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30
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Shen L, Ouyang L, Zhu Y, Trimmer M. Spatial separation of anaerobic ammonium oxidation and nitrite‐dependent anaerobic methane oxidation in permeable riverbeds. Environ Microbiol 2019; 21:1185-1195. [DOI: 10.1111/1462-2920.14554] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural MeteorologyDepartment of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology Nanjing 210044 China
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London E1 4NS, London UK
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31
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Anaerobic Methane Oxidation in High-Arctic Alaskan Peatlands as a Significant Control on Net CH4 Fluxes. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3010007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Terrestrial consumption of the potent greenhouse gas methane (CH4) is a critical aspect of the future climate, as CH4 concentrations in the atmosphere are projected to play an increasingly important role in global climate forcing. Anaerobic oxidation of methane (AOM) has only recently been considered a relevant control on methane fluxes from terrestrial systems. We performed in vitro anoxic incubations of intact peat from Utqiaġvik (Barrow), Alaska using stable isotope tracers. Our results showed an average potential AOM rate of 15.0 nmol cm3 h−1, surpassing the average rate of gross CH4 production (6.0 nmol cm3 h−1). AOM and CH4 production rates were positively correlated. While CH4 production was insensitive to additions of Fe(III), there was a depth:Fe(III) interaction in the kinetic reaction rate constant for AOM, suggestive of stimulation by Fe(III), particularly in shallow soils (<10 cm). We estimate AOM would consume 25–34% of CH4 produced under ambient conditions. Soil genetic surveys showed phylogenetic links between soil microbes and known anaerobic methanotrophs in ANME groups 2 and 3. These results suggest a prevalent role of AOM to net CH4 fluxes from Arctic peatland ecosystems, and a probable link with Fe(III)-reduction.
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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Wang B, Huang S, Zhang L, Zhao J, Liu G, Hua Y, Zhou W, Zhu D. Diversity of NC10 bacteria associated with sediments of submerged Potamogeton crispus (Alismatales: Potmogetonaceae). PeerJ 2018; 6:e6041. [PMID: 30533317 PMCID: PMC6284450 DOI: 10.7717/peerj.6041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/30/2018] [Indexed: 12/15/2022] Open
Abstract
Background The nitrite-dependent anaerobic methane oxidation (N-DAMO) pathway, which plays an important role in carbon and nitrogen cycling in aquatic ecosystems, is mediated by “Candidatus Methylomirabilis oxyfera” (M. oxyfera) of the NC10 phylum. M. oxyfera-like bacteria are widespread in nature, however, the presence, spatial heterogeneity and genetic diversity of M. oxyfera in the rhizosphere of aquatic plants has not been widely reported. Method In order to simulate the rhizosphere microenvironment of submerged plants, Potamogeton crispus was cultivated using the rhizobox approach. Sediments from three compartments of the rhizobox: root (R), near-rhizosphere (including five sub-compartments of one mm width, N1–N5) and non-rhizosphere (>5 mm, Non), were sampled. The 16S rRNA gene library was used to investigate the diversity of M. oxyfera-like bacteria in these sediments. Results Methylomirabilis oxyfera-like bacteria were found in all three sections, with all 16S rRNA gene sequences belonging to 16 operational taxonomic units (OTUs). A maximum of six OTUs was found in the N1 sub-compartment of the near-rhizosphere compartment and a minimum of four in the root compartment (R) and N5 near-rhizosphere sub-compartment. Indices of bacterial community diversity (Shannon) and richness (Chao1) were 0.73–1.16 and 4–9, respectively. Phylogenetic analysis showed that OTU1-11 were classified into group b, while OTU12 was in a new cluster of NC10. Discussion Our results confirmed the existence of M. oxyfera-like bacteria in the rhizosphere microenvironment of the submerged plant P. crispus. Group b of M. oxyfera-like bacteria was the dominant group in this study as opposed to previous findings that both group a and b coexist in most other environments. Our results indicate that understanding the ecophysiology of M. oxyfera-like bacteria group b may help to explain their existence in the rhizosphere sediment of aquatic plant.
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Affiliation(s)
- Binghan Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Shanshan Huang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Liangmao Zhang
- Laboratory of Environmental Planning and Management, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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Fernández-Baca CP, Truhlar AM, Omar AEH, Rahm BG, Walter MT, Richardson RE. Methane and nitrous oxide cycling microbial communities in soils above septic leach fields: Abundances with depth and correlations with net surface emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:429-441. [PMID: 29860012 DOI: 10.1016/j.scitotenv.2018.05.303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Onsite septic systems use soil microbial communities to treat wastewater, in the process creating potent greenhouse gases (GHGs): methane (CH4) and nitrous oxide (N2O). Subsurface soil dispersal systems of septic tank overflow, known as leach fields, are an important part of wastewater treatment and have the potential to contribute significantly to GHG cycling. This study aimed to characterize soil microbial communities associated with leach field systems and quantify the abundance and distribution of microbial populations involved in CH4 and N2O cycling. Functional genes were used to target populations producing and consuming GHGs, specifically methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) for CH4 and nitric oxide reductase (cnorB) and nitrous oxide reductase (nosZ) for N2O. All biomarker genes were found in all soil samples regardless of treatment (leach field, sand filter, or control) or depth (surface or subsurface). In general, biomarker genes were more abundant in surface soils than subsurface soils suggesting the majority of GHG cycling is occurring in near-surface soils. Ratios of production to consumption gene abundances showed a positive relationship with CH4 emissions (mcrA:pmoA, p < 0.001) but not with N2O emission (cnorB:nosZ, p > 0.05). Of the three measured soil parameters (volumetric water content (VWC), temperature, and conductivity), only VWC was significantly correlated to a biomarker gene, mcrA (p = 0.0398) but not pmoA or either of the N2O cycling genes (p > 0.05 for cnorB and nosZ). 16S rRNA amplicon library sequencing results revealed soil VWC, CH4 flux and N2O flux together explained 64% of the microbial community diversity between samples. Sequencing of mcrA and pmoA amplicon libraries revealed treatment had little effect on diversity of CH4 cycling organisms. Overall, these results suggest GHG cycling occurs in all soils regardless of whether or not they are associated with a leach field system.
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Affiliation(s)
- Cristina P Fernández-Baca
- Department of Civil and Environmental Engineering, 220 Hollister Hall, Cornell University, Ithaca, NY, United States.
| | - Allison M Truhlar
- New York State Water Resources Institute, 230 Riley-Robb Hall, Cornell University, Ithaca, NY, United States
| | - Amir-Eldin H Omar
- Department of Molecular Biology and Genetics, 107 Biotechnology Building, Cornell University, Ithaca, NY, United States
| | - Brian G Rahm
- New York State Water Resources Institute, 230 Riley-Robb Hall, Cornell University, Ithaca, NY, United States
| | - M Todd Walter
- Department of Biological and Environmental Engineering, 232 Riley-Robb Hall, Cornell University, Ithaca, NY, United States
| | - Ruth E Richardson
- Department of Civil and Environmental Engineering, 220 Hollister Hall, Cornell University, Ithaca, NY, United States
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Shen LD, Ouyang L, Zhu Y, Trimmer M. Active pathways of anaerobic methane oxidation across contrasting riverbeds. ISME JOURNAL 2018; 13:752-766. [PMID: 30375505 PMCID: PMC6461903 DOI: 10.1038/s41396-018-0302-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/19/2018] [Accepted: 09/30/2018] [Indexed: 12/26/2022]
Abstract
Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO2 g−1 (dry sediment) d−1, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 105 to 1.5 × 107 and 2.1 × 104 to 2.5 × 105 copies g−1 dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.,School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Liao Ouyang
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Yizhu Zhu
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Mark Trimmer
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
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Li W, Lu P, Chai F, Zhang L, Han X, Zhang D. Long-term nitrate removal through methane-dependent denitrification microorganisms in sequencing batch reactors fed with only nitrate and methane. AMB Express 2018; 8:108. [PMID: 29961200 PMCID: PMC6026486 DOI: 10.1186/s13568-018-0637-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022] Open
Abstract
Denitrifying anaerobic methane oxidation (damo) bioprocesses can remove nitrate using methane as the electron donor, which gains great concern due to the current stringent discharge standard of nitrogen in wastewater treatment plants. To obtain an engineering acceptable nitrogen removal rate (NRR) and demonstrate the long-term stable ability of damo system under conditions of nitrate and methane, two sequencing batch reactors (SBRs) fed with only nitrate and methane were operated for more than 600 days at 30 °C. The NRR of 21.91 ± 0.73 mg NO3--N L-1 day-1 was obtained which is, to the best of our knowledge, the highest rate observed in the literatures under such conditions. The temperature was found to significantly affect the system performance. Furthermore, the microbial community was analyzed by using real-time PCR technique. The results showed that the microbial consortium contained damo archaea and bacteria. These two microbes cooperated to maintain the long-term stability. And the number of damo archaea was higher than that of damo bacteria with the ratio of 1.77. By using methane as the electron donor, damo archaea reduced nitrate to nitrite coupled to methane oxidation and damo bacteria reduce the generated nitrite to nitrogen gas. The first step of nitrate to nitrite taken by damo archaea might be the limiting step of this cooperation system. SBR could be a suitable reactor configuration to enrich slow-growing microbes like damo culture. These results demonstrated the potential application of damo processes for nitrogen removal of wastewater containing low C/N ratios.
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Affiliation(s)
- Weiwei Li
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Fengguang Chai
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Xinkuan Han
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
| | - Daijun Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044 People’s Republic of China
- Department of Environmental Science, Chongqing University, Chongqing, 400044 People’s Republic of China
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in ‘t Zandt MH, de Jong AEE, Slomp CP, Jetten MSM. The hunt for the most-wanted chemolithoautotrophic spookmicrobes. FEMS Microbiol Ecol 2018; 94:4966976. [PMID: 29873717 PMCID: PMC5989612 DOI: 10.1093/femsec/fiy064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are the drivers of biogeochemical methane and nitrogen cycles. Essential roles of chemolithoautotrophic microorganisms in these cycles were predicted long before their identification. Dedicated enrichment procedures, metagenomics surveys and single-cell technologies have enabled the identification of several new groups of most-wanted spookmicrobes, including novel methoxydotrophic methanogens that produce methane from methylated coal compounds and acetoclastic 'Candidatus Methanothrix paradoxum', which is active in oxic soils. The resultant energy-rich methane can be oxidized via a suite of electron acceptors. Recently, 'Candidatus Methanoperedens nitroreducens' ANME-2d archaea and 'Candidatus Methylomirabilis oxyfera' bacteria were enriched on nitrate and nitrite under anoxic conditions with methane as an electron donor. Although 'Candidatus Methanoperedens nitroreducens' and other ANME archaea can use iron citrate as an electron acceptor in batch experiments, the quest for anaerobic methane oxidizers that grow via iron reduction continues. In recent years, the nitrogen cycle has been expanded by the discovery of various ammonium-oxidizing prokaryotes, including ammonium-oxidizing archaea, versatile anaerobic ammonium-oxidizing (anammox) bacteria and complete ammonium-oxidizing (comammox) Nitrospira bacteria. Several biogeochemical studies have indicated that ammonium conversion occurs under iron-reducing conditions, but thus far no microorganism has been identified. Ultimately, iron-reducing and sulfate-dependent ammonium-oxidizing microorganisms await discovery.
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Affiliation(s)
- Michiel H in ‘t Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Anniek EE de Jong
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Department of Earth Sciences, Geochemistry, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Mike SM Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Netherlands Earth System Science Center, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Shen LD, Wu HS, Liu X, Li J. Cooccurrence and potential role of nitrite- and nitrate-dependent methanotrophs in freshwater marsh sediments. WATER RESEARCH 2017; 123:162-172. [PMID: 28668629 DOI: 10.1016/j.watres.2017.06.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Revised: 05/31/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
Nitrite- and nitrate-dependent anaerobic methane oxidation are mediated by the NC10 bacteria closely related to "Candidatus Methylomirabilis oxyfera" (M. oxyfera) and the ANME-2d archaea closely related to "Candidatus Methanoperedens nitroreducens" (M. nitroreducens), respectively. Here, we investigated the occurrence and activity of both M. oxyfera-like bacteria and M. nitroreducens-like archaea in the sediment of freshwater marshes in Eastern China. The presence of diverse M. oxyfera-like bacteria (>87% identity to M. oxyfera) and M. nitroreducens-like archaea (>96% identity to M. nitroreducens) was confirmed by using Illumina-based total bacterial and archaeal 16S rRNA gene sequencing, respectively. The recovered M. oxyfera-like bacterial sequences accounted for 1.6-4.3% of the total bacterial 16S rRNA pool, and M. nitroreducens-like archaeal sequences accounted for 0.2-1.8% of the total archaeal 16S rRNA pool. The detected numbers of OTUs of the 16S rRNA genes of M. oxyfera-like bacteria and M. nitroreducens-like archaea were 78 and 72, respectively, based on 3% sequence difference. Quantitative PCR showed that the 16S rRNA gene abundance of M. oxyfera-like bacteria (6.1 × 106-3.2 × 107 copies g-1 sediment) was 2-4 orders of magnitude higher than that of M. nitroreducens-like archaea (1.4 × 103-3.2 × 104 copies g-1 sediment). Stable isotope experiments showed that the addition of both nitrite and nitrate stimulated the anaerobic methane oxidation, while the stimulation by nitrite is more significant than nitrate. Our results provide the first evidence that the M. oxyfera-like bacteria play a more important role than the M. nitroreducens-like archaea in methane cycling in wetland systems.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China.
| | - Hong-Sheng Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China; Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xu Liu
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ji Li
- Department of Agricultural Resource and Environment, College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
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Ghashghavi M, Jetten MSM, Lüke C. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers. AMB Express 2017; 7:162. [PMID: 28831762 PMCID: PMC5567572 DOI: 10.1186/s13568-017-0466-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023] Open
Abstract
Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.
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Vaksmaa A, Guerrero-Cruz S, van Alen TA, Cremers G, Ettwig KF, Lüke C, Jetten MSM. Enrichment of anaerobic nitrate-dependent methanotrophic 'Candidatus Methanoperedens nitroreducens' archaea from an Italian paddy field soil. Appl Microbiol Biotechnol 2017; 101:7075-7084. [PMID: 28779290 PMCID: PMC5569662 DOI: 10.1007/s00253-017-8416-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 01/06/2023]
Abstract
Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by ‘Candidatus Methanoperedens nitroreducens’ archaea and ‘Candidatus Methylomirabilis oxyfera’ NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, ‘Candidatus Methanoperedens nitroreducens’ had the highest abundance of (2.2 ± 0.4 × 108) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described ‘Candidatus Methanoperedens nitroreducens ANME2D’ (96% identity) and ‘Candidatus Methylomirabilis oxyfera’ (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of ‘Candidatus Methanoperedens nitroreducens Vercelli’ that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to ‘Candidatus Methanoperedens nitroreducens ANME2D’ (WP_048089615.1) at the protein level. The ‘Candidatus Methylomirabilis oxyfera’ draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for ‘Candidatus Methanoperedens nitroreducens’. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Katharina F Ettwig
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands
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Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland. Appl Environ Microbiol 2017; 83:AEM.00782-17. [PMID: 28526796 DOI: 10.1128/aem.00782-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/14/2017] [Indexed: 02/01/2023] Open
Abstract
Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably, there was an increasing abundance of sulfate reducers (Desulfococcus and other Deltaproteobacteria) and anammox microorganisms (Brocadiaceae) with depth. Pore water profiles demonstrated that nitrate and sulfate concentrations exhibited a commensurate decrease with biomat depth accompanied by the accumulation of ammonium. Quantitative PCR targeting the anammox hydrazine synthase gene, hzsA, revealed a 3-fold increase in abundance with biomat depth as well as a 2-fold increase in the sulfate reductase gene, dsrA These microbial and geochemical trends were most pronounced in proximity to the influent region of the wetland where the biomat was thickest and influent nitrate concentrations were highest. While direct genetic queries for dissimilatory nitrate reduction to ammonium (DNRA) microorganisms proved unsuccessful, an increasing depth-dependent dominance of Gammaproteobacteria and diatoms that have previously been functionally linked to DNRA was observed. To further explore this potential, a series of microcosms containing field-derived biomat material confirmed the ability of the community to produce sulfide and reduce nitrate; however, significant ammonium production was observed only in the presence of hydrogen sulfide. Collectively, these results suggest that biogenic sulfide induces DNRA, which in turn can explain the requisite coproduction of ammonium and nitrite from nitrified effluent necessary to sustain the anammox community.IMPORTANCE This study aims to increase understanding of why and how anammox is occurring in an engineered wetland with limited exogenous contributions of ammonium and nitrite. In doing so, the study has implications for how geochemical parameters could potentially be leveraged to impact nutrient cycling and attenuation during the operation of treatment wetlands. The work also contributes to ongoing discussions about biogeochemical signatures surrounding anammox processes and enhances our understanding of the contributions of anammox processes in freshwater environments.
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Vaksmaa A, Jetten MSM, Ettwig KF, Lüke C. McrA primers for the detection and quantification of the anaerobic archaeal methanotroph 'Candidatus Methanoperedens nitroreducens'. Appl Microbiol Biotechnol 2017; 101:1631-1641. [PMID: 28084539 PMCID: PMC5266762 DOI: 10.1007/s00253-016-8065-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of ‘Candidatus M. nitroreducens’. The first primer pair produces a fragment of 186-bp that can be used to quantify ‘Candidatus M. nitroreducens’ cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the ‘Candidatus M. nitroreducens’ mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106 copies g−1 wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102 copies g−1 wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104 copies g−1 wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known ‘Candidatus M. nitroreducens’ archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of ‘Candidatus M. nitroreducens’ sequences, which have been only poorly captured by general methanogenic mcrA primers.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, The Netherlands
| | - Katharina F Ettwig
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Reverse Methanogenesis and Respiration in Methanotrophic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:1654237. [PMID: 28154498 PMCID: PMC5244752 DOI: 10.1155/2017/1654237] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.
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