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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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Yan A, Pan Z, Liang Y, Mo X, Guo T, Li J. Archaea communities in aerobic granular sludge: A mini-review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174974. [PMID: 39053544 DOI: 10.1016/j.scitotenv.2024.174974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/27/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.
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Affiliation(s)
- Anqi Yan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zengrui Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yifan Liang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinyan Mo
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tao Guo
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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3
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Hu R, He Z, Wang C. Rethinking microbially driven methane formation in mangrove wetlands. Trends Microbiol 2024; 32:832-835. [PMID: 38897853 DOI: 10.1016/j.tim.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
Mangrove wetlands contribute to climate change mitigation through efficient carbon burial, yet microbial methanogenesis offsets these climate benefits. We review the diversity of methanogenic microorganisms in mangrove sediments, present the unrecognized role of bacteria on methanogenesis, and highlight the significance of distinguishing various methanogenic pathways to assess mangrove climate benefits.
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Affiliation(s)
- Ruiwen Hu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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Wang Q, Zheng G, Ni L, Wang H, Li W, Guo P, Wang Y, Zheng D, Wu J, Zhang D. Colonization characteristics and dynamic transition of archaea communities on polyethylene and polypropylene microplastics in the sediments of mangrove ecosystems. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134343. [PMID: 38640671 DOI: 10.1016/j.jhazmat.2024.134343] [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: 12/03/2023] [Revised: 02/28/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Microplastics are a growing concern in mangrove ecosystems; however, their effects on archaeal communities and related ecological processes remain unclear. We conducted in situ biofilm-enrichment experiments to investigate the ecological influence of polyethylene (PE) and polypropylene microplastics on archaeal communities in the sediments of mangrove ecosystems. The archaeal community present on microplastics was distinct from that of the surrounding sediments at an early stage but became increasingly similar over time. Bathyarchaeota, Thaumarchaeota, Euryarchaeota, and Asgardaeota were the most abundant phyla. Methanolobus, an archaeal biomarker, was enriched in PE biofilms, and significantly controlled by homogeneous selection in the plastisphere, indicating an increased potential risk of methane emission. The dominant archaeal assembly process in the sediments was deterministic (58.85%-70.47%), while that of the PE biofilm changed from stochastic to deterministic during the experiment. The network of PE plastispheres showed less complexity and competitive links, and higher modularity and stability than that of sediments. Functional prediction showed an increase in aerobic ammonia oxidation during the experiment, whereas methanogenesis and chemoheterotrophy were significantly higher in the plastisphere. This study provides novel insights into the impact of microplastic pollution on archaeal communities and their mediating ecological functions in mangrove ecosystems.
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Affiliation(s)
- Qiong Wang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China; Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Gang Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Xianghu Laboratory, Hangzhou 311231, Zhejiang, China
| | - Lingfang Ni
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Heng Wang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316021, Zhejiang, China
| | - Weiye Li
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Daoqiong Zheng
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China
| | - Jiaping Wu
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China; Donghai Laboratory, Zhoushan 316021, Zhejiang, China; Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan 316021, Zhejiang, China.
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5
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Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [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: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
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Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
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6
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Qu Y, Zhao Y, Yao X, Wang J, Liu Z, Hong Y, Zheng P, Wang L, Hu B. Salinity causes differences in stratigraphic methane sources and sinks. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 19:100334. [PMID: 38046178 PMCID: PMC10692758 DOI: 10.1016/j.ese.2023.100334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 12/05/2023]
Abstract
Methane metabolism, driven by methanogenic and methanotrophic microorganisms, plays a pivotal role in the carbon cycle. As seawater intrusion and soil salinization rise due to global environmental shifts, understanding how salinity affects methane emissions, especially in deep strata, becomes imperative. Yet, insights into stratigraphic methane release under varying salinity conditions remain sparse. Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata (15-40 m depth) through in situ and microcosm simulation studies. Coastal strata, exhibiting a salinity level five times greater than terrestrial strata, manifested a 12.05% decrease in total methane production, but a staggering 687.34% surge in methane oxidation, culminating in 146.31% diminished methane emissions. Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics, impacting the methanogenic archaeal, methanotrophic archaeal, and methanotrophic bacterial communities by 16.53%, 27.25%, and 22.94%, respectively. Furthermore, microbial interactions influenced strata system methane metabolism. Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition, facilitating methane production via Methanofastidiosales. This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.
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Affiliation(s)
- Ying Qu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yi Hong
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Lizhong Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
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Yeo J, Jeon YW. Impact of Polyethylene-Glycol-Induced Water Potential on Methane Yield and Microbial Consortium Dynamics in the Anaerobic Degradation of Glucose. Bioengineering (Basel) 2024; 11:433. [PMID: 38790299 PMCID: PMC11117670 DOI: 10.3390/bioengineering11050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
This study investigated the relationship between water potential (Ψ) and the cation-induced inhibition of methane production in anaerobic digesters. The Ψ around methanogens was manipulated using polyethylene glycol (PEG) in a batch anaerobic reactor, ranging from -0.92 to -5.10 MPa. The ultimate methane potential (Bu) decreased significantly from 0.293 to 0.002 Nm3 kg-1-VSadded as Ψ decreased. When Ψ lowered from -0.92 MPa to -1.48 MPa, the community distribution of acetoclastic Methanosarcina decreased from 59.62% to 40.44%, while those of hydrogenotrophic Methanoculleus and Methanobacterium increased from 17.70% and 1.30% to 36.30% and 18.07%, respectively. These results mirrored changes observed in methanogenic communities affected by cation inhibition with KCl. Our findings strongly indicate that the inhibitory effect of cations on methane production may stem more from the water stress induced by cations than from their direct toxic effects. This study highlights the importance of considering Ψ dynamics in understanding cation-mediated inhibition in anaerobic digesters, providing insights into optimizing microbial processes for enhanced methane production from organic substrates.
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Affiliation(s)
- Jin Yeo
- Biogas Research Center, Hankyong National University, Anseong 17579, Republic of Korea;
| | - Yong-Woo Jeon
- Environmental Technology Division, Korea Testing Laboratory, Seoul 08389, Republic of Korea
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Yang M, Liu N, Wang B, Li Y, Li W, Shi X, Yue X, Liu CQ. Stepwise degradation of organic matters driven by microbial interactions in China΄s coastal wetlands: Evidence from carbon isotope analysis. WATER RESEARCH 2024; 250:121062. [PMID: 38157604 DOI: 10.1016/j.watres.2023.121062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
The microbial "unseen majority" as drivers of carbon cycle represent a significant source of uncertain climate change. To comprehend the resilience of life forms on Earth to climate change, it is crucial to incorporate knowledge of intricate microbial interactions and their impact to carbon transformation. Combined with carbon stable isotope analysis and high-throughput sequencing technology, the underlying mechanism of microbial interactions for organic carbon degradation has been elucidated. Niche differentiation enabled archaea to coexist with bacteria mainly in a cooperative manner. Bacteria composed of specialists preferred to degrade lighter carbon, while archaea were capable of utilizing heavier carbon. Microbial resource-dependent interactions drove stepwise degradation of organic matter. Bacterial cooperation directly facilitated the degradation of algae-dominated particulate organic carbon, while competitive feeding of archaea caused by resource scarcity significantly promoted the mineralization of heavier particulate organic carbon and then the release of dissolved inorganic carbon. Meanwhile, archaea functioned as a primary decomposer and collaborated with bacteria in the gradual degradation of dissolved organic carbon. This study emphasized microbial interactions driving carbon cycle and provided new perspectives for incorporating microorganisms into carbon biogeochemical models.
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Affiliation(s)
- Meiling Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China
| | - Na Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Baoli Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China.
| | - Yajun Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Wanzhu Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xinjie Shi
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xinrui Yue
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Bohai Coastal Critical Zone National Observation and Research Station, Tianjin University, Tianjin 300072, China
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Wang L, Lin Y, Li J, Yu Q, Xu K, Ren H, Geng J. Deciphering Microbe-Mediated Dissolved Organic Matter Reactome in Wastewater Treatment Plants Using Directed Paired Mass Distance. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:739-750. [PMID: 38147428 DOI: 10.1021/acs.est.3c06871] [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: 12/28/2023]
Abstract
Understanding the reaction mechanism of dissolved organic matter (DOM) during wastewater biotreatment is crucial for optimal DOM control. Here, we develop a directed paired mass distance (dPMD) method that constructs a molecular network displaying the reaction pathways of DOM. It couples direction inference and PMD analysis to extract the substrate-product relationships and delta masses of potentially paired reactants directly from sequential mass spectrometry data without formula assignment. Using this method, we analyze the influent and effluent samples from the bioprocesses of 12 wastewater treatment plants (WWTPs) and build a dPMD network to characterize the core reactome of DOM. The network shows that the first step of the transformation triggers reaction cascades that diversify the DOM, but the highly overlapped subsequent reaction pathways result in similar effluent DOM compositions across WWTPs despite varied influents. Mass changes exhibit consistent gain/loss preferences (e.g., +3.995 and -16.031) but different occurrences across WWTPs. Combined with genome-centric metatranscriptomics, we reveal the associations among dPMDs, enzymes, and microbes. Most enzymes are involved in oxygenation, (de)hydrogenation, demethylation, and hydration-related reactions but with different target substrates and expressed by various taxa, as exemplified by Proteobacteria, Actinobacteria, and Nitrospirae. Therefore, a functionally diverse community is pivotal for advanced DOM degradation.
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Affiliation(s)
- Liye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Yuan Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Juechun Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Qingmiao Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400044, P. R. China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Jinju Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400044, P. R. China
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10
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Chen X, Cai R, Zhuo X, Chen Q, He C, Sun J, Zhang Y, Zheng Q, Shi Q, Jiao N. Niche differentiation of microbial community shapes vertical distribution of recalcitrant dissolved organic matter in deep-sea sediments. ENVIRONMENT INTERNATIONAL 2023; 178:108080. [PMID: 37429058 DOI: 10.1016/j.envint.2023.108080] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023]
Abstract
Sedimentary organic matter provides carbon substrates and energy sources for microorganisms, which drive benthic biogeochemical processes and in turn modify the quantity and quality of dissolved organic matter (DOM). However, the molecular composition and distribution of DOM and its interactions with microbes in deep-sea sediments remain poorly understood. Here, molecular composition of DOM and its relationship with microbes were analyzed in samples collected from two sediment cores (∼40 cm below the sea floor), at depths of 1157 and 2253 m from the South China Sea. Results show that niche differentiation was observed on a fine scale in different sediment layers, with Proteobacteria and Nitrososphaeria dominating the shallow sediments (0-6 cm) and Chloroflexi and Bathyarchaeia prevailing in deeper sediments (6-40 cm), indicating correspondence of microbial community composition with both geographical isolation and the availability of organic matter. An intimate link between the DOM composition and microbial community further indicates that, microbial mineralization of fresh organic matter in the shallow layer potentially resulted in the accumulation of recalcitrant DOM (RDOM), while relatively low abundance of RDOM was linked to anaerobic microbial utilization in deeper sediment layers. In addition, higher RDOM abundance in the overlying water, as compared to that in the surface sediment, suggests that sediment might be a source of deep-sea RDOM. These results emphasize the close relation between the distribution of sediment DOM and different microbial community, laying a foundation for understanding the complex dynamics of RDOM in deep-sea sediment and water column.
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Affiliation(s)
- Xiaoxia Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Ruanhong Cai
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China.
| | - Xiaocun Zhuo
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Quanrui Chen
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Jia Sun
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Qiang Zheng
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, Research Centre for Geomicrobial Resources and Application, China University of Petroleum, Beijing 102249, China
| | - Nianzhi Jiao
- College of Ocean and Earth Sciences and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361005, China; Carbon Neutral Innovation Research Center, Xiamen University, Xiamen 361005, China.
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Lu J, Sha H, Chen J, Yi X, Xiong J. Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12572-7. [PMID: 37191684 DOI: 10.1007/s00253-023-12572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023]
Abstract
Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.
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Affiliation(s)
- Jiaqi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Haonan Sha
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xianghua Yi
- Lanshion Marine Science and Technology Co., Ltd, Ningbo, 315715, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, 315211, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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