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Feng G, Gong S. Functional Genes and Transcripts Indicate the Existent and Active Microbial Mercury-Methylating Community in Mangrove Intertidal Sediments of an Urbanized Bay. Microorganisms 2024; 12:1245. [PMID: 38930626 PMCID: PMC11205478 DOI: 10.3390/microorganisms12061245] [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: 05/27/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely investigated. An effort to assess the diversity and abundance of hgcA genes and transcripts and link them to Hg and MeHg contents was made in the mangrove intertidal sediments along the urbanized Shenzhen Bay, China. The hgcA genes and transcripts associated with Thermodesulfobacteria [mainly Geobacteraceae, Syntrophorhabdaceae, Desulfobacterales, and Desulfarculales (these four lineages were previously classified into the Deltaproteobacteria taxon)], as well as Euryarchaeota (mainly Methanomicrobia and Theionarchaea) dominated the hgcA-harboring communities, while Chloroflexota, Nitrospirota, Planctomycetota, and Lentisphaerota-like hgcA sequences accounted for a small proportion. The hgcA genes appeared in greater abundance and diversity than their transcript counterparts in each sampling site. Correlation analysis demonstrated that the MeHg content rather than Hg content significantly correlated with the structure of the existent/active hgcA-harboring community and the abundance of hgcA genes/transcripts. These findings provide better insights into the microbial Hg methylation drivers in mangrove sediments, which could be helpful for understanding the MeHg biotransformation therein.
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Affiliation(s)
- Guofang Feng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China;
- Shenzhen Key Lab of Industrial Water Saving & Municipal Sewage Reclamation Technology, Shenzhen Polytechnic University, Shenzhen 518055, China
| | - Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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2
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OuYang S, Li Y, Liu M, Zhao Q, Wang J, Xia J, He J, Jiang F. Elimination of methylmercury production potential in excessive sludge in wastewater treatment plants by sulfur addition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169934. [PMID: 38199371 DOI: 10.1016/j.scitotenv.2024.169934] [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: 10/21/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Mercury ions (Hg(II)) in wastewater can accumulate and transform into the highly neurotoxic methylmercury (MeHg) in activated sludge. The release of MeHg can have severe environmental consequences, making the treatment of MeHg-contaminated sludge a pressing concern. In this study, we found that all the collected activated sludge samples, from different wastewater treatment plants in four cities, had the potential for Hg methylation. The Hg-methylating capacity reached a maximum level of 0.70-0.92 μg/g volatile suspended solids after 48 h of exposure to 5 μg/L Hg(II) and showed an average MeHg production rate of 4.8±0.5%. Accordingly, a sludge treatment method involving the addition of elemental sulfur (S0) for a short-term or long-term duration (3 or 180 days, respectively) was proposed. The results demonstrated that this treatment approach effectively mitigated and potentially eliminated MeHg formation by simultaneously reducing Hg bioavailability and Hg-methylating bioactivity. We found that bioavailable Hg(II) ions were converted to a secondary phase similar to insoluble HgS after S0 addition treatment, leading to a decrease in Hg bioavailability in sludge. The enhancement of Hg and extracellular polymeric substances (EPS) complexation via the increasing amount of thiol groups in EPS also reduced the Hg bioavailability after the long-term treatment. Furthermore, the long-term S0 addition significantly reduced the abundance of Hg-methylators with hgcA gene and promoted the growth of Hg-reducers with merA gene, which ensured the complete elimination of MeHg production potential of the excessive activated sludge. Our findings demonstrated that the proposed S0-addition sludge treatment is a promising and safe biotechnology for treating Hg-contaminated sludge. This approach has the potential to contribute significantly to the mitigation of MeHg pollution within environmental contexts.
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Affiliation(s)
- Shenyu OuYang
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Yu Li
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Ming Liu
- State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510655, China
| | - Qingxia Zhao
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Jinting Wang
- Department of Civil and Environmental Engineering, Hong Kong University of Science & Technology, Hong Kong
| | - Juntao Xia
- School of Environmental Science & Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Junfeng He
- School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Jiang
- School of Environmental Science & Engineering, Sun Yat-sen University, Guangzhou 510275, China.
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3
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Hao X, Zhao Q, Zhou X, Huang Q, Liu YR. Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133122. [PMID: 38056276 DOI: 10.1016/j.jhazmat.2023.133122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2-8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.
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Affiliation(s)
- Xiuli Hao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinquan Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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4
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Cardona GI, Escobar MC, Acosta-González A, Díaz-Ruíz N, Niño-García JP, Vasquez Y, Marrugo-Negrete J, Marqués S. Microbial diversity and abundance of Hg related genes from water, sediment and soil the Colombian amazon ecosystems impacted by artisanal and small-scale gold mining. CHEMOSPHERE 2024; 352:141348. [PMID: 38340998 DOI: 10.1016/j.chemosphere.2024.141348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
The Amazon region abounds in precious mineral resources including gold, copper, iron, and coltan. Artisanal and small-scale gold mining (ASGM) poses a severe risk in this area due to considerable mercury release into the surrounding ecosystems. Nonetheless, the impact of mercury on both the overall microbiota and the microbial populations involved in mercury transformation is not well understood. In this study we evaluated microbial diversity in samples of soil, sediment and water potentially associated with mercury contamination in two localities (Taraira and Tarapacá) in the Colombian Amazon Forest. To this end, we characterized the bacterial community structure and mercury-related functions in samples from sites with a chronic history of mercury contamination which today have different levels of total mercury content. We also determined mercury bioavailability and mobility in the samples with the highest THg and MeHg levels (up to 43.34 and 0.049 mg kg-1, respectively, in Taraira). Our analysis of mercury speciation showed that the immobile form of mercury predominated in soils and sediments, probably rendering it unavailable to microorganisms. Despite its long-term presence, mercury did not appear to alter the microbial community structure or composition, which was primarily shaped by environmental and physicochemical factors. However, an increase in the relative abundance of merA genes was detected in polluted sediments from Taraira. Several Hg-responsive taxa in soil and sediments were detected in sites with high levels of THg, including members of the Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi phyla. The results suggest that mercury contamination at the two locations sampled may select mercury-adapted bacteria carrying the merA gene that could be used in bioremediation processes for the region.
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Affiliation(s)
- Gladys Inés Cardona
- Instituto Amazónico de Investigaciones Científicas SINCHI. Laboratorio de Biotecnología y Recursos Genéticos, Bogotá, Colombia.
| | - Maria Camila Escobar
- Instituto Amazónico de Investigaciones Científicas SINCHI. Laboratorio de Biotecnología y Recursos Genéticos, Bogotá, Colombia; Escuela de Microbiología. Universidad de Antioquia, Medellín, Colombia
| | | | - Natalie Díaz-Ruíz
- Escuela de Microbiología. Universidad de Antioquia, Medellín, Colombia
| | | | - Yaneth Vasquez
- Chemistry Department, Universidad de Córdoba, Montería, Colombia
| | - José Marrugo-Negrete
- Convergence Science and Technology Cluster, Universidad Central, Bogotá, Colombia
| | - Silvia Marqués
- Department of Biotechnology and Environmental Protection. Estación Experimental Del Zaidín. Consejo Superior de Investigaciones Científicas, Granada, Spain
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Liu YR, Guo L, Yang Z, Xu Z, Zhao J, Wen SH, Delgado-Baquerizo M, Chen L. Multidimensional Drivers of Mercury Distribution in Global Surface Soils: Insights from a Global Standardized Field Survey. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12442-12452. [PMID: 37506289 DOI: 10.1021/acs.est.3c04313] [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] [Indexed: 07/30/2023]
Abstract
Soil stores a large amount of mercury (Hg) that has adverse effects on human health and ecosystem safety. Significant uncertainties still exist in revealing environmental drivers of soil Hg accumulation and predicting global Hg distribution owing to the lack of field data from global standardized analyses. Here, we conducted a global standardized field survey and explored a holistic understanding of the multidimensional environmental drivers of Hg accumulation in global surface soils. Hg content in surface soils from our survey ranges from 3.8 to 618.2 μg kg-1 with an average of 74.0 μg kg-1 across the globe. Atmospheric Hg deposition, particularly vegetation-induced elemental Hg0 deposition, is the major source of surface soil Hg. Soil organic carbon serves as the major substrate for sequestering Hg in surface soils and is significantly influenced by agricultural management, litterfall, and elevation. For human activities, changing land-use could be a more important contributor than direct anthropogenic emissions. Our prediction of a new global Hg distribution highlights the hot spots (high Hg content) in East Asia, the Northern Hemispheric temperate/boreal regions, and tropical areas, while the cold spots (low Hg content) are in arid regions. The holistic understanding of multidimensional environmental drivers helps to predict the Hg distribution in global surface soils under a changing global environment.
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Affiliation(s)
- Yu-Rong Liu
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Guo
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, United States
| | - Zeng Xu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Jiating Zhao
- Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Shu-Hai Wen
- College of Resources and Environment and State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla 41012, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla 41013, Spain
| | - Long Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
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6
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Zhang R, Aris-Brosou S, Storck V, Liu J, Abdelhafiz MA, Feng X, Meng B, Poulain AJ. Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation. ISME COMMUNICATIONS 2023; 3:74. [PMID: 37454192 PMCID: PMC10349881 DOI: 10.1038/s43705-023-00277-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21-513 mg kg-1 dry wt. soil; MeHg: 1.21-6.82 ng g-1 dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria.
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Affiliation(s)
- Rui Zhang
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Veronika Storck
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC, H3C 3A7, Canada
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Mahmoud A Abdelhafiz
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China.
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He Z, Shen J, Li Q, Yang Y, Zhang D, Pan X. Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162148. [PMID: 36758696 DOI: 10.1016/j.scitotenv.2023.162148] [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: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.
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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
| | - Jiaquan Shen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qunqun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yingli Yang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Daoyong Zhang
- 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.
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Lü J, Wang S, Liu B, Song X. Spatiotemporal heterogeneity of nitrogen transformation potentials in a freshwater estuarine system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160335. [PMID: 36414069 DOI: 10.1016/j.scitotenv.2022.160335] [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: 07/11/2022] [Revised: 10/31/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Under the influence of water diversion, the microbial community composition of estuarine waters and sediments might have complex spatiotemporal variations. Microbial interactions with N are significant for lake water quality. Therefore, the largest lake receiving seasonal water diversion in the North China Plain was selected as the study area. Based on 16S rRNA high-throughput sequencing and metagenomic sequencing techniques, this study analysed temporal (June-December) and spatial (estuary-pelagic zone) changes in the microbial community and functional gene composition of water and sediment. The results showed that the water microbial community composition had temporality, while sediment microbes had spatiality. The main causes of temporality in the aquatic microbial community were temperature and nitrate-N concentration, while those of sediment were flow velocity and N content. Additionally, there were complex interactions between microbial communities and N. In water, temporal variation in the relative abundance of N-related functional genes might have indirectly contributed to inorganic N composition in June (nitrite-N > ammonia-N > nitrate-N) and August (nitrite-N > nitrate-N > ammonia-N). High nitrate-N concentrations in December influenced the microbial community composition. In sediment, the estuary had higher N functional genes than the pelagic estuary, creating a relatively active N cycle and reducing total N levels in the estuary. This study revealed a potentially overlooked N sink and a flow velocity threshold that has great impacts on microbial community composition. This research contributes to a deeper understanding of the estuarine N cycle under the influence of water diversions, with implications for the calculation of global N balances and the management of lake water environments.
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Affiliation(s)
- Jiali Lü
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research, Beijing 101408, China; Key Laboratory of Water Cycle & Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen 999017, Denmark
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Xiongan Institute of Innovation, Chinese Academy of Science, China.
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China; Xiongan Institute of Innovation, Chinese Academy of Science, China
| | - Xianfang Song
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research, Beijing 101408, China; Key Laboratory of Water Cycle & Related Land Surface Processes, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
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9
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Calboli FCF, Delahaut V, Deflem I, Hablützel PI, Hellemans B, Kordas A, Raeymaekers JAM, Bervoets L, De Boeck G, Volckaert FAM. Association between Chromosome 4 and mercury accumulation in muscle of the three-spined stickleback ( Gasterosteus aculeatus). Evol Appl 2021; 14:2553-2567. [PMID: 34745343 PMCID: PMC8549617 DOI: 10.1111/eva.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 08/18/2021] [Accepted: 08/29/2021] [Indexed: 11/29/2022] Open
Abstract
Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome-wide association study (GWAS) between 28,450 single nucleotide polymorphisms (SNPs) and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on Chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kb distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback.
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Affiliation(s)
- Federico C. F. Calboli
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Present address:
Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Vyshal Delahaut
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
| | - Io Deflem
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | | | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | - Anna Kordas
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | | | - Lieven Bervoets
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
| | - Gudrun De Boeck
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
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10
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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11
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Hao X, Zhu J, Rensing C, Liu Y, Gao S, Chen W, Huang Q, Liu YR. Recent advances in exploring the heavy metal(loid) resistant microbiome. Comput Struct Biotechnol J 2020; 19:94-109. [PMID: 33425244 PMCID: PMC7771044 DOI: 10.1016/j.csbj.2020.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.
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Affiliation(s)
- Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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Colby GA, Ruuskanen MO, St.Pierre KA, St.Louis VL, Poulain AJ, Aris-Brosou S. Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake. Front Microbiol 2020; 11:561194. [PMID: 33133035 PMCID: PMC7579425 DOI: 10.3389/fmicb.2020.561194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2022] Open
Abstract
Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.
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Affiliation(s)
- Graham A. Colby
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Kyra A. St.Pierre
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Vincent L. St.Louis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON, Canada
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