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Yan Y, Ma JJ, Liang XP, Yin Y, Wu YQ, Yu RL, Hu GR, Zhu YG, Li H. Occurrence and spatiotemporal distribution of arsenic biotransformation genes in urban dust. ENVIRONMENT INTERNATIONAL 2024; 190:108823. [PMID: 38908273 DOI: 10.1016/j.envint.2024.108823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/18/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Microbially-mediated arsenic biotransformation plays a pivotal role in the biogeochemical cycling of arsenic; however, the presence of arsenic biotransformation genes (ABGs) in urban dust remains unclear. To investigate the occurrence and spatiotemporal distributions of ABGs, a total of one hundred and eighteen urban dust samples were collected from different districts of Xiamen city, China in summer and winter. Although inorganic arsenic species, including arsenate [As(V)] and arsenite [As(III)], were found to be predominant, the methylated arsenicals, particularly trimethylarsine oxide [TMAs(V)O] and dimethylarsenate [DMAs(V)], were detected in urban dust. Abundant ABGs were identified in urban dust via AsChip analysis (a high-throughput qPCR chip for ABGs), of which As(III) S-adenosylmethionine methyltransferase genes (arsM), As(V) reductase genes (arsC), As(III) oxidase genes (aioA), As(III) transporter genes (arsB), and arsenic-sensing regulator genes (arsR) were the most prevalent, collectively constituting more than 90 % of ABGs in urban dust. Microbes involved in arsenic methylation were assigned to bacteria (e.g., Actinomycetes and Alphaproteobacteria), archaea (e.g., Halobacteria), and eukaryotes (e.g., Chlamydomonadaceae) in urban dust via the arsM amplicon sequencing. Temperature, a season-dependent environmental factor, profoundly affected the abundance of ABGs and the composition of microbes involved in arsenic methylation. This study provides new insights into the presence of ARGs within the urban dust.
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Affiliation(s)
- Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jin-Jin Ma
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiu-Peng Liang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yi Yin
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Ya-Qing Wu
- Instrumental Analysis Center of Huaqiao University, Huaqiao University, Xiamen 361021, China
| | - Rui-Lian Yu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Gong-Ren Hu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Liu ZT, Ma RA, Zhu D, Konstantinidis KT, Zhu YG, Zhang SY. Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome. Nat Commun 2024; 15:5168. [PMID: 38886447 PMCID: PMC11183072 DOI: 10.1038/s41467-024-49165-5] [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: 02/19/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
Antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) coexist in organic fertilized agroecosystems based on their correlations in abundance, yet evidence for the genetic linkage of ARG-MRGs co-selected by organic fertilization remains elusive. Here, an analysis of 511 global agricultural soil metagenomes reveals that organic fertilization correlates with a threefold increase in the number of diverse types of ARG-MRG-carrying contigs (AMCCs) in the microbiome (63 types) compared to non-organic fertilized soils (22 types). Metatranscriptomic data indicates increased expression of AMCCs under higher arsenic stress, with co-regulation of the ARG-MRG pairs. Organic fertilization heightens the coexistence of ARG-MRG in genomic elements through impacting soil properties and ARG and MRG abundances. Accordingly, a comprehensive global map was constructed to delineate the distribution of coexistent ARG-MRGs with virulence factors and mobile genes in metagenome-assembled genomes from agricultural lands. The map unveils a heightened relative abundance and potential pathogenicity risks (range of 4-6) for the spread of coexistent ARG-MRGs in Central North America, Eastern Europe, Western Asia, and Northeast China compared to other regions, which acquire a risk range of 1-3. Our findings highlight that organic fertilization co-selects genetically linked ARGs and MRGs in the global soil microbiome, and underscore the need to mitigate the spread of these co-resistant genes to safeguard public health.
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Affiliation(s)
- Zi-Teng Liu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Rui-Ao Ma
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Si-Yu Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.
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Prieto-Fernández F, Lambert S, Kujala K. Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms. Front Microbiol 2024; 15:1386120. [PMID: 38855773 PMCID: PMC11160943 DOI: 10.3389/fmicb.2024.1386120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/23/2024] [Indexed: 06/11/2024] Open
Abstract
Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.
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Sonthiphand P, Rueangmongkolrat N, Uthaipaisanwong P, Kusonmano K, Mhuantong W, Termsaithong T, Limthamprasert C, Chotpantarat S, Luepromchai E. Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2024; 112:49. [PMID: 38466428 DOI: 10.1007/s00128-024-03866-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/31/2024] [Indexed: 03/13/2024]
Abstract
Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.
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Affiliation(s)
- Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.
| | - Nattanan Rueangmongkolrat
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Pichahpuk Uthaipaisanwong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok, Thailand
| | - Kanthida Kusonmano
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bang Khun Thian, Bangkok, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Teerasit Termsaithong
- Learning Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Theoretical and Computational Physics (TCP) group, Center of Excellence in Theoretical and Computational Science (TaCS-CoE), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chanida Limthamprasert
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Srilert Chotpantarat
- Department of Geology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand
- Research Unit of Site Remediation on Metals Management from Industry and Mining (Site Rem), Chulalongkorn University, Bangkok, Thailand
| | - Ekawan Luepromchai
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Kuo J, Liu D, Wen WH, Chiu CY, Chen W, Wu YW, Lai FT, Lin CH. Different microbial communities in paddy soils under organic and nonorganic farming. Braz J Microbiol 2024; 55:777-788. [PMID: 38147271 PMCID: PMC10920611 DOI: 10.1007/s42770-023-01218-5] [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: 10/04/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
Organic agriculture is a farming method that provides healthy food and is friendly to the environment, and it is developing rapidly worldwide. This study compared microbial communities in organic farming (Or) paddy fields to those in nonorganic farming (Nr) paddy fields based on 16S rDNA sequencing and analysis. The predominant microorganisms in both soils were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, and Nitrospirota. The alpha diversity of the paddy soil microbial communities was not different between the nonorganic and organic farming systems. The beta diversity of nonmetric multidimensional scaling (NMDS) revealed that the two groups were significantly separated. Distance-based redundancy analysis (db-RDA) suggested that soil pH and electrical conductivity (EC) had a positive relationship with the microbes in organic paddy soils. There were 23 amplicon sequence variants (ASVs) that showed differential abundance. Among them, g_B1-7BS (Proteobacteria), s_Sulfuricaulis limicola (Proteobacteria), g_GAL15 (p_GAL15), c_Thermodesulfovibrionia (Nitrospirota), two of f_Anaerolineaceae (Chloroflexi), and two of g_S085 (Chloroflexi) showed that they were more abundant in organic soils, whereas g_11-24 (Acidobacteriota), g__Subgroup_7 (Acidobacteriota), and g_Bacillus (Firmicutes) showed differential abundance in nonorganic paddy soils. Functional prediction of microbial communities in paddy soils showed that functions related to carbohydrate metabolism could be the major metabolic activities. Our work indicates that organic farming differs from nonorganic farming in terms of microbial composition in paddy soils and provides specific microbes that might be helpful for understanding soil fertility.
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Affiliation(s)
- Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung, 94450, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, 94450, Taiwan
| | - Daniel Liu
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wei Hao Wen
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Ching Yuan Chiu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Wanyu Chen
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Yun Wen Wu
- Department of Bioresources, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Fang-Ting Lai
- Department of Medicinal Botanicals and Foods On Health Applications, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan
| | - Chorng-Horng Lin
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua, 51591, Taiwan.
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Qiao J, Chen M, Zhong S, Tong H, Li F. Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2303-2312. [PMID: 38263620 DOI: 10.1021/acs.est.3c07753] [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: 01/25/2024]
Abstract
Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.
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Affiliation(s)
- Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Manjia Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Songxiong Zhong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
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Gao AX, Chen C, Gao ZY, Zhai ZQ, Wang P, Zhang SY, Zhao FJ. Soil redox status governs within-field spatial variation in microbial arsenic methylation and rice straighthead disease. THE ISME JOURNAL 2024; 18:wrae057. [PMID: 38564256 PMCID: PMC11031232 DOI: 10.1093/ismejo/wrae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024]
Abstract
Microbial arsenic (As) methylation in paddy soil produces mainly dimethylarsenate (DMA), which can cause physiological straighthead disease in rice. The disease is often highly patchy in the field, but the reasons remain unknown. We investigated within-field spatial variations in straighthead disease severity, As species in rice husks and in soil porewater, microbial composition and abundance of arsM gene encoding arsenite S-adenosylmethionine methyltransferase in two paddy fields. The spatial pattern of disease severity matched those of soil redox potential, arsM gene abundance, porewater DMA concentration, and husk DMA concentration in both fields. Structural equation modelling identified soil redox potential as the key factor affecting arsM gene abundance, consequently impacting porewater DMA and husk DMA concentrations. Core amplicon variants that correlated positively with husk DMA concentration belonged mainly to the phyla of Chloroflexi, Bacillota, Acidobacteriota, Actinobacteriota, and Myxococcota. Meta-omics analyses of soil samples from the disease and non-disease patches identified 5129 arsM gene sequences, with 71% being transcribed. The arsM-carrying hosts were diverse and dominated by anaerobic bacteria. Between 96 and 115 arsM sequences were significantly more expressed in the soil samples from the disease than from the non-disease patch, which were distributed across 18 phyla, especially Acidobacteriota, Bacteroidota, Verrucomicrobiota, Chloroflexota, Pseudomonadota, and Actinomycetota. This study demonstrates that even a small variation in soil redox potential within the anoxic range can cause a large variation in the abundance of As-methylating microorganisms, thus resulting in within-field variation in rice straighthead disease. Raising soil redox potential could be an effective way to prevent straighthead disease.
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Affiliation(s)
- A-Xiang Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Chuan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Zi-Yu Gao
- School of Ecological and Environmental Sciences, East China Normal University, NO. 500 Dongchuan Street, Minghang, Shanghai 200241, China
| | - Zhi-Qiang Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Peng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
| | - Si-Yu Zhang
- School of Ecological and Environmental Sciences, East China Normal University, NO. 500 Dongchuan Street, Minghang, Shanghai 200241, China
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Center of Agricultural Health, Academy for Advanced Interdisciplinary, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, NO. 1 Weigang, Xuanwu district, Nanjing 210095, China
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Qiao J, Liu J, Palomo A, Bostick BC, Phan K, Zheng Y, Li F. Prevalence of Methylated Arsenic and Microbial Arsenic Methylation Genes in Paddy Soils of the Mekong Delta. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37354103 DOI: 10.1021/acs.est.3c00210] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Abstract
Microbially mediated inorganic-methylated arsenic (As) transformation in paddy soil is crucial to rice safety; however, the linkages between the microbial As methylation process and methylated As species remain elusive. Here, 62 paddy soils were collected from the Mekong River delta of Cambodia to profile As-related functional gene composition involved in the As cycle. The soil As concentration ranged from <1 to 16.6 mg kg-1, with average As contents of approximately 81% as methylated As and 54% as monomethylarsenate (MMAs(V)) in the phosphate- and oxalate-extractable fractions based on As sequential extraction analysis. Quantitative PCR revealed high arsenite-methylating gene (arsM) copy numbers, and metagenomics identified consistently high arsM gene abundance. The abundance of As-related genes was the highest in bacteria, followed by archaea and fungi. Pseudomonas, Bradyrhizobium, Burkholderia, and Anaeromyxobacter were identified as bacteria harboring the most genes related to As biotransformation. Moreover, arsM and arsI (As demethylation) gene-containing operons were identified in the metagenome-assembled genomes (MAGs), implying that arsM and arsI could be transcribed together. The prevalence of methylated As and arsM genes may have been overlooked in tropical paddy fields. The As methylation-demethylation cycle should be considered when manipulating the methylated As pool in paddy fields for rice safety.
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Affiliation(s)
- Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, Guangdong 510650, China
| | - Jingyu Liu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Queensland Alliance for Environmental Health Science (QAEHS), The University of Queensland, Brisbane 4108, Australia
| | - Alejandro Palomo
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Benjamin C Bostick
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, United States
| | - Kongkea Phan
- Faculty of Science and Technology, International University, Phnom Penh 12101, Cambodia
| | - Yan Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, Guangdong 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, Guangdong 510650, China
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Zhang C, Liu X, Shi LD, Li J, Xiao X, Shao Z, Dong X. Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments. NPJ Biofilms Microbiomes 2023; 9:13. [PMID: 36991068 PMCID: PMC10060404 DOI: 10.1038/s41522-023-00382-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.
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Affiliation(s)
- Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xi Xiao
- Key Laboratory of Marine Mineral Resources, Ministry of Natural Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Ke T, Zhang D, Guo H, Xiu W, Zhao Y. Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158549. [PMID: 36075436 DOI: 10.1016/j.scitotenv.2022.158549] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
High arsenic (As) in groundwater is an environmental issue of global concern, which is closely related to microbe-mediated As biogeochemical cycling. However, the distribution of genes related to As cycling and underlying microbial As biogeochemical processes in high As groundwater remain elusive. Hence, we profiled the As cycling genes (arsC, arrA, and aioA genes) and indigenous microbial communities in groundwater from a typical high As area, the Hetao Basin from China, using amplicon sequencing and qPCR techniques. Here, we revealed the significant difference in microbial community structure between low As groundwater samples (LG) and high As groundwater samples (HG). Acinetobacter, Thiovirga, Hydrogenophaga, and Sulfurimonas were dominant in LG, while Aquabcterium, Acinetobacter, Sphingomonas, Pseudomonas, Desulfomicrobium, Hydrogenophaga, and Nitrospira were predominant in HG. Shannon and Chao indices of the microbial communities in HG were significantly higher than those of in LG. Alpha diversity and abundance of arsC and arrA genes were higher than those of aioA genes. The significant positive correlation was uncovered between the abundances of arsC and aioA genes, suggesting the cooccurrence of As functional genes in groundwater. Sphingopyxis, Agrobacterium, Klebsiella, Hoeflea, and Aeromonas represented the dominant taxa within the As (V) reducers communities. Distance-based redundancy analysis showed that ORP, pH, Astot, Mn, and DOC were the key factors shaping the diverse microbial populations, while ORP, S2-, As(III), Fe(II), NH4+, pH, Mn, SO42-, As(V), temperature, and P as the main drivers affecting arsenotrophic microbiota. This work provides an insight into microbial communities linked to As biogeochemical processes in high As groundwater, playing a fundamental role in groundwater As cycling.
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Affiliation(s)
- Tiantian Ke
- Ministry of Education, Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing, China
| | - Di Zhang
- Ministry of Education, Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing, China
| | - Huaming Guo
- Ministry of Education, Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing, China.
| | - Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Beijing), Beijing, China
| | - Yi Zhao
- Ministry of Education, Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
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Cantillo-González A, Anguita J, Rojas C, Vargas IT. Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments. MICROMACHINES 2022; 13:1953. [PMID: 36422381 PMCID: PMC9692521 DOI: 10.3390/mi13111953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm-2. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.
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Affiliation(s)
- Angela Cantillo-González
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 6640064, Chile
| | - Javiera Anguita
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Claudia Rojas
- Laboratory of Soil Microbial Ecology and Biogeochemistry (LEMiBiS), Institute of Agri-Food, Animal and Environmental Sciences (ICA3), Universidad de O’Higgins, San Fernando 3070000, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago 8331150, Chile
| | - Ignacio T. Vargas
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago 6640064, Chile
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12
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. FRONTIERS IN PLANT SCIENCE 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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