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Liu J, Pei R, Liu R, Jing C, Liu W. Arsenic methylation and microbial communities in paddy soils under alternating anoxic and oxic conditions. J Environ Sci (China) 2025; 148:468-475. [PMID: 39095181 DOI: 10.1016/j.jes.2023.10.030] [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: 07/25/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 08/04/2024]
Abstract
Arsenic (As) methylation in soils affects the environmental behavior of As, excessive accumulation of dimethylarsenate (DMA) in rice plants leads to straighthead disease and a serious drop in crop yield. Understanding the mobility and transformation of methylated arsenic in redox-changing paddy fields is crucial for food security. Here, soils including un-arsenic contaminated (N-As), low-arsenic (L-As), medium-arsenic (M-As), and high-arsenic (H-As) soils were incubated under continuous anoxic, continuous oxic, and consecutive anoxic/oxic treatments respectively, to profile arsenic methylating process and microbial species involved in the As cycle. Under anoxic-oxic (A-O) treatment, methylated arsenic was significantly increased once oxygen was introduced into the incubation system. The methylated arsenic concentrations were up to 2-24 times higher than those in anoxic (A), oxic (O), and oxic-anoxic (O-A) treatments, under which arsenic was methylated slightly and then decreased in all four As concentration soils. In fact, the most plentiful arsenite S-adenosylmethionine methyltransferase genes (arsM) contributed to the increase in As methylation. Proteobacteria (40.8%-62.4%), Firmicutes (3.5%-15.7%), and Desulfobacterota (5.3%-13.3%) were the major microorganisms related to this process. These microbial increased markedly and played more important roles after oxygen was introduced, indicating that they were potential keystone microbial groups for As methylation in the alternating anoxic (flooding) and oxic (drainage) environment. The novel findings provided new insights into the reoxidation-driven arsenic methylation processes and the model could be used for further risk estimation in periodically flooded paddy fields.
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Affiliation(s)
- Jing Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Rui Pei
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Runzeng Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Wenjing Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
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Ito K, Kuramata M, Tanikawa H, Suda A, Yamaguchi N, Ishikawa S. Diversity and transcription of genes involved in respiratory As(V) reduction and As(III) methylation in Japanese paddy soils. BMC Microbiol 2024; 24:396. [PMID: 39379826 PMCID: PMC11462812 DOI: 10.1186/s12866-024-03562-4] [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: 05/20/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Arsenic (As) metabolism by soil microorganisms has an impact on As geochemical cycling in paddy soils, which in turn affects As uptake in rice. However, little is known about the key microorganisms involved in this process in Japanese paddy soil. RESULTS Total RNA was extracted from Japanese paddy soils with different levels of dissolved As under flooded conditions, and the transcription of As metabolic genes (arrA, ttrA and arsM) was analyzed via a metatranscriptomic approach. The results showed that ttrA was the predominant respiratory arsenate reductase gene transcribed in these soils rather than arrA, suggesting that ttrA contributes to the reductive dissolution of As. The predominant taxa expressing ttrA differed among soils but were mostly associated with genera known for their iron- and/or sulfate-reduction activity. In addition, a wide variety of microorganisms expressed and upregulated arsM approximately 5.0- to 13.2-fold at 9 d compared with 3 d of incubation under flooded conditions in flasks. CONCLUSIONS Our results support the involvement of microbial activity in the geochemical cycling of As in Japanese paddy soils and suggest that ttrA may be one of the key genes involved in the formation of arsenite, an inorganic species taken up by rice.
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Affiliation(s)
- Koji Ito
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Masato Kuramata
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hachidai Tanikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Aomi Suda
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Noriko Yamaguchi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Satoru Ishikawa
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
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Hemmat-Jou MH, Liu S, Liang Y, Chen G, Fang L, Li F. Microbial arsenic methylation in soil-water systems and its environmental significance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173873. [PMID: 38879035 DOI: 10.1016/j.scitotenv.2024.173873] [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: 03/27/2024] [Revised: 05/20/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
In this review, we have summarized the current knowledge about the environmental importance, relevance, and consequences of microbial arsenic (As) methylation in various ecosystems. In this regard, we have presented As biomethylation in terrestrial and aquatic ecosystems particularly in rice paddy soils and wetlands. The functions of As biomethylation by microbial consortia in anaerobic and aerobic conditions are extensively discussed. In addition, we have tried to explain the interconnections between As transformation and carbon (C), such as microbial degradation of organic compounds and methane (CH4) emission. These processes can cause As release because of the reduction of arsenate (As(V)) to the more mobile arsenite (As(III)) as well as As methylation and the formation of toxic trivalent methylated As species in anaerobic conditions. Furthermore, the sulfur (S) transformation can form highly toxic thiolated As species owing to its interference with As biomethylation. Besides, we have focused on many other mutual interlinks that remain elusive between As and C, including As biomethylation, thiolation, and CH4 emission, in the soil-water systems. Recent developments have clarified the significant and complex interactions between the coupled microbial process in anoxic and submerged soils. These processes, performed by little-known/unknown microbial taxa or well-known members of microbial communities with unrecognized metabolic pathways, conducted several concurrent reactions that contributed to global warming on our planet and have unfavorable impacts on water quality and human food resources. Finally, some environmental implications in rice production and arsenic removal from soil-water systems are discussed. Generally, our understanding of the ecological and metabolic evidence for the coupling and synchronous processes of As, C, and S are involved in environmental contamination-caused toxicity in human food, including high As content in rice grain, water resources, and global warming through methanogenesis elucidate combating global rice safety, drinking water, and climate changes.
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Affiliation(s)
- Mohammad Hossein Hemmat-Jou
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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
| | - Sujie Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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
| | - Yongmei Liang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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
| | - Guanhong Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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
| | - Liping Fang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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.
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, 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
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Naiel MAE, Taher ES, Rashed F, Ghazanfar S, Shehata AM, Mohammed NA, Pascalau R, Smuleac L, Ibrahim AM, Abdeen A, Shukry M. The arsenic bioremediation using genetically engineered microbial strains on aquatic environments: An updated overview. Heliyon 2024; 10:e36314. [PMID: 39286167 PMCID: PMC11402758 DOI: 10.1016/j.heliyon.2024.e36314] [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: 02/19/2024] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024] Open
Abstract
Heavy metal contamination threatens the aquatic environment and human health. Different physical and chemical procedures have been adopted in many regions; however, their adoption is usually limited since they take longer time, are more expensive, and are ineffective in polluted areas with high heavy metal contents. Thus, biological remediation is considered a suitable applicable method for treating contaminates due to its aquatic-friendly features. Bacteria possess an active metabolism that enables them to thrive and develop in highly contaminated water bodies with arsenic (As). They achieve this by utilizing their genetic structure to selectively target As and deactivate its toxic influences. Therefore, this review extensively inspects the bacterial reactions and interactions with As. In addition, this literature demonstrated the potential of certain genetically engineered bacterial strains to upregulate the expression and activity of specific genes associated with As detoxification. The As resistant mechanisms in bacteria exhibit significant variation depending on the genetics and type of the bacterium, which is strongly affected by the physical water criteria of their surrounding aquatic environment. Moreover, this literature has attempted to establish scientific connections between existing knowledge and suggested sustainable methods for removing As from aquatic bodies by utilizing genetically engineered bacterial strains. We shall outline the primary techniques employed by bacteria to bioremediate As from aquatic environments. Additionally, we will define the primary obstacles that face the wide application of genetically modified bacterial strains for As bioremediation in open water bodies. This review can serve as a target for future studies aiming to implement real-time bioremediation techniques. In addition, potential synergies between the bioremediation technology and other techniques are suggested, which can be employed for As bioremediation.
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Affiliation(s)
- Mohammed A E Naiel
- Animal Production Department, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Ehab S Taher
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, 13110, Jordan
| | - Fatema Rashed
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa, 13110, Jordan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Abdelrazeq M Shehata
- Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Nourelhuda A Mohammed
- Department of Physiology and Biochemistry, Faculty of Medicine, Mutah University, Mutah, 61710, Al-Karak, Jordan
| | - Raul Pascalau
- Department of Agricultural Technologies, Faculty of Agriculture, University of Life Sciences "King Mihai I" from Timisoara, Romania
| | - Laura Smuleac
- Department of Sustainable Development and Environmental Engineering Faculty of Agriculture, University of Life Sciences "King Mihai I" from Timisoara, Timisoara, Roman, Romania
| | - Ateya Megahed Ibrahim
- Department of Administration and Nursing Education, College of Nursing, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Department of Family and Community Health Nursing, Faculty of Nursing, Port-Said University, Egypt
| | - Ahmed Abdeen
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Benha University, Toukh, 13736, Egypt
- Department of Biochemistry, Faculty of Veterinary Medicine, South Valley University, Qena, 83523, Egypt
| | - Mustafa Shukry
- Department of Physiology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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Song Y, Prather KLJ. Strategies in engineering sustainable biochemical synthesis through microbial systems. Curr Opin Chem Biol 2024; 81:102493. [PMID: 38971129 DOI: 10.1016/j.cbpa.2024.102493] [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: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 07/08/2024]
Abstract
Growing environmental concerns and the urgency to address climate change have increased demand for the development of sustainable alternatives to fossil-derived fuels and chemicals. Microbial systems, possessing inherent biosynthetic capabilities, present a promising approach for achieving this goal. This review discusses the coupling of systems and synthetic biology to enable the elucidation and manipulation of microbial phenotypes for the production of chemicals that can substitute for petroleum-derived counterparts and contribute to advancing green biotechnology. The integration of artificial intelligence with metabolic engineering to facilitate precise and data-driven design of biosynthetic pathways is also discussed, along with the identification of current limitations and proposition of strategies for optimizing biosystems, thereby propelling the field of chemical biology towards sustainable chemical production.
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Affiliation(s)
- Yoseb Song
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Limmer MA, Seyfferth AL. Controlling exposure to As and Cd from rice via irrigation management. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:339. [PMID: 39073464 PMCID: PMC11286649 DOI: 10.1007/s10653-024-02116-x] [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: 04/17/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024]
Abstract
Irrigation management controls biogeochemical cycles in rice production. Under flooded paddy conditions, arsenic becomes plant-available as iron-reducing conditions ensue, while oxic conditions lead to increased plant availability of Cd in acidic soils. Because Cd enters rice through Mn transporters, we hypothesized that irrigation resulting in intermediate redox could simultaneously limit both As and Cd in rice grain due to As retention in soil and Mn competition for Cd uptake. In a 2 year field study, we used 6 irrigation managements that varied in extent and frequency of inundation, and we observed strong effects of irrigation management on porewater chemistry, soil redox potentials, plant As and Cd concentrations, plant nutrient concentrations, and methane emissions. Plant As decreased with drier irrigation management, but in the grain this effect was stronger for organic As than for inorganic As. Grain organic As, but not inorganic As, was strongly and positively correlated with cumulative methane emissions. Conversely, plant Cd increased under more aerobic irrigation management and grain Cd was negatively correlated with porewater Mn. A hazard index approach showed that in the tested soil with low levels of As and Cd (5.4 and 0.072 mg/kg, respectively), irrigation management could not simultaneously decrease grain As and Cd. Many soil properties, such as reducible As, available Cd, soil pH, available S, and soil organic matter should be considered when attempting to optimize irrigation management when the goal is decreasing the risk of As and Cd in rice grain.
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Affiliation(s)
- Matt A Limmer
- Department of Plant and Soil Science, University of Delaware, Newark, DE, USA
| | - Angelia L Seyfferth
- Department of Plant and Soil Science, University of Delaware, Newark, DE, USA.
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7
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Hu L, Huang F, Qian Y, Ding T, Yang Y, Shen D, Long Y. Pathways and contributions of sulfate reducing-bacteria to arsenic cycling in landfills. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134582. [PMID: 38776810 DOI: 10.1016/j.jhazmat.2024.134582] [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: 01/03/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Sulfate-reducing bacteria (SRB) are generally found in sanitary landfills and play a role in sulfur (S) and metal/metalloid geochemical cycling. In this study, we investigated the influence of SRB on arsenic (As) metabolic pathways in refuse-derived cultures. The results indicated that SRB promote As(III) methylation and are beneficial for controlling As levels. Heterotrophic and autotrophic SRB showed significant differences during As cycling. In heterotrophic SRB cultures, the As methylation rate increased with As(III) concentration in the medium and reached a peak (85.1%) in cultures containing 25 mg L-1 As(III). Moreover, 4.0-12.6% of SO42- was reduced to S2-, which then reacted with As(III) to form realgar (AsS). In contrast, autotrophic SRB oxidized As(III) to less toxic As(V) under anaerobic conditions. Heterotrophic arsM-harboring SRB, such as Desulfosporosinus, Desulfocurvibacter, and Desulfotomaculum, express As-related genes and are considered key genera for As methylation in landfills. Thiobacillus are the main autotrophic SRB in landfills and can derive energy by oxidizing sulfur compounds and metal(loid)s. These results suggest that different types of SRB drive As methylation, redox reaction, and mineral formation in landfills. These study findings have implications for the management of As pollutants in landfills and other contaminated environments.
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Affiliation(s)
- Lifang Hu
- College of Energy Environment and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Feng Huang
- College of Energy Environment and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Yating Qian
- College of Energy Environment and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Tao Ding
- College of Energy Environment and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China.
| | - Yuzhou Yang
- College of Energy Environment and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yuyang Long
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
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8
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Teng ZJ, Li J, Wang P, Li CY, Peng M, Qin QL, Chen XL, Chen Y, Fu HH, Wang N, Zhang YZ. Meta-omics analysis reveals the marine arsenic cycle driven by bacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135137. [PMID: 39024770 DOI: 10.1016/j.jhazmat.2024.135137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/16/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
Arsenic is a toxic element widely distributed in the Earth's crust and ranked as a class I human carcinogen. Microbial metabolism makes significant contributions to arsenic detoxification, migration and transformation. Nowadays, research on arsenic is primarily in areas affected by arsenic pollution associated with human health activities. However, the biogeochemical traits of arsenic in the global marine ecosystem remain to be explicated. In this study, we revealed that seawater environments were primarily governed by the process of arsenate reduction to arsenite, while arsenite methylation was predominant in marine sediments which may serve as significant sources of arsenic emission into the atmosphere. Significant disparities existed in the distribution patterns of the arsenic cycle between surface and deep seawaters at middle and low latitudes, whereas these situations tend to be similar in the Arctic and Antarctic oceans. Significant variations were also observed in the taxonomic diversity and core microbial community of arsenic cycling across different marine environments. Specifically, γ-proteobacteria played a pivotal role in the arsenic cycle in the whole marine environment. Temperature, dissolved oxygen and phosphate were the crucial factors that related to these differentiations in seawater environments. Overall, our study contributes to a deeper understanding of the marine arsenic cycle.
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Affiliation(s)
- Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Jian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Pan H, Wattiez R, Gillan D. Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges. Curr Microbiol 2024; 81:257. [PMID: 38955825 DOI: 10.1007/s00284-024-03781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.
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Affiliation(s)
- Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology (Panjin Campus), Panjin, China.
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
| | - David Gillan
- Proteomics and Microbiology Department, University of Mons, Avenue du champ de Mars 6, 7000, Mons, Belgium
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10
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Chen X, Yu T, Xiao L, Zeng XC. Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa? JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134135. [PMID: 38574656 DOI: 10.1016/j.jhazmat.2024.134135] [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: 03/03/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024]
Abstract
Sb(III) and As(III) share similar chemical features and coexist in the environment. However, their oxidase enzymes have completely different sequences and structures. This raises an intriguing question: Could Sb(III)-oxidizing prokaryotes (SOPs) also oxidize As(III), and vice versa? Regarding this issue, previous investigations have yielded unclear, incorrect and even conflicting data. This work aims to address this matter. First, we prepared an enriched population of SOPs that comprises 55 different AnoA genes, lacking AioAB and ArxAB genes. We found that these SOPs can oxidize both Sb(III) and As(III) with comparable capabilities. To further confirm this finding, we isolated three cultivable SOP strains that have AnoA gene, but lack AioAB and ArxAB genes. We observed that they also oxidize both Sb(III) and As(III) under both anaerobic and aerobic conditions. Secondly, we obtained an enriched population of As(III)-oxidizing prokaryotes (AOPs) from As-contaminated soils, which comprises 69 different AioA genes, lacking AnoA gene. We observed that the AOP population has significant As(III)-oxidizing activities, but lack detectable Sb(III)-oxidizing activities under both aerobic and anaerobic conditions. Therefore, we convincingly show that SOPs can oxidize As(III), but AOPs cannot oxidize Sb(III). These findings clarify the previous ambiguities, confusion, errors or contradictions regarding how SOPs and AOPs oxidize each other's substrate.
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Affiliation(s)
- Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Tingting Yu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Linhai Xiao
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China.
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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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12
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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13
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Li J, Yin Z, Xu K, Yan L, Ye L, Du J, Jing C, Shi J. Arsenite S-Adenosylmethionine Methyltransferase Is Responsible for Antimony Biomethylation in Nostoc sp. PCC7120. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1934-1943. [PMID: 38180751 DOI: 10.1021/acs.est.3c07367] [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: 01/06/2024]
Abstract
Antimony (Sb) biomethylation is an important but uninformed process in Sb biogeochemical cycling. Methylated Sb species have been widely detected in the environment, but the gene and enzyme for Sb methylation remain unknown. Here, we found that arsenite S-adenosylmethionine methyltransferase (ArsM) is able to catalyze Sb(III) methylation. The stepwise methylation by ArsM forms mono-, di-, and trimethylated Sb species. Sb(III) is readily coordinated with glutathione, forming the preferred ArsM substrate which is anchored on three conserved cysteines. Overexpressing arsM in Escherichia coli AW3110 conferred resistance to Sb(III) by converting intracellular Sb(III) into gaseous methylated species, serving as a detoxification process. Methylated Sb species were detected in paddy soil cultures, and phylogenetic analysis of ArsM showed its great diversity in ecosystems, suggesting a high metabolic potential for Sb(III) methylation in the environment. This study shows an undiscovered microbial process methylating aqueous Sb(III) into the gaseous phase, mobilizing Sb on a regional and even global scale as a re-emerging contaminant.
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Affiliation(s)
- Jianwei Li
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhipeng Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Kun Xu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Li Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Li Ye
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Jingjing Du
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chuanyong Jing
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
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14
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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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15
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William VU, Magpantay HD. Arsenic and Microorganisms: Genes, Molecular Mechanisms, and Recent Advances in Microbial Arsenic Bioremediation. Microorganisms 2023; 12:74. [PMID: 38257901 PMCID: PMC10820871 DOI: 10.3390/microorganisms12010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Throughout history, cases of arsenic poisoning have been reported worldwide, and the highly toxic effects of arsenic to humans, plants, and animals are well documented. Continued anthropogenic activities related to arsenic contamination in soil and water, as well as its persistency and lethality, have allowed arsenic to remain a pollutant of high interest and concern. Constant scrutiny has eventually resulted in new and better techniques to mitigate it. Among these, microbial remediation has emerged as one of the most important due to its reliability, safety, and sustainability. Over the years, numerous microorganisms have been successfully shown to remove arsenic from various environmental matrices. This review provides an overview of the interactions between microorganisms and arsenic, the different mechanisms utilized by microorganisms to detoxify arsenic, as well as current trends in the field of microbial-based bioremediation of arsenic. While the potential of microbial bioremediation of arsenic is notable, further studies focusing on the field-scale applicability of this technology is warranted.
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Affiliation(s)
| | - Hilbert D. Magpantay
- Department of Chemistry, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines;
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16
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Chen C, Li L, Wang Y, Dong X, Zhao FJ. Methylotrophic methanogens and bacteria synergistically demethylate dimethylarsenate in paddy soil and alleviate rice straighthead disease. THE ISME JOURNAL 2023; 17:1851-1861. [PMID: 37604918 PMCID: PMC10579292 DOI: 10.1038/s41396-023-01498-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023]
Abstract
Microorganisms play a key role in arsenic (As) biogeochemistry, transforming As species between inorganic and organic forms and different oxidation states. Microbial As methylation is enhanced in anoxic paddy soil, producing primarily dimethylarsenic (DMAs), which can cause rice straighthead disease and large yield losses. DMAs can also be demethylated in paddy soil, but the microorganisms driving this process remain unclear. In this study, we showed that the enrichment culture of methylotrophic methanogens from paddy soil demethylated pentavalent DMAs(V) efficiently. DMAs(V) was reduced to DMAs(III) before demethylation. 16S rRNA gene diversity and metagenomic analysis showed that Methanomassiliicoccus dominated in the enrichment culture, with Methanosarcina and Methanoculleus also being present. We isolated Methanomassiliicoccus luminyensis CZDD1 and Methanosarcina mazei CZ1 from the enrichment culture; the former could partially demethylate trivalent DMAs(III) but not DMAs(V) and the latter could demethylate neither. Addition of strain CZDD1 to the enrichment culture greatly accelerated DMAs(V) demethylation. Demethylation of DMAs(V) in the enrichment culture was suppressed by ampicillin, suggesting the involvement of bacteria. We isolated three anaerobic bacterial strains including Clostridium from the enrichment culture, which could produce hydrogen and reduce DMAs(V) to DMAs(III). Furthermore, augmentation of the Methanomassiliicoccus-Clostridium coculture to a paddy soil decreased DMAs accumulation by rice and alleviated straighthead disease. The results reveal a synergistic relationship whereby anaerobic bacteria reduce DMAs(V) to DMAs(III) for demethylation by Methanomassiliicoccus and also produce hydrogen to promote the growth of Methanomassiliicoccus; enhancing their populations in paddy soil can help alleviate rice straighthead disease.
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Affiliation(s)
- Chuan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lingyan Li
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
| | - Xiuzhu Dong
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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17
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Chao H, Balcazar JL, Wu Y, Cai A, Ye M, Sun M, Hu F. Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil. ENVIRONMENT INTERNATIONAL 2023; 179:108175. [PMID: 37683504 DOI: 10.1016/j.envint.2023.108175] [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: 03/20/2023] [Revised: 08/13/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023]
Abstract
Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils.
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Affiliation(s)
- Huizhen Chao
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
| | - Jose Luis Balcazar
- Catalan Institute for Water Research (ICRA), Girona 17003, Spain; University of Girona, Girona 17004, Spain
| | - Yunling Wu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
| | - Anjuan Cai
- Jiangsu Environmental Engineering Technology Co., Ltd., 210019, China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mingming Sun
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China.
| | - Feng Hu
- Soil Ecology Lab, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization & Jiangsu Key Laboratory for Solid Organic Waste Utilization, Nanjing 210095, China
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18
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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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19
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Wang L, Guo Q, Wu G, Yu Z, Ninin JML, Planer-Friedrich B. Methanogens-Driven Arsenic Methylation Preceding Formation of Methylated Thioarsenates in Sulfide-Rich Hot Springs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7410-7420. [PMID: 37134202 DOI: 10.1021/acs.est.2c08814] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hot springs represent a major source of arsenic release into the environment. Speciation is typically reported to be dominated by arsenite, arsenate, and inorganic thiolated arsenates. Much less is known about the relevance and formation of methylated thioarsenates, a group with species of high mobility and toxicity. In hot spring samples taken from the Tengchong volcanic region in China, methylated thioarsenates contributed up to 13% to total arsenic. Enrichment cultures were obtained from the corresponding sediment samples and incubated to assess their capability to convert arsenite into methylated thioarsenates over time and in the presence of different microbial inhibitors. In contrast to observations in other environmental systems (e.g., paddy soils), there was no solid evidence, supporting that the sulfate-reducing bacteria contributed to the arsenic methylation. Methanosarcina, the sole genus of methanogens detected in the enrichment cultures, as well as Methanosarcina thermophila TM-1, a pure strain within the genus, did methylate arsenic. We propose that methylated thioarsenates in a typical sulfide-rich hot spring environment like Tengchong form via a combination of biotic arsenic methylation driven by thermophilic methanogens and arsenic thiolation with either geogenic sulfide or sulfide produced by sulfate-reducing bacteria.
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Affiliation(s)
- Luxia Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Qinghai Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - Zhicheng Yu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, Hubei, P. R. China
| | - José Miguel Léon Ninin
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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20
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Liu J, Zhang D, Luo Y, Ding T, Hu L. Microbial mediated arsenate reducing behavior in landfill leachate-saturated zone. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120281. [PMID: 36167165 DOI: 10.1016/j.envpol.2022.120281] [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: 07/27/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
As(V) reduction mediated by microorganisms might be an essential process in resisting As toxicity since As(V) is the major species in the landfill. LSZ has been considered as a trigger of all types of microbial activity inside a landfill site. This research investigated the microbial As(V)-reducing behavior in LSZ. The results revealed that higher As(V)-reduction efficiency in higher As(V) content-stress LSZ scenario. The corresponding microbial diversity also varied with the As(V) content. The microbial community structure was related to arrA and arsC distribution, which encode respiratory As(V) reductase and cytoplasmic As(V) reductase, respectively. The landfill As bio-reduction pathways were modeled, as well as the As functional gene distribution among different As(V) contents at different landfill stages. The C, N, and S metabolic processes generally affected the As(V)-resistance genes distribution. Thiosulfate oxidation, denitrification, and dissimilatory nitrate reduction positively affected arsC, while dissimilatory sulfate reduction and methanogenesis trended to play a negative role. This research provides new insight into As(V) bio-reduction inside a landfill site in terms of functional genes distribution and correlation with nutrient elements metabolic processes.
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Affiliation(s)
- Jinbao Liu
- Zhejiang Tongji Vocational College of Science and Technology, Hangzhou, 311231, China
| | - Dongchen Zhang
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Yongjun Luo
- Zhejiang Guangchuan Engineering Consulting Co. Ltd., Hangzhou, Zhejiang, 310020, China
| | - Tao Ding
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China.
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Yin Z, Ye L, Jing C. Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16473-16482. [PMID: 36227700 DOI: 10.1021/acs.est.2c05764] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.
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Affiliation(s)
- Zhipeng Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Ye
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
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Hu L, Qian Y, Ci M, Long Y, Zheng H, Xu K, Wang Y. Localized intensification of arsenic methylation within landfill leachate-saturated zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156979. [PMID: 35764148 DOI: 10.1016/j.scitotenv.2022.156979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/05/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Leachate-saturated zone (LSZ) of landfills is a complicated biogeochemical hotspot due to the continuous input of electron donors and acceptors from the top refuse layer with leachate migration. In this study, the methylation behavior of the arsenic (As) was investigated. The results indicate that As-methylation processes are influenced by temperature fields in LSZ. The dimethylarsinic acid biotransformation capability can be enhanced with an increase in temperature. Microbial diversity, quantification of functional gene (arsM), and co-occurrence network analysis further characterized the drivers of As methylation in LSZ. As-biogeochemical cycle pathways, as well as As-functional gene distribution among different temperature fields, were modeled on the basis of KEGG annotation. Binning analysis was further employed to assemble As-methylated metagenomes, enabling the identification of novel species for As methylation in landfills. Then, 87 high-quality draft metagenome-assembled genomes (MAGs) were reconstructed from LSZ refuse samples; nearly 15 % (13 of 87) belonged to putative As-methylates functional MAGs. Combined with the model of the As-biogeochemical cycle, nine putative functional species could complete methylation processes alone. The findings of this study highlighted the temperature influence on the As-methylation behavior in LSZ and could facilitate the management of As contamination in landfills.
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Affiliation(s)
- Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Yating Qian
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Manting Ci
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Instrumental Analysis Center, Zhejiang Gongshang University, Hangzhou 310012, China.
| | - Haozhe Zheng
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Ke Xu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Yuqian Wang
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
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Zhao M, Zhao Y, Lin W, Xiao KQ. An overview of experimental simulations of microbial activity in early Earth. Front Microbiol 2022; 13:1052831. [PMID: 36713221 PMCID: PMC9878457 DOI: 10.3389/fmicb.2022.1052831] [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: 09/24/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
Microbial activity has shaped the evolution of the ocean and atmosphere throughout the Earth history. Thus, experimental simulations of microbial metabolism under the environment conditions of the early Earth can provide vital information regarding biogeochemical cycles and the interaction and coevolution between life and environment, with important implications for extraterrestrial exploration. In this review, we discuss the current scope and knowledge of experimental simulations of microbial activity in environments representative of those of early Earth, with perspectives on future studies. Inclusive experimental simulations involving multiple species, and cultivation experiments with more constraints on environmental conditions similar to early Earth would significantly advance our understanding of the biogeochemical cycles of the geological past.
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Affiliation(s)
- Mingyu Zhao
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Yao Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Ke-Qing Xiao
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
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