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de Menezes AB, Gashchak S, Wood MD, Beresford NA. Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175381. [PMID: 39122033 DOI: 10.1016/j.scitotenv.2024.175381] [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: 03/05/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.
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Affiliation(s)
- Alexandre Barretto de Menezes
- University of Galway, School of Biological and Chemical Sciences, Ryan Institute, University Road, H91 TK33, Galway, Ireland.
| | - Sergii Gashchak
- Chornobyl Center for Nuclear Safety, Radioactive Waste & Radioecology, International Radioecology Laboratory, Slavutych, Kyiv Region, Ukraine.
| | - Michael D Wood
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom.
| | - Nicholas A Beresford
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom; Centre for Ecology & Hydrology, CEH Lancaster, Lancaster Environment Centre, Library Av., Bailrigg, Lancaster LA1 4AP, United Kingdom
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2
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Cheng D, Xiong J, Dong L, Wong JWC, Liu X. Spatial distribution of PAHs and microbial communities in intertidal sediments of the Pearl River Estuary, South China. Comp Biochem Physiol C Toxicol Pharmacol 2024; 284:109992. [PMID: 39084352 DOI: 10.1016/j.cbpc.2024.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/02/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
The exploration of sediment pollution caused by PAHs and its impact on microbial communities can provide valuable insights for the remediation of sediments. The spatial distribution of PAHs and their impact on the microbial community within the Pearl River Estuary were investigated in this study. The findings revealed that the total concentration ranges of 16 PAHs were between 24.26 and 3075.93 ng/g, with naphthalene, fluorene, and phenanthrene potentially exerting adverse biological effects. More PAHs were found to accumulate in subsurface sediments, and their average accumulation rates gradually decreased as the number of rings in PAHs increased, ranging from 180 % for 2-ring to 36 % for 6-ring. The phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi were found to dominate both surface and subsurface sediments The correlation between microbial genera and PAHs contents was weak in sediments with low levels of PAHs contamination, while a more significant positive relationship was observed in sediments with high levels of PAHs contamination. The physicochemical properties of sediments, such as pH, soil structure and Cu significantly influence bacterial community composition in highly contaminated sediments. Additionally, the network analysis revealed that certain bacterial genera, including Novosphingobium, Robiginitalea and Synechococcus_CC9902, played a pivotal role in the degradation of PAHs. These findings are significant in comprehending the correlation between bacterial communities and environmental factors in intertidal ecosystems, and establish a scientific foundation for bioremediation of intertidal zones.
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Affiliation(s)
- Dengmiao Cheng
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China
| | - Jisen Xiong
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China
| | - Lu Dong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Jonathan Woon Chung Wong
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan 523808, PR China
| | - Xinhui Liu
- Research and Development Center for Watershed Environmental Eco-Engineering, Beijing Normal University, Zhuhai 519087, PR China; State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
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3
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Liu ZS, Wang KH, Han Q, Jiang CY, Liu SJ, Li DF. Sphingobium sp. SJ10-10 encodes a not-yet-reported chromate reductase and the classical Rieske dioxygenases to simultaneously degrade PAH and reduce chromate. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134889. [PMID: 38878436 DOI: 10.1016/j.jhazmat.2024.134889] [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: 04/13/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024]
Abstract
Both polycyclic aromatic hydrocarbons (PAHs) and heavy metals persist in the environment and are toxic to organisms. Their co-occurrence makes any of them difficult to remove during bioremediation and poses challenges to environmental management and public health. Microorganisms capable of effectively degrading PAHs and detoxifying heavy metals concurrently are required to improve the bioremediation process. In this study, we isolated a new strain, Sphingobium sp. SJ10-10, from an abandoned coking plant and demonstrated its capability to simultaneously degrade 92.6 % of 75 mg/L phenanthrene and reduce 90 % of 3.5 mg/L hexavalent chromium [Cr(VI)] within 1.5 days. Strain SJ10-10 encodes Rieske non-heme iron ring-hydroxylating oxygenases (RHOs) to initiate PAH degradation. Additionally, a not-yet-reported protein referred to as Sphingobium chromate reductase (SchR), with low sequence identity to known chromate reductases, was identified to reduce Cr(VI). SchR is distributed across different genera and can be classified into two classes: one from Sphingobium members and the other from non-Sphingobium species. The widespread presence of SchR in those RHO-containing Sphingobium members suggests that they are excellent candidates for bioremediation. In summary, our study demonstrates the simultaneous removal of PAHs and Cr(VI) by strain SJ10-10 and provides valuable insights into microbial strategies for managing complex pollutant mixtures.
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Affiliation(s)
- Ze-Shen Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke-Huan Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qun Han
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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4
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Gao T, Tian H, Xiang L, Wang Z, Fu Y, Shi J, Wen X, Jiang X, He W, Hashsham SA, Wang F. Characteristics of bacterial community and extracellular enzymes in response to atrazine application in black soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123286. [PMID: 38171425 DOI: 10.1016/j.envpol.2023.123286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/31/2023] [Indexed: 01/05/2024]
Abstract
The ecological functioning of black soil largely depends on the activities of various groups of microorganisms. However, little is known about how atrazine, a widely used herbicide with known harmful effects on the environment, influences the microbial ecology of black soil, and the extracellular enzymes related to the carbon, nitrogen and phosphorus cycles. Here, we evaluated the change in extracellular enzymes and bacterial community characteristics in black soil after exposure to various concentrations of atrazine. Low concentrations of applied atrazine (10 - 20 mg kg-1) were almost completely degraded after 120 days. At high concentrations (80 - 100 mg kg-1), about 95% of the applied atrazine was degraded over the same period. Additionally, linear fitting of data indicated that the total enzymatic activity index (TEI) and bacterial α-diversity index were negatively correlated with atrazine applied concentration. The atrazine had a greater effect on bacterial beta diversity after 120 days, which differentiated species clusters treated with low and high atrazine concentrations. Soil bacterial community structure and function were affected by atrazine, especially at high atrazine concentrations (80 - 100 mg kg-1). Key microorganisms such as Sphingomonas and Nocardioides were identified as biomarkers for atrazine dissipation. Functional prediction indicated that most metabolic pathways might be involved in atrazine dissipation. Overall, the findings enhance our understanding of the factors driving atrazine degradation in black soil and supports the use of biomarkers as indicators of atrazine dissipation.
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Affiliation(s)
- Tiancong Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziqi Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Shi
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Xin Wen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, China
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Center for Microbial Ecology, Michigan State University, USA
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li N, Wang Y, Zhou L, Fu D, Chen T, Chen X, Wang Q, Zhu W. The joint action of biochar and plant roots on U-stressed soil remediation: Insights from bacteriomics and metabolomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132635. [PMID: 37793252 DOI: 10.1016/j.jhazmat.2023.132635] [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: 04/18/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
Although biological remediation of U-stressed soil has been studied for a long time, the combined effects of biochar and plant roots are rarely discussed and its influence on rhizosphere microecology are still unknown. Based on pot experiments, we explored the combined efforts of biochar addition and plant roots on U-stressed rhizosphere soil in several ways, including soil physicochemical properties, soil enzyme activities, uranium chemical speciation, bacterial community structure and metabolic pathways. Our results indicates that the content of DTPA-extractable U decreased by 49.31% after biochar and plant roots application, whereas plant roots only treatment just decreased by 25.46%. Further research has found that the pH, CEC, enzyme activities and nutritional level of rhizosphere soil were more significantly improved after biochar and plant roots application. Meanwhile, the abundance and diversity of bacterial community was also upregulated, which was also suggested by the stronger metabolisms of lipids, carbohydrate, nucleotides as well as amino acids. Correlation analyses also certified the positive associations between soil properties, bacterial communities and metabolism. We speculated that the uranium immobilization was mainly attributed to the direct fixation of biochar for its alkalinity, CEC, DOC, etc. and the joint action of biochar and plant roots for their stimulating effects on bacteria. Our findings suggested that combination of biochar and plant roots could limit bioaccessibility of U in a larger extend than plant roots only, which may be a better strategy for rapid remediation of U-streesed soil.
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Affiliation(s)
- Nan Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Yilin Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Li Zhou
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Dengjiang Fu
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Tao Chen
- School of National Defense & Nuclear Science and Technology, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Xiaoming Chen
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Qing Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
| | - Wenkun Zhu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China.
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6
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Lu J, Liu Y, Zhang R, Hu Z, Xue K, Dong B. Biochar inoculated with Pseudomonas putida alleviates its inhibitory effect on biodegradation pathways in phenanthrene-contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132550. [PMID: 37729712 DOI: 10.1016/j.jhazmat.2023.132550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Controversial results are reported whereby biodegradation of polycyclic aromatic hydrocarbons (PAHs) can be promoted or inhibited by biochar amendment of soil. Metabolomics was applied to analyze the metabolic profiles of amendment with biochar (BB) and biochar inoculated with functional bacteria (Pseudomonas putida) (BP) involved in phenanthrene (PHE) degradation. Additionally, metagenomic analysis was utilized to assess the impact of different treatments on PHE degradation by soil microorganisms. Results indicated that BB treatment decreased the PHE biodegradation of the soil indigenous bacterial consortium, but BP treatment alleviated this inhibitory effect. Metabolomics revealed the differential metabolite 9-phenanthrol was absent in the BB treatment, but was found in the control group (CK), and in the treatment inoculated with the Pseudomonas putida (Ps) and the BP treatment. Metagenomic analysis showed that biochar decreased the abundance of the cytochrome P450 monooxygenase (CYP116), which was detected in the Pseudomonas putida, thus alleviating the inhibitory effect of biochar on PHE degradation. Moreover, a noticeable delayed increase of functional gene abundance and enzymes abundance in the BB treatment was observed in the PHE degradation pathway. Our findings elucidate the mechanism of inhibition with biochar amendment and the alleviating effect of biochar inoculated with degrading bacteria.
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Affiliation(s)
- Jinfeng Lu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuexian Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ruili Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengyi Hu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Biya Dong
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Sun H, Chen Q, Chen W, Qu C, Mo J, Song J, Guo J, Tian Y. Assessment of biological community in riparian zone contaminated by PAHs: Linking source apportionment to biodiversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158121. [PMID: 35988620 DOI: 10.1016/j.scitotenv.2022.158121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Riparian zone, an important land-water interface, plays an essential role in maintaining the ecological health of rivers, whereas the effects of Polycyclic aromatic hydrocarbons (PAHs) on the health of biological communities in riparian groundwater remain undetermined. To understand the responses of multiple communities to environmental variables, the distribution and ecosystem risk of 16 PAHs have been investigated in the Beiluo River, China. The distribution of multiple communities in riparian groundwater was investigated by environmental DNA metabarcoding, including 16S rRNA, 18S rRNA, and COI gene sequencing for bacteria, microbial eukaryotes (including algae, fungi, and protozoa), and metazoan, respectively, followed by correlation analysis between multiple communities and PAH contamination levels. The concentration of PAHs in the Beiluo River ranged largely from 35.32 to 728.59 ng/L. Here, the Shannon's diversity index of bacteria (Firmicutes) decreased possibly due to the occurrence of Pyrene, which mainly derives from coal and biomass combustion. Furthermore, the reduced richness of fungi (Ascomycota, Basidiomycota) and algae (Chlorophyta, Chrysophyceae) can be attributed to the presence of medium molecular weight (MMW) PAHs (Pyrene, Benz(a)anthracene, Chrysene), and low molecular weight (LMW) PAHs (Naphthalene, Fluorene, Phenanthrene). The richness and Shannon's diversity index of metazoan (Arthropoda) were promoted owing to MMW PAHs (Chrysene, Fluoranthene) generated from coal and biomass combustion and traffic emission. The ecological risk of PAHs in the groundwater environment of the Beiluo River was characterized as low to medium, where LMW and MMW PAHs posed higher risk than the high molecular weight (HMW) compounds. Overall, this study provides insights into the structures of riparian multi-biological communities altered by PAHs.
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Affiliation(s)
- Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Qiqi Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Wenwu Chen
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Chengkai Qu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jiezhang Mo
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
| | - Yulu Tian
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
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8
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Tian Z, Li G, Bai M, Hou X, Li X, Zhao C, Zhu Q, Du C, Li M, Liu W, Zhang L. Microbial mechanisms of refractory organics degradation in old landfill leachate by a combined process of UASB-A/O-USSB. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157737. [PMID: 35926627 DOI: 10.1016/j.scitotenv.2022.157737] [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: 04/25/2022] [Revised: 07/05/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
A combined process of anaerobic digestion (UASB), shortcut nitrification-denitrification (A/O), and semi-anoxic co-metabolism (operated by an up-flow semi-anoxic sludge bed; USSB) was constructed for the treatment of old landfill leachate (>10 years). The performance and mechanism of refractory organics degradation by the combined process (UASB-A/O-USSB) were investigated. The results showed that the semi-anoxic co-metabolism contributes 57 % of the totally degraded refractory organics. Specific microorganisms and their corresponding metabolic functions drive the degradation of refractory organics in each unit of the UASB-A/O-USSB process. In detail, organics with simple molecular structures were preferentially degraded by anaerobic digestion and shortcut denitrification, whereas those with complex structures were subsequently degraded in the oxic tanks and USSB reactor by shortcut nitrification and semi-anoxic co-metabolism. The structural equation model showed that the combined process of shortcut nitrification and semi-anoxic co-metabolism had a better effect on the degradation of recalcitrant organics than the single process. These findings provide information on how refractory organics are metabolically degraded in a combined process.
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Affiliation(s)
- Zhenjun Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Guowen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Miaoxin Bai
- Inner Mongolia Enterprise Key Laboratory of Damaged Environment Appraisal, Evaluation and Restoration, Hohhot 010020, China; Inner Mongolia Ecological Environment Scientific Research Institute Limited, Hohhot 010020, China
| | - Xiaolin Hou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaoguang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Chen Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qiuheng Zhu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Caili Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Maotong Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Wenjie Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lieyu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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9
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Teng T, Liang J, Zhu J, Jin P, Zhang D. Altered active pyrene degraders in biosurfactant-assisted bioaugmentation as revealed by RNA stable isotope probing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120192. [PMID: 36126767 DOI: 10.1016/j.envpol.2022.120192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Bioaugmentation is an effective approach for removing pyrene from contaminated sites, and its performance is enhanced by a biosurfactant. To reveal the mechanisms of biosurfactant-assisted bioaugmentation, we introduced RNA stable isotope probing (RNA-SIP) in the pyrene-contaminated soils and explored the impacts of rhamnolipid on the pyrene degradation process. After 12-day degradation, residual pyrene was the lowest in the bioaugmentation treatment (7.76 ± 1.57%), followed by biosurfactant-assisted bioaugmentation (9.86 ± 2.58%) and enhanced natural attenuation (23.97 ± 1.05%). Thirteen well-known and two novel pyrene-degrading bacteria were confirmed to participate in the pyrene degradation. Pyrene degradation was accelerated in the biosurfactant-assisted bioaugmentation, manifested by the high diversity of active pyrene degraders. Our findings expand the knowledge on pyrene degrading bacteria and the mechanisms of pyrene degradation in a bioaugmentation process.
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Affiliation(s)
- Tingting Teng
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
| | - Jidong Liang
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China.
| | - Jinwei Zhu
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China; Shaanxi Electrical Equipment Institute, Xi'an, 710025, PR China
| | - Pengkang Jin
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co.,Ltd and Xi'an Jiaotong University, Xi'an, 710049, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun, 130021, PR China
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10
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Khan AL, Numan M, Bilal S, Asaf S, Crafword K, Imran M, Al-Harrasi A, Al-Sabahi JN, Rehman NU, A-Rawahi A, Lee IJ. Mangrove's rhizospheric engineering with bacterial inoculation improve degradation of diesel contamination. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127046. [PMID: 34481398 DOI: 10.1016/j.jhazmat.2021.127046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Mangroves (Avicennia marina) growing in intertidal areas are often exposed to diesel spills, adversely damaging the ecosystem. Herein, we showed for the first time that mangrove seedlings' associations with bacteria could reprogram host-growth, physiology, and ability to degrade diesel. We found four bacterial strains [Sphingomonas sp.-LK11, Rhodococcus corynebacterioides-NZ1, Bacillus subtilis-EP1 Bacillus safensis-SH10] exhibiting significant growth during diesel degradation (2% and 5%, v/v) and higher expression of alkane monooxygenase compared to control. This is in synergy with reduced long-chain n-alkanes (C24-C30) during microbe-diesel interactions in the bioreactor. Among individual strains, SH10 exhibited significantly higher potential to improve mangrove seedling's morphology, anatomy and growth during diesel treatment in rhizosphere compared to control. This was also evidenced by reduced activities and gene expression of antioxidant enzymes (catalases, peroxidases, ascorbic peroxidases, superoxide dismutases and polyphenol peroxidases) and lipid peroxidation during microbe-diesel interactions. Interestingly, we noticed significantly higher soil-enzyme activities (phosphatases and glucosidases) and essential metabolites in seedling's rhizosphere after bacteria and diesel treatments. Degradation of longer n-alkane chains in the rhizosphere also revealed a potential pathway that benefits mangroves by bacterial strains during diesel contaminations. Current results support microbes' application to rhizoengineer plant growth, responses, and phytoextraction abilities in environments contaminated with diesel spills. AVAILABILITY OF DATA AND MATERIALS: The datasets generated during the current study are available in the NCBI GenBank ((https://www.ncbi.nlm.nih.gov).
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Affiliation(s)
- Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, 616, Oman; Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA.
| | - Muhammad Numan
- Department of Biology, University of North Carolina at Greensboro, NC 27412, USA
| | - Saqib Bilal
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Sajjad Asaf
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Kerri Crafword
- Department of Biology and Biochemistry, College of Natural Science and Mathematics, University of Houston, TX, USA
| | - Muhammad Imran
- School of Applied Biosciences, Kyungpook National University, Daegu Korea, South Korea
| | - Ahmed Al-Harrasi
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA.
| | - Jamal Nasser Al-Sabahi
- Central Instrument Laboratory, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Najeeb Ur Rehman
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - Ahmed A-Rawahi
- Department of Engineering Technology, College of Technology, University of Houston, Sugar Land, 77479 TX, USA
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu Korea, South Korea.
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11
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Zhao H, Gu Y, Liu X, Liu J, Waigi MG. Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15. Front Microbiol 2021; 12:792698. [PMID: 34899673 PMCID: PMC8660855 DOI: 10.3389/fmicb.2021.792698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/29/2021] [Indexed: 12/04/2022] Open
Abstract
Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.
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Affiliation(s)
- Hui Zhao
- College of Resources and Environmental Sciences, Institute of Organic Contaminant Control and Soil Remediation, Nanjing Agricultural University, Nanjing, China
| | - Yujun Gu
- College of Resources and Environmental Sciences, Institute of Organic Contaminant Control and Soil Remediation, Nanjing Agricultural University, Nanjing, China
| | - Xiangyu Liu
- College of Resources and Environmental Sciences, Institute of Organic Contaminant Control and Soil Remediation, Nanjing Agricultural University, Nanjing, China
| | - Juan Liu
- College of Resources and Environmental Sciences, Institute of Organic Contaminant Control and Soil Remediation, Nanjing Agricultural University, Nanjing, China
| | - Michael Gatheru Waigi
- College of Resources and Environmental Sciences, Institute of Organic Contaminant Control and Soil Remediation, Nanjing Agricultural University, Nanjing, China
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12
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Liu J, Zhang AN, Liu YJ, Liu Z, Liu Y, Wu XJ. Analysis of the mechanism for enhanced pyrene biodegradation based on the interactions between iron-ions and Rhodococcus ruber strain L9. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112789. [PMID: 34560613 DOI: 10.1016/j.ecoenv.2021.112789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
A slow degradation rate and low transformation efficiency are the main problems in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). This study selected pyrene as the target PAH to investigate the effect of ferrous ion and ferric ion on pyrene degradation. The driving effect and mechanism, including the interaction between pyrene and iron ions and the bacterial physiological response during the biodegradation process by Rhodococcus ruber strain L9, were investigated. The results showed that iron ions did not enhance bacterial growth but improved bacteria's pyrene removal capacity, contributing to the total efficiency of pyrene biodegradation. The process started with an initial formation of "cation-π" between Fe (III) and pyrene, which subsequently drove the pyrene removal process and accelerated the bacterial metabolic process. Moreover, a significant increase in the protein concentration, catechol dioxygenase (C12O and C23O) activities, and intracellular protein regulation in crude enzyme solution indicate a positive response of the bacteria during the iron ion-enhanced pyrene degradation process.
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Affiliation(s)
- Jing Liu
- School of Civil Engineering, Yulin University, Yulin 719000, China; Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Ai-Ning Zhang
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yong-Jun Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China.
| | - Zhe Liu
- Key Lab of Northwest Water Resource, Ecology and Environment, Ministry of Education, Xi'an University of Architecture and Technology, No. 13 Yanta Road, Xi'an 710055, China
| | - Yu Liu
- School of Petroleum and Environment Engineering, Yanan University, Yanan 716000, China
| | - Xi-Jun Wu
- School of Civil Engineering, Yulin University, Yulin 719000, China
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13
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Chen S, Li Y, Fan Z, Liu F, Liu H, Wang L, Wu H. Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil. CHEMOSPHERE 2021; 282:130976. [PMID: 34089999 DOI: 10.1016/j.chemosphere.2021.130976] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 04/13/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Atrazine is one of the most widely used herbicides, however it and its metabolites cause widespread contamination in soil and ground water. Bioaugmentation is an effective method for remediation of environmental organic pollutants. High-throughput sequencing provides an important tool for understanding the changes of microbial community and function in response to pollutants degradation based on bioaugmentation. In this study, the effect of biodegradation with Paenarthrobacter sp. W11 and the change of microbial community during atrazine degradation were investigated. The results showed that bioaugmentation significantly accelerated the degradation rate of atrazine in soil and reduced the toxic effect of atrazine residues on wheat growth. The extra available NH4+ through atrazine mineralization could serve as a nitrogen source to increase microbial numbers. High-throughput sequencing further revealed that the microbial community restored a new balance. The function of microbial community predicted by PICRUSt2 suggested that the biodegradation process of atrazine affected not only the atrazine degradation pathway, but also the nitrogen metabolism pathway. Methylobacillus and Pseudomonas were considered as the most important indigenous atrazine-degrading microorganisms, because their relative abundances were positively correlated with the relative abundance of Paenarthrobacter and atrazine degradation pathway. This study provides insight into the cooperation between indigenous microorganisms and external inoculums on atrazine degradation process.
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Affiliation(s)
- Shuaimin Chen
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China
| | - Yangyang Li
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China
| | - Zuowei Fan
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China
| | - Fangming Liu
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China
| | - Huitao Liu
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China
| | - Lichun Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China.
| | - Haiyan Wu
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, 1363 Shengtai Street, Changchun, 130033, China.
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14
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Leng Q, Mu J, Yang G. Efficient anaerobic bioremediation of high-concentration benzo[a]pyrene in marine environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117210. [PMID: 33932831 DOI: 10.1016/j.envpol.2021.117210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Benzo[a]pyrene (BaP), a persistent organic pollutant that may accumulate in sea sediments after oil spill or BaP chemical leakage accidents, considerably harms marine ecosystems and human health. Previous studies have been predominantly focused on its degradation at low concentrations, while the remediation of BaP pollution with high concentrations was neglected. Additionally, the metabolic pathways associated with its anaerobic degradation remain unclear. As a first attempt, super-efficient systems for BaP anaerobic degradation were established, and the corresponding metabolic pathways were elucidated in this study. The results showed that the BaP removal rate in BaP-only system with initial concentrations of 200 mg/L reached 3.09 mg/(L·d) within 45 days. Co-solvent, acetone promoted anaerobic BaP degradation (4.252 mg/(L·d)), while dichloromethane showed a newly-discovered co-metabolic effect. In the system with 500 mg/L of BaP and dichloromethane addition, the removal rate increased drastically (14.64 mg/(L·d)) at 400 mg/L turn point of BaP. Additionally, the corresponding microbial community-level metabolic network was firstly proposed.
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Affiliation(s)
- Qingxue Leng
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
| | - Jun Mu
- School of Ecological & Environment, Hainan Tropical Ocean University, Sanya, Hainan, 572022, China.
| | - Guangfeng Yang
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
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15
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Liu X, Liu M, Zhou L, Hou L, Yang Y, Wu D, Meadows ME, Li Z, Tong C, Gu J. Occurrence and distribution of PAHs and microbial communities in nearshore sediments of the Knysna Estuary, South Africa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 270:116083. [PMID: 33280920 DOI: 10.1016/j.envpol.2020.116083] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/13/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
This study investigated the polycyclic aromatic hydrocarbons (PAHs) occurrence, and their impact on the microbial community and PAH-degrading genera and genes in the Knysna Estuary of South Africa. The results reveal that the estuary exhibits low PAH levels (114.1-356.0 ng g-1). Ignavibacteriae and Deferribacteres, as well as Proteobacteria and Bacteroidetes, are keystone phyla. Among measured environmental factors, total organic carbon (TOC), nutrients such as nitrite and nitrate, metals as Al, Cr, Cu, Ni, Pb and Zn, and environmental properties (pH and salinity) are primary contributors to structuring the bacterial community assemblage. The abundance of alpha subunit genes of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of Gram-negative bacteria lies in the range of (2.0-4.2) × 105 copies g-1, while that of Gram-positive bacteria ranges from 3.0 × 105 to 1.3 × 107 copies g-1. The PAH-degrading bacteria account for up to 0.1% of the bacterial community and respond mainly to nitrate, TOC and salinity, while PAHs at low concentration are not significant influencing factors. PAH degraders such as Xanthomonadales, Pseudomonas, and Mycobacterium, which play a central role in PAH-metabolization coupled with other biogeochemical processes (e.g. iron cycling), may contribute to maintaining a healthy estuarine ecosystem. These results are important for developing appropriate utilization and protection strategies for pristine estuaries worldwide.
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Affiliation(s)
- Xinran Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), 3663 North Zhongshan Road, Shanghai, 200062, China.
| | - Limin Zhou
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Dianming Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; Institute of Eco-Chongming (IEC), 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Michael E Meadows
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; Department of Environmental & Geographical Science, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa
| | - Zhanhai Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Chunfu Tong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Jinghua Gu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
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16
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Rodrigues EM, Cesar DE, Santos de Oliveira R, de Paula Siqueira T, Tótola MR. Hydrocarbonoclastic bacterial species growing on hexadecane: Implications for bioaugmentation in marine ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115579. [PMID: 33254655 DOI: 10.1016/j.envpol.2020.115579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/24/2020] [Accepted: 08/30/2020] [Indexed: 06/12/2023]
Abstract
of bioaugmentation strategies are an obstacle for damage mitigation caused by oil spills in marine environments. Cells added to the contaminated sites are quickly lost by low adherence to the contaminants, rendering ineffective. This study used two hydrocarbonoclastic species - Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 cells - growing in mineral medium containing hexadecane to evaluate cell distribution in a crude-oil contaminated marine water. Cell affinity to hydrophobic compounds was quantified using Microbial Adhesion to Hydrocarbons test and analysis of fatty acids profile was performed using the Microbial Identification System. Bioremediation simulations were set up and cell populations of both strains were quantified by Fluorescent in situ Hybridization. R. rhodochrous and N. farcinica reached up to 97% and 60% of adhesion to hexadecane, respectively. The carbon source had more influence on the fatty acid profiles of both strains than the microbial species. The presence of 45.24% of 13:0 anteiso on total fatty acids in R. rhodochrous and 12.35% of saturated fatty acids with less than 13 carbons atoms in N. farcinica, as well as the occurrence of fatty alcohols only in presence of hexadecane in both species, are indicators that fatty acid changes are involved in the adaptation of the cells to remain at the water/oil interface. Cell quantification after bioremediation simulations revealed an increase in the density of both species, suggesting that the bioremediation strategies resulted on the increase of hydrocarbonoclastic species and up to 27.9% of all prokaryotic microbial populations in the microcosms were composed of R. rhodochrous or N. farcinica. These findings show the potential of application of these two bacterial strains in bioaugmentation of hydrocarbon-contaminated marine ecosystems.R. rhodochrous TRN7 and N. farcinica TRH1 hydrocarbonoclastic strains modify the fatty acid profile and increases density, optimizing hydrocarbons biodegradation.
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Affiliation(s)
- Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil; Instituto Federal de Educação, Ciência e Tecnologia Do Ceará - IFCE - Campus Camocim, Camocim, Ceará, Brazil.
| | - Dionéia Evangelista Cesar
- Laboratório de Ecologia e Biologia Molecular de Microorganismos, Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Renatta Santos de Oliveira
- Laboratório de Ecologia e Biologia Molecular de Microorganismos, Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Tatiane de Paula Siqueira
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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17
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Li X, Song Y, Bian Y, Gu C, Yang X, Wang F, Jiang X. Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics. ENVIRONMENT INTERNATIONAL 2020; 144:105995. [PMID: 32758715 DOI: 10.1016/j.envint.2020.105995] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.
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Affiliation(s)
- Xiaona Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenggang Gu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglun Yang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
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18
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Vaidya SS, Patel AB, Jain K, Amin S, Madamwar D. Characterizing the bacterial consortium ASDF capable of catabolic degradation of fluoranthene and other mono- and poly-aromatic hydrocarbons. 3 Biotech 2020; 10:491. [PMID: 33134009 DOI: 10.1007/s13205-020-02478-w] [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: 06/02/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022] Open
Abstract
In this study, a bacterial consortium ASDF was developed, capable of degrading fluoranthene (a non-alternant poly-aromatic hydrocarbon). It comprised of three bacterial strains: Pseudomonas sp. ASDF1, Burkholderia sp. ASDF2 and Mycobacterium sp. ASDF3 capable of degrading 100 mg/L of fluoranthene under experimentally defined and optimum conditions (37 °C, pH 7.0, 150 rpm) within 7 days. Consortium had metabolized fluoranthene as sole source of carbon and energy with maximum degradation rate of 0.52 mg/L/h and growth rate of 0.054/h. Fluoranthene degradation is an aerobic process, therefore with increasing the gyratory shaking from 50 to 150 rpm, degradation was concurrently enhanced by 7.1-fold. The synthetic surfactants SDS and CTAB had antagonistic effect on fluoranthene degradation (decreased up to 2.8-fold). The proficiency of consortium was assessed for its inherent ability to degrade seven other hydrocarbons both individually as well as in mixture. The degradation profile was studied using HPLC and the detection of two degraded intermediates (salicylic acid and derivatives of phthalic acid) suggested that fluoranthene degradation might have occurred via ortho- and meta-cleavage pathways. The competency of consortium was further validated through simulated microcosm studies, which showed 96% degradation of fluoranthene in soil ecosystem under the ambient conditions. Hence, the study suggested that the consortium ASDF has an inherent potential for its wide applicability in bioremediation of hydrocarbon-contaminated sites.
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Affiliation(s)
- Sagar S Vaidya
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Avani Bharatkumar Patel
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Kunal Jain
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India
| | - Seema Amin
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa, Anand, Gujarat 388 421 India
| | - Datta Madamwar
- Post Graduate Department of Biosciences, UGC Centre of Advanced Study, Satellite Campus, Vadtal Road, Sardar Patel University, Bakrol, Anand, Gujarat 388 315 India.,P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Charusat Campus, Changa, Anand, Gujarat 388 421 India
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19
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Hao DC, Li XJ, Xiao PG, Wang LF. The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design. Front Microbiol 2020; 11:557400. [PMID: 33193139 PMCID: PMC7644954 DOI: 10.3389/fmicb.2020.557400] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/25/2020] [Indexed: 12/27/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs), especially high molecular weight PAHs, are carcinogenic and mutagenic organic compounds that are difficult to degrade. Microbial remediation is a popular method for the PAH removal in diverse environments and yet it is limited by the lack of electron acceptors. An emerging solution is to use the microbial electrochemical system, in which the solid anode is used as an inexhaustible electron acceptor and the microbial activity is stimulated by biocurrent in situ to ensure the PAH removal and avoid the defects of bioremediation. Based on the extensive investigation of recent literatures, this paper summarizes and comments on the research progress of PAH removal by the microbial electrochemical system of diversified design, enhanced measures and functional microorganisms. First, the bioelectrochemical degradation of PAHs is reviewed in separate and mixed PAH degradation, and the removal performance of PAHs in different system configurations is compared with the anode modification, the enhancement of substrate and electron transfer, the addition of chemical reagents, and the combination with phytoremediation. Second, the key functional microbiota including PAH degrading microbes and exoelectrogens are overviewed as well as the reduced microbes without competitive advantage. Finally, the typical representations of electrochemical activity especially the internal resistance, power density and current density of systems and influence factors are reviewed with the correlation analysis between PAH removal and energy generation. Presently, most studies focused on the anode modification in the bioelectrochemical degradation of PAHs and actually more attentions need to be paid to enhance the mass transfer and thus larger remediation radius, and other smart designs are also proposed, especially that the combined use of phytoremediation could be an eco-friendly and sustainable approach. Additionally, exoelectrogens and PAH degraders are partially overlapping, but the exact functional mechanisms of interaction network are still elusive, which could be revealed with the aid of advanced bioinformatics technology. In order to optimize the efficacy of functional community, more advanced techniques such as omics technology, photoelectrocatalysis and nanotechnology should be considered in the future research to improve the energy generation and PAH biodegradation rate simultaneously.
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Affiliation(s)
- Da-Cheng Hao
- School of Environmental and Chemical Engineering, Dalian Jiaotong University, Dalian, China
| | - Xiao-Jing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs/Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
| | - Lian-Feng Wang
- School of Environmental and Chemical Engineering, Dalian Jiaotong University, Dalian, China
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Liang J, Wang Q, Yoza BA, Li QX, Chen C, Ming J, Yu J, Li J, Ke M. Rapid granulation using calcium sulfate and polymers for refractory wastewater treatment in up-flow anaerobic sludge blanket reactor. BIORESOURCE TECHNOLOGY 2020; 305:123084. [PMID: 32135348 DOI: 10.1016/j.biortech.2020.123084] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
Long start-up period and slow granulation are major restraints in up-flow anaerobic sludge blanket (UASB) reactors for the treatment of refractory wastewater. In this study, Calcium sulfate (CaSO4), CaSO4/guar gum (GG), and CaSO4/cationic polyacrylamide (CPAM) were used to enhance granulation during the treatment of phenolic wastewaters in UASB reactors. Use of CaSO4, CaSO4/GG, and CaSO4/CPAM increased formation of granules (>0.25 mm) by 7%, 21% and 40%, respectively, after 90 days in comparison with the control. Use of CaSO4/GG and CaSO4/CPAM at an organic loading rate of 2.89 kg chemical oxygen demand (COD) m-3 d-1 increased the COD removal efficiency by 9% and 3%, respectively, in comparison with the control (75%). The CaSO4 enhanced the granulation rate as nuclei and the subsequent dissolution of CaSO4 improves the activity of methanogens. Polymers facilitated bacteria adhesion and improved the diversity of phenols-degrading bacteria. This study describes a new method for rapid granulation in UASB reactors when treating toxic and refractory wastewaters.
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Affiliation(s)
- Jiahao Liang
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Qinghong Wang
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Brandon A Yoza
- Hawaii Natural Energy Institute, University of Hawaii at Manoa, Honolulu, HI 96822, United States
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, United States
| | - Chunmao Chen
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China.
| | - Jie Ming
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Jingshi Yu
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Jin Li
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
| | - Ming Ke
- State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum-Beijing, Beijing 102249, China
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21
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Li H, Qiu Y, Yao T, Ma Y, Zhang H, Yang X, Li C. Evaluation of seven chemical pesticides by mixed microbial culture (PCS-1): Degradation ability, microbial community, and Medicago sativa phytotoxicity. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121834. [PMID: 31843407 DOI: 10.1016/j.jhazmat.2019.121834] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Environmental problems caused by the large-scale use of chemical pesticides are becoming more and more serious, and the removal of chemical pesticides from the ecological environment by microbial degradation has attracted wide attention. In this study, using enrichment screening with seven chemical pesticides as the sole carbon source, a mixed microbial culture (PCS-1) was obtained from the continuous cropping of strawberry fields. The microbial community composition, degradation ability, and detoxification effect of PCS-1 was determined for the seven pesticides. Inoculation with PCS-1 showed significant degradation of and tolerance to the seven pesticides. Microbial community composition analysis indicated that Pseudomonas, Enterobacter, Aspergillus, and Rhodotorula were the dominant genera for the degradation of the seven pesticides by PCS-1. The concentration of the seven pesticides was 10 mg L-1 in hydroponic and soil culture experiments. The fresh weight, plant height, and root length of PCS-1-inoculated alfalfa (Medicago sativa) significantly increased compared with those of non-PCS-1-inoculated M. sativa. PCS-1 not only effectively degraded the residual content of the seven pesticides in water and soil but also reduced the pesticide residues in the roots, stems, and leaves of M. sativa. This study shows that PCS-1 may be important in environmental remediation involving the seven pesticides.
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Affiliation(s)
- Haiyun Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
| | - Yizhi Qiu
- School of Life Science, Lanzhou University, Lanzhou, China
| | - Tuo Yao
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China.
| | - Yachun Ma
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
| | - Huirong Zhang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
| | - Xiaolei Yang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
| | - Changning Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China; Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education, Lanzhou, China
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Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis. Bioprocess Biosyst Eng 2020; 43:1521-1531. [PMID: 32303845 DOI: 10.1007/s00449-020-02345-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L-1. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.
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Man Y, Wang J, Tam NFY, Wan X, Huang W, Zheng Y, Tang J, Tao R, Yang Y. Responses of rhizosphere and bulk substrate microbiome to wastewater-borne sulfonamides in constructed wetlands with different plant species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135955. [PMID: 31855648 DOI: 10.1016/j.scitotenv.2019.135955] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/01/2019] [Accepted: 12/04/2019] [Indexed: 05/20/2023]
Abstract
Constructed wetlands (CWs) have been used to remove organic pollutants including antibiotics based on the roles of plants and microbial communities, but how rhizosphere and bulk substrate-associated microbiomes respond to antibiotics during biodegradation have seldom been researched. The effects of sulfonamides (SAs) on the microbiome composition in different compartments, namely rhizosphere, near rhizosphere and bulk substrate, in CWs planted with either Cyperus alternifolius, Cyperus papyrus or Juncus effuses were evaluated using specially designed rhizoboxes and 16S rRNA gene high-throughput sequencing. Results revealed that wastewater-borne SAs significantly reduced the microbial biodiversity in CWs, and inhibited the functional bacterial groups related to sulphur and nitrogen cycles. On the contrary, SAs significantly enriched methylotrophs with potential to initially biodegrade SAs, such as Methylosinus, Methylotenera, Methylocaldum and Methylomonas, and such enrichment was more significant in rhizosphere than in bulk substrate. The network analysis indicated that a more complex network in bulk substrate was more fragile to SA stress. The presence of wetland plants significantly influenced the bacterial community structure in CWs, but in the same compartment, the difference among the three plants species was not obvious. Wetland plants ensured the stability of rhizosphere microorganisms and increased their ability to tolerate SA stress. The present study enhances our understanding of the importance of plant-bacteria interactions in CWs and responses of substrate microbiome to antibiotics.
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Affiliation(s)
- Ying Man
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Jiaxi Wang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Nora Fung-Yee Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region
| | - Xiang Wan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing 210008, China
| | - Wenda Huang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Yu Zheng
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Jinpeng Tang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China
| | - Ran Tao
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China.
| | - Yang Yang
- Research Center of Hydrobiology, Jinan University, Guangzhou 510632, China; Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China.
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Wang C, Huang Y, Zhang Z, Hao H, Wang H. Absence of the nahG-like gene caused the syntrophic interaction between Marinobacter and other microbes in PAH-degrading process. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121387. [PMID: 31648897 DOI: 10.1016/j.jhazmat.2019.121387] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
In this study, Marinobacter sp. N4 isolated from the halophilic consortium CY-1 was found to degrade phenanthrene as a sole carbon source with the accumulation of 1-Hydroxy-2-naphthoic acid (1H2N). With the assistance of Halomonas sp. G29, phenanthrene could be completely mineralized. The hpah1 and hpah2 gene cluster was amplified from the genome of strain N4, that were responsible for upstream and downstream of PAH degradation. Strain N4 was predicted for the transformation from phenanthrene to 1H2N, and strain G29 could transform the produced 1H2N into 1,2-dihydroxynaphthalene (1,2-DHN). The produced 1,2-DHN could be further transformed into salicylic acid (SALA) by strain N4. SALA could be catalyzed into catechol by strain G29 and further utilized by strains N4 and G29 via the catechol 2,3-dioxygenase pathway and catechol 1,2-dioxygenase pathway, respectively. NahG, encoding salicylate hydroxylase, was absent from the hpah2 gene cluster and predicted to be the reason for 1H2N accumulation in the PAH-degrading process by pure culture of strain N4. The syntrophic interaction mode among Marinobacter and other microbes was also predicted. According to our knowledge, this is the first report of the PAH-degrading gene cluster in Marinobacter and the syntrophic interaction between Marinobacter and other microbes in the PAH-degrading process.
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Affiliation(s)
- Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | - Yong Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | - Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | - Han Hao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
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Remizovschi A, Carpa R, Forray FL, Chiriac C, Roba CA, Beldean-Galea S, Andrei AȘ, Szekeres E, Baricz A, Lupan I, Rudi K, Coman C. Mud volcanoes and the presence of PAHs. Sci Rep 2020; 10:1253. [PMID: 31988316 PMCID: PMC6985136 DOI: 10.1038/s41598-020-58282-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 01/08/2020] [Indexed: 02/01/2023] Open
Abstract
A mud volcano (MV) is a naturally hydrocarbon-spiked environment, as indicated by the presence of various quantities of PAHs and aromatic isotopic shifts in its sediments. Recurrent expulsion of various hydrocarbons consolidates the growth of hydrocarbonoclastic bacterial communities in the areas around MVs. In addition to the widely-known availability of biologically malleable alkanes, MVs can represent hotbeds of polyaromatic hydrocarbons (PAHs), as well - an aspect that has not been previously explored. This study measured the availability of highly recalcitrant PAHs and the isotopic signature of MV sediments both by GC-MS and δ13C analyses. Subsequently, this study highlighted both the occurrence and distribution of putative PAH-degrading bacterial OTUs using a metabarcoding technique. The putative hydrocarbonoclastic taxa incidence are the following: Enterobacteriaceae (31.5%), Methylobacteriaceae (19.9%), Bradyrhizobiaceae (16.9%), Oxalobacteraceae (10.2%), Comamonadaceae (7.6%) and Sphingomonadaceae (5.5%). Cumulatively, the results of this study indicate that MVs represent polyaromatic hydrocarbonoclastic hotbeds, as defined by both natural PAH input and high incidence of putative PAH-degrading bacterial OTUs.
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Affiliation(s)
- Alexei Remizovschi
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Rahela Carpa
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania.
| | - Ferenc L Forray
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Geology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Cecilia Chiriac
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Carmen-Andreea Roba
- Babeş-Bolyai University, Faculty of Environmental Science and Engineering, 30 Fântânele Street, 400294, Cluj-Napoca, Romania
| | - Simion Beldean-Galea
- Babeş-Bolyai University, Faculty of Environmental Science and Engineering, 30 Fântânele Street, 400294, Cluj-Napoca, Romania
| | - Adrian-Ștefan Andrei
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Center of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Iulia Lupan
- Babeş-Bolyai University, Faculty of Biology and Geology, Department of Molecular Biology and Biotechnology, 1, M. Kogalniceanu Street, 400084, Cluj-Napoca, Cluj, Romania
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, As, Norway
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, 48 Republicii Street, 400015, Cluj-Napoca, Romania
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Macchi M, Festa S, Vega-Vela NE, Morelli IS, Coppotelli BM. Assessing interactions, predicting function, and increasing degradation potential of a PAH-degrading bacterial consortium by effect of an inoculant strain. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:25932-25944. [PMID: 31273663 DOI: 10.1007/s11356-019-05760-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/14/2019] [Indexed: 05/22/2023]
Abstract
A natural phenanthrene-degrading consortium CON was inoculated with an exogenous strain Sphingobium sp. (ex Sp. paucimobilis) 20006FA yielding the consortium called I-CON, in order to study ecological interactions into the bacterial community. DGGE and proteomic profiles and analyses by HTS (High-Throughput Sequencing) technologies demonstrated inoculant establishment and changes on CON composition. Inoculation increased degradation efficiency in I-CON and prevented intermediate HNA accumulation. This could be explained not only by the inoculation, but also by enrichment in Achromobacter genus at expense of a decrease in Klebsiella genus. After inoculation, cooperation between Sphingobium and Achromobacter genera were improved, thereby, some competition could have been generated, and as a consequence, species in minor proportion (cheaters), as Inquilinus sp. and Luteibacter sp., were not detected. Sequences of Sphingobium (corresponding to the inoculated strain) did not vary. PICRUSt predicted a network with bacterial phylotypes connected with enzymes, showing functional redundancy in the phenanthrene pathway, with exception of the first enzymes biphenyl-2,3-diol 1,2-dioxygenase and protocatechuate 4,5-dioxygenase that were only encoded in Sphingobium sp. This is the first report where a natural consortium that has been characterized by HTS technologies is inoculated with an exogenous strain in order to study competitiveness and interactions.
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Affiliation(s)
- Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), Street 50 N°227, 1900, La Plata, Argentina
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), Street 50 N°227, 1900, La Plata, Argentina
| | - Nelson E Vega-Vela
- Pontificia Universidad Javeriana, Bogotá, Colombia
- Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), Street 50 N°227, 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP; CCT-La Plata, CONICET), Street 50 N°227, 1900, La Plata, Argentina.
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27
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Liu Q, Tang J, Liu X, Song B, Zhen M, Ashbolt NJ. Vertical response of microbial community and degrading genes to petroleum hydrocarbon contamination in saline alkaline soil. J Environ Sci (China) 2019; 81:80-92. [PMID: 30975332 DOI: 10.1016/j.jes.2019.02.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
A column microcosm was conducted by amending crude oil into Dagang Oilfield soil to simulate the bioremediation process. The dynamic change of microbial communities and metabolic genes in vertical depth soil from 0 to 80 cm were characterized to evaluate the petroleum degradation potential of indigenous microorganism. The influence of environmental variables on the microbial responds to petroleum contamination were analyzed. Degradation extent of 42.45% of n-alkanes (C8-C40) and 34.61% of 16ΣPAH were reached after 22 weeks. Relative abundance of alkB, nah, and phe gene showed about 10-fold increment in different depth of soil layers. Result of HTS profiles demonstrated that Pseudomonas, Marinobacter and Lactococcus were the major petroleum-degrading bacteria in 0-30 and 30-60 cm depth of soils. Fusarium and Aspergillus were the dominant oil-degrading fungi in the 0-60 cm depth of soils. In 60-80 cm deep soil, anaerobic bacteria such as Bacteroidetes, Lactococcus, and Alcanivorax played important roles in petroleum degradation. Redundancy analysis (RDA) and correlation analysis demonstrated that petroleum hydrocarbons (PHs) as well as soil salinity, clay content, and anaerobic conditions were the dominant effect factors on microbial community compositions in 0-30, 30-60, and 60-80 cm depth of soils, respectively.
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Affiliation(s)
- Qinglong Liu
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China..
| | - Jingchun Tang
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China.; Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin 300071, China; Tianjin Engineering Research Center of Environmental Diagnosis and Contamination Remediation, Tianjin 300071, China.
| | - Xiaomei Liu
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Benru Song
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Meinan Zhen
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada
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28
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Yu Y, Yin H, Peng H, Lu G, Dang Z. Biodegradation of decabromodiphenyl ether (BDE-209) using a novel microbial consortium GY1: Cells viability, pathway, toxicity assessment, and microbial function prediction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:958-965. [PMID: 31018474 DOI: 10.1016/j.scitotenv.2019.03.078] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
GY1, a novel microbial consortium with efficient ability to degrade decabromodiphenyl ether (BDE-209) has been isolated and the sequencing analysis has been conducted. The results revealed that Hyphomicrobium, Pseudomonas, Aminobacter, Sphingopyxis, Chryseobacterium, Bacillus, Pseudaminobacter, Stenotrophomonas, Sphingobacterium and Microbacterium were the dominant genera, and the function genes involved in BDE-209 conversion were predicted by PICRUSt. When BDE-209 concentration increased from 0.5 to 10mg/L, its degradation efficiency declined from 57.2% to 22.3%. Various kinds of debrominated metabolites were detected during the biodegradation process, including BDE-208, BDE-207, BDE-206, BDE-205, BDE-190, BDE-181, BDE-155, BDE-154, BDE-99, BDE-47, BDE-17 and BDE-7. Also, the proportion of necrotic cells was observed during GY1 mediated degradation of BDE-209 to reveal the changes of cells viability under BDE-209 stress. Subsequent analysis showed that the reaction of BDE-209 with GY1 was a detoxification process and bioaugmentation with GY1 effectively enhanced BDE-209 degradation in actual water and water-sediment system.
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Affiliation(s)
- Yuanyuan Yu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Hua Yin
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China.
| | - Hui Peng
- Department of Chemistry, Jinan University, Guangzhou 510632, Guangdong, China
| | - Guining Lu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
| | - Zhi Dang
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, China
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29
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Liu X, Liu M, Chen X, Yang Y, Hou L, Wu S, Zhu P. Indigenous PAH degraders along the gradient of the Yangtze Estuary of China: Relationships with pollutants and their bioremediation implications. MARINE POLLUTION BULLETIN 2019; 142:419-427. [PMID: 31232319 DOI: 10.1016/j.marpolbul.2019.03.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/21/2019] [Accepted: 03/31/2019] [Indexed: 06/09/2023]
Abstract
This study investigated the network of polycyclic aromatic hydrocarbon (PAH) degraders in the Yangtze estuarine and coastal areas. Along the estuarine gradients, Proteobacteria and Bacteroidetes were the dominant bacterial phyla, and forty-six potential PAH degraders were identified. The abundance of genes encoding the alpha subunit of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of gram-negative bacteria ranged from 5.5 × 105 to 5.8 × 107 copies g-1, while that of gram-positive bacteria ranged from 1.3 × 105 to 2.0 × 107 copies g-1. The PAH-degraders could represent up to 0.2% of the total bacterial community and mainly respond to PAHs and Cu concentrations, which indicate anthropogenic activities. Salinity and pH showed negative regulating effects on the PAH-degrading potential and the tolerance of bacteria to pollutants. PAH degraders such as Novosphingobium and Mycobacterium exhibit heavy-metal tolerance and core roles in the network of PAH degraders. These outcomes have important implications for bioremediation.
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Affiliation(s)
- Xinran Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Institute of Eco-Chongming (IEC), 3663 North Zhongshan Road, Shanghai 200062, China.
| | - Xing Chen
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Yi Yang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Shixue Wu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Pinkuan Zhu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
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30
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Storey S, Ashaari MM, Clipson N, Doyle E, de Menezes AB. Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study. Front Microbiol 2018; 9:2815. [PMID: 30519226 PMCID: PMC6258822 DOI: 10.3389/fmicb.2018.02815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.
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Affiliation(s)
- Sean Storey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Mardiana Mohd Ashaari
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Malaysia, Malaysia
| | - Nicholas Clipson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Earth Institute, University College Dublin, Dublin, Ireland
| | - Alexandre B de Menezes
- Microbiology, School of Natural Sciences, Ryan Institute, National University of Ireland, Galway, Ireland
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31
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Qu W, Liu T, Wang D, Hong G, Zhao J. Metagenomics-Based Discovery of Malachite Green-Degradation Gene Families and Enzymes From Mangrove Sediment. Front Microbiol 2018; 9:2187. [PMID: 30258430 PMCID: PMC6143792 DOI: 10.3389/fmicb.2018.02187] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
Malachite green (MG) is an organic contaminant and the effluents with MG negatively influence the health and balance of the coastal and marine ecosystem. The diverse and abundant microbial communities inhabiting in mangroves participate actively in various ecological processes. Metagenomic sequencing from mangrove sediments was applied to excavate the resources MG-degradation genes (MDGs) and to assess the potential of their corresponding enzymes. A data set of 10 GB was assembled into 33,756 contigs and 44,743 ORFs were predicted. In the data set, 666 bacterial genera and 13 pollutant degradation pathways were found. Proteobacteria and Actinobacteria were the most dominate phyla in taxonomic assignment. A total of 44 putative MDGs were revealed and possibly derived from 30 bacterial genera, most of which belonged to the phyla of Proteobacteria and Bacteroidetes. The MDGs belonged to three gene families, including peroxidase genes (up to 93.54% of total MDGs), laccase (3.40%), and p450 (3.06%). Of the three gene families, three representatives (Mgv-rLACC, Mgv-rPOD, and Mgv-rCYP) which had lower similarities to the closest sequences in GenBank were prokaryotic expressed and their enzymes were characterized. Three recombinant proteins showed different MG-degrading activities. Mgv-rPOD had the strongest activity which decolorized 97.3% of MG (300 mg/L) within 40 min. In addition, Mgv-rPOD showed a more complete process of MG degradation compared with other two recombinant proteins according to the intermediates detected by LC-MS. Furthermore, the high MG-degrading activity was maintained at low temperature (20°C), wider pH range, and the existence of metal ions and chelating agent. Mgv-rLACC and Mgv-rCYP also removed 63.7% and 54.1% of MG (20 mg/L) within 24 h, respectively. The results could provide a broad insight into discovering abundant genetic resources and an effective strategy to access the eco-friendly way for preventing coastal pollution.
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Affiliation(s)
- Wu Qu
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Tan Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dexiang Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Guolin Hong
- The Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jing Zhao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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32
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Wang C, Huang Y, Zhang Z, Wang H. Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium. AMB Express 2018; 8:67. [PMID: 29696463 PMCID: PMC5918149 DOI: 10.1186/s13568-018-0594-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 04/13/2018] [Indexed: 11/15/2022] Open
Abstract
With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.
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33
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Yang L, Wang YH, Zhu HZ, Muhadesi JB, Wang BJ, Liu SJ, Jiang CY. Parapedobacter defluvii sp. nov., isolated from the sewage treatment packing of a coking chemical plant. Int J Syst Evol Microbiol 2017; 67:4698-4703. [PMID: 28984570 DOI: 10.1099/ijsem.0.002360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain WY-1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from the sewage treatment packing of a coking chemical plant. Strain WY-1T grew over a temperature range of 15-45 °C (optimum, 30-37 °C), a pH range of 5.5-11.0 (optimum, pH 6.5-7.0) and an NaCl concentration range of 0-3 % (w/v; optimum, 0 %). 16S rRNA gene sequence analysis showed that strain WY-1T was closely related to Parapedobacter indicus RK1T with the highest sequence similarity of 96.0 %. The predominant cellular fatty acids of the novel strain were iso-C15 : 0, summed feature 3(C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C17 : 1ω9c, iso-C15 : 0 3-OH and C16 : 0. The respiratory quinone of the cells was menaquinone 7 (MK-7). The main polar lipid was phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and two unknown lipids. The G+C content of the DNA was 47.1 mol%. Chemotaxonomic characteristics and phylogenetic analyses revealed that strain WY-1T belonged to the genus Parapedobacter. Strain WY-1T showed a range of phenotypic characteristics that differentiated it from species of the genus Parapedobacter with validly published names, including its assimilation from carbon sources, enzyme activities and having a wider pH range for growth. Based on these results, it is concluded that strain WY-1T represents a novel species of the genus Parapedobacter, for which the name Parapedobacter defluvii sp. nov. is proposed. The type strain is WY-1T (=NBRC 112611T=CGMCC 1.15342T).
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Affiliation(s)
- Lan Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jiang-Baota Muhadesi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China.,RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China
| | - Cheng-Ying Jiang
- RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
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34
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Zhang M, Liu X, Li Y, Wang G, Wang Z, Wen J. Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation. Sci Rep 2017; 7:474. [PMID: 28352108 PMCID: PMC5428726 DOI: 10.1038/s41598-017-00580-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/06/2017] [Indexed: 11/24/2022] Open
Abstract
To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.
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Affiliation(s)
- Mingjiang Zhang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Xingyu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China.
| | - Yibin Li
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Guangyuan Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Zining Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - Jiankang Wen
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
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35
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Zhang M, Huang F, Wang G, Liu X, Wen J, Zhang X, Huang Y, Xia Y. Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident. Sci Rep 2017; 7:227. [PMID: 28331217 PMCID: PMC5427973 DOI: 10.1038/s41598-017-00280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2017] [Indexed: 12/14/2022] Open
Abstract
A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.
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Affiliation(s)
- MingJiang Zhang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - FuKe Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - GuangYuan Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XingYu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China.
| | - JianKang Wen
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XiaoSheng Zhang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - YaoSi Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - Yu Xia
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
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