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Rong L, Wu L, Zong L, Wang W, Xiao Y, Yang C, Pan H, Zou X. Evolution of the Black solider fly larvae gut antibiotic resistome during kitchen waste disposal. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135878. [PMID: 39321479 DOI: 10.1016/j.jhazmat.2024.135878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/21/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024]
Abstract
Kitchen waste (KW) is an important reservoir of antibiotic resistance genes (ARGs). Black solider fly larvae (BSFL) are extensively employed in KW disposal, closely linking to their robust gut microbes. However, antibiotic resistome in BSFL gut during the KW disposal processes and the mechanism remain unclear. In the present study, the antibiotic resistome in BSFL gut within the 12 days KW disposal processes were investigated. Results showed that, ARGs abundance initially increased and subsequently decreased, the five most prevalent core ARG classes were tetracycline, aminoglycoside, cephalosporin, lincosamide and multidrug. A total of 7 MGE types were observed and the horizontal gene transfer (HGT) of ARGs was predominantly mediated by plasmids. Host microbes were mainly categorized into Proteobacteria (98.12 %) and their assemblies were mainly classified into the deterministic processes. To elucidate the driving mechanisms, the mantel test and the structural equation model (SEM) were developed. Results indicated that microbial functions (0.912, p < 0.0001) and microbial community (1.014, p = 0.036), consistently showed very significant relationships with the patterns of ARGs, which presented higher direct effects than indirect effects. Overall, this study makes an initial contribution to a more deepgoing comprehension of the gut antibiotic resistome of BSFL during KW disposal.
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Affiliation(s)
- Lingling Rong
- School of Life Science, Jinggangshan University, Ji'an 343009, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Ligui Wu
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Lihui Zong
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Wei Wang
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Yi Xiao
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Chunyan Yang
- School of Life Science, Jinggangshan University, Ji'an 343009, China
| | - Hongcheng Pan
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin 541004, China.
| | - Xiaoming Zou
- School of Life Science, Jinggangshan University, Ji'an 343009, China.
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2
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Lu W, Zheng Y, Wang Y, Song J, Weng Y, Ma W, Arslan M, Gamal El-Din M, Wang D, Wang Q, Chen C. Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils. ENVIRONMENTAL RESEARCH 2024; 262:119857. [PMID: 39197484 DOI: 10.1016/j.envres.2024.119857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/14/2024] [Accepted: 08/26/2024] [Indexed: 09/01/2024]
Abstract
This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.
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Affiliation(s)
- Wenyi Lu
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Yi Zheng
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Yi Wang
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
| | - Jiayu Song
- CNPC Research Institute of Safety and Environmental Technology, Beijing, 102200, China
| | - Yibin Weng
- CNPC Research Institute of Safety and Environmental Technology, Beijing, 102200, China
| | - Wenfeng Ma
- Shandong Institute of Petroleum and Chemical Technology, Dongying, 257061, China
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Dingyuan Wang
- School of Petroleum Engineering, China University of Petroleum, Qingdao, 266580, China
| | - Qinghong Wang
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China.
| | - Chunmao Chen
- State Key Laboratory of Petroleum Pollution Control, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum-Beijing, Beijing, 102249, China
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3
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Yang L, Chen Q, Wei J, Fan T, Kong L, Long T, Zhang S, Deng S. Response of microbial communities in aquifers with multiple organic solvent contamination: Implications for MNA remedy. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134798. [PMID: 38843633 DOI: 10.1016/j.jhazmat.2024.134798] [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: 03/04/2024] [Revised: 05/07/2024] [Accepted: 06/01/2024] [Indexed: 06/26/2024]
Abstract
The application of Monitored Natural Attenuation (MNA) technology has been widespread, while there is a paucity of data on groundwater with multiple co-contaminants. This study focused on high permeability, low hydraulic gradient groundwater with co-contamination of benzene, toluene, ethylbenzene, and xylenes (BTEX), chlorinated aliphatic hydrocarbons (CAHs), and chlorinated aromatic hydrocarbons (CPs). The objective was to investigate the responses of microbial communities during natural attenuation processes. Results revealed greater horizontal variation in groundwater microbial community composition compared to vertical variation. The variation was strongly correlated with the total contaminant quantity (r = 0.722, p < 0.001) rather than individual contaminants. BTEX exerted a more significant influence on community diversity than other contaminants. The assembly of groundwater microbial communities was primarily governed by deterministic processes (βNTI < -2) in high contaminant concentration zones, while stochastic processes (|βNTI| < 2) dominated in low-concentration zones. Moreover, the microbial interactions shifted at different depths indicating the degradation rate variation in the vertical. This study makes fundamental contribution to the understanding for the effects of groundwater flow and material fields on indigenous microbial communities, which will provide a scientific basis for more precise adoption of microbial stimulation/augmentation to accelerate the rate of contaminant removal.
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Affiliation(s)
- Lu Yang
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Qiang Chen
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Jing Wei
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Tingting Fan
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Lingya Kong
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China.
| | - Tao Long
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Shengtian Zhang
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Shaopo Deng
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China.
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Yan K, You Q, Wang S, Zou Y, Chen J, Xu J, Wang H. Depth-dependent patterns of soil microbial community in the E-waste dismantling area. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130379. [PMID: 36427484 DOI: 10.1016/j.jhazmat.2022.130379] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
The long-term dismantling of electronic waste (E-waste) has contaminated the soil environment considerably. In spite of this, it is unknown if it affects the depth-resolved microbial communities. In the present research, six soil profiles (dismantling sites and the surrounding farmland) were collected from one of the largest Chinese E-waste disposal centers to identify depth-resolved microbiota and assess how heavy metal contamination affects microbial adaptation. Results suggested that cadmium (0.12-7.22 mg kg-1) and copper (18.99-11282.03 mg kg-1) were the main pollutants in the test soil profiles, and their concentrations gradually decreased with depth. The surrounding contaminated farmland has a more complex interaction and higher modularity (0.77-0.85) among microbes, indicating a stronger niche differentiation to enhance functional diversity. The proportion of positive interactions between taxa decreased with depth, as high heavy metals contamination in the topsoil results in the co-occurrence of microorganisms with the same ecological niche that collaborated to face environmental stress. Soil physicochemical properties, heavy metals concentration, and soil depth critically affect microbial communities. Microbial community assembly processes in the topsoil were affected by environmental filtering, i.e., by deterministic processes (NST: 13-52%), while were more stochastic (NST: 46-72%) in the subsoil due to the environment of soil becoming more homogeneous as soil depth increased.
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Affiliation(s)
- Kang Yan
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi You
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Suyuan Wang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yiyang Zou
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jian Chen
- Plant Protection, Fertilizer and Rural Energy Agency of Wenling, Wenling 317500, Zhejiang Province, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haizhen Wang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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5
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Yang S, Chen Q, Zheng T, Chen Y, Zhao X, He Y, Sun W, Zhong S, Li Z, Wang J. Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129186. [PMID: 35643011 DOI: 10.1016/j.jhazmat.2022.129186] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Archaea are important participants in biogeochemical cycles of metal(loid)-polluted ecosystems, whereas archaeal structure and function in response to metal(loid) contamination remain poorly understood. Here, the effects of multiple metal(loid) pollution on the structure and function of archaeal communities were investigated in three zones within an abandoned sewage reservoir. We found that the high-contamination zone (Zone I) had higher archaeal diversity but a lower habitat niche breadth, relative to the mid-contamination zone (Zone II) and low-contamination zone (Zone III). Particularly, metal-resistant species represented by potential methanogens were markedly enriched in Zone I (cumulative relative abundance: 32.24%) compared to Zone II (1.93%) and Zone III (0.10%), and closer inter-taxon connections and higher network complexity (based on node number, edge number, and degree) were also observed compared to other zones. Meanwhile, the higher abundances of potential metal-resistant and methanogenic functions in Zone I (0.24% and 9.24%, respectively) than in Zone II (0.08% and 7.52%) and Zone III (0.01% and 1.03%) suggested archaeal functional adaptation to complex metal(loid) contamination. More importantly, six bioavailable metal(loid)s (titanium, tin, nickel, chromium, cobalt, and zinc) were the main contributors to archaeal community variations, and metal(loid) pollution reinforced the role of deterministic processes, particularly homogeneous selection, in the archaeal community assembly. Overall, this study provides the first integrated insight into the survival strategies of archaeal communities under multiple metal(loid) contamination, which will be of significant guidance for future bioremediation and environmental governance of metal(loid)-contaminated environments.
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Affiliation(s)
- Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tong Zheng
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
| | - Ying Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xiaohui Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Yifan He
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Sining Zhong
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fuzhou 350002, China
| | - Zhilong Li
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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6
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Zhu N, Wang J, Wang Y, Li S, Chen J. Differences in geological conditions have reshaped the structure and diversity of microbial communities in oily soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119404. [PMID: 35523380 DOI: 10.1016/j.envpol.2022.119404] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 03/27/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
High-throughput sequencing was used to study the microbial community structure diversity changes in oil-contaminated soils under different spatial distances and environmental conditions. 239 Phyla, 508 Classes, 810 Orders, 1417 Families, 2048 Genera, 511 Species of microbial communities were obtained from 16 samples in three regions. The physicochemical properties of the soil, microorganisms' community structure has been changed by Petroleum hydrocarbon (PHA). Alpha diversity results showed that the soil contained high bacterial diversity, especially in Qingyang's loess soil. The bacterial abundance was in the order of loess soil > black soil > sandy soil. Beta diversity revealed that spatial distance limitation and random variation of repeated samples may be the main factors leading to soil heterogeneity and microbial community structure differences. The dominant bacteria phyla with broad petroleum hydrocarbon degradation ability such as Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were identified. Pseudomonas, Bacillus, Nocardioides, Oceanobacillus, Sphingomonas, Alkanindiges and Streptomyces were identified as functional microbial for the PHA degradation. The microbial communities manifested the co-exclusion under different geological conditions, and played the key role in the soil PHA degradation through amino acid metabolism, energy metabolism and carbohydrate metabolism. The correlation results of amos structural equation showed that the diversity and abundance of soil microorganisms in different regions were controlled by soil PHA content and environmental factors. Altitude, annual average temperature and annual rainfall were positively correlated with microbial diversity. Annual rainfall and soil physical and chemical factors exhibited the most significant influence on it. Microbial diversity indirectly affected the PHA content in different type soil. We believe that reshape the structure and diversity of microbial communities in soil could be changed and reshaped by different geological conditions, pollutants and soil type. This study can provide helps for understanding the ecological effect of geomicrobiology formation under the driving force of geographic environment and other factors.
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Affiliation(s)
- Ning Zhu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Jiangqin Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China.
| | - Shaowei Li
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
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Zhang H, Wu C, Wang F, Wang H, Chen G, Cheng Y, Chen J, Yang J, Ge T. Wheat yellow mosaic enhances bacterial deterministic processes in a plant-soil system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:151430. [PMID: 34748834 DOI: 10.1016/j.scitotenv.2021.151430] [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: 08/26/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Understanding the mechanisms that govern microbial community assembly across soil-plant continuum is crucial for predicting the response of ecosystems to environmental changes. However, the impact of the health status of plant on microbial assembly across this continuum still remain poorly understood. Here, we investigated how wheat yellow mosaic (WYM), caused by the wheat mosaic virus transmitted by Polymyxa graminis, affected microbial assembly across soil (bulk soil, rhizosphere soil), and plant (roots and leaves) continuum in a winter wheat (Triticum aestivum L.) system in northern China, using null model analysis. The results showed that deterministic processes dominated the bacterial community assembly, whereas stochastic processes were primarily responsible for the assembly of the fungal communities. With increasing levels of WYM, deterministic processes were greatly enhanced for bacterial community assembly, accompanied by a decrease in community niche breadth. Intensified competition between bacteria and fungi and increased soil total nitrogen (TN) and soil organic carbon (SOC) contents were mainly responsible for the enhanced deterministic processes for bacterial community assembly. Random forest modeling indicated a strong potential of rhizosphere bacterial community assembly for predicting the pathological conditions of wheat. Structural equation modeling showed that disease level was positively correlated with SOC and TN contents, competitions between bacteria and fungi, and the contribution of variable selection processes to the bacterial community assembly in the wheat rhizosphere. Our study revealed the ecological mechanisms underlying the associations between microbial communities and soil-borne disease, and highlighted the significance of microbial community assembly for maintaining soil and plant health.
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Affiliation(s)
- Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Fangyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haiting Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guixian Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou 341000, China
| | - Ye Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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Chen K, He R, Wang L, Liu L, Huang X, Ping J, Huang C, Wang X, Liu Y. The dominant microbial metabolic pathway of the petroleum hydrocarbons in the soil of shale gas field: Carbon fixation instead of CO 2 emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151074. [PMID: 34678370 DOI: 10.1016/j.scitotenv.2021.151074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 05/20/2023]
Abstract
In shale gas mining areas, indigenous microorganisms degrade organic pollutants such as petroleum hydrocarbons into carbon dioxide (CO2) and water (H2O) through aerobic metabolism. A large quantity of CO2 emissions will exacerbate the "Greenhouse effect". Based on the clean sieved soil and oil-based drilling fluid in the shale gas mining area, this experiment set three concentration gradients (3523 ± 159 mg/kg, 8715 ± 820 mg/kg and 22,031 ± 1533 mg/kg) to treat the soil, and each group was disposed for the same amount of time (63 days). By analyzing the dynamic changes of microbial diversity and the abundance of key functional genes for carbon fixation, the impact of petroleum hydrocarbons on carbon fixation potential was discovered, and the natural attenuation law of petroleum hydrocarbons in contaminated soil was explored. It provided the scientific research basis of ecology for the carbon cycle, carbon allocation, and carbon fixation in microbial remediation of petroleum hydrocarbon contaminated soil. The results obtained indicated the following: i) The removal rate of petroleum hydrocarbons under high-concentration pollution (45.33 ± 3.90%) was significantly lower than low and medium-concentration pollution. The TPH concentration removal rate of each group was the largest in the early stage of culture (1-5d), and there was no significant correlation between the TPH content and the community composition (R2 = 0.0736, P > 0.05). ii) Composition and function of Carbon Fixation associated microbiota were assessed by 16S rRNA sequencing and PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) analysis. The main carbon fixation pathway in this study is the reductive citric acid cycle, because there was no shortage of enzymes that can affect subsequent reactions.
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Affiliation(s)
- Kejin Chen
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Rong He
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Li'ao Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Lingyue Liu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Xin Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Juan Ping
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Chuan Huang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China
| | - Xiang Wang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China.
| | - Yuanyuan Liu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, PR China.
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9
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Gao Y, Yuan L, Du J, Wang H, Yang X, Duan L, Zheng L, Bahar MM, Zhao Q, Zhang W, Liu Y, Fu Z, Wang W, Naidu R. Bacterial community profile of the crude oil-contaminated saline soil in the Yellow River Delta Natural Reserve, China. CHEMOSPHERE 2022; 289:133207. [PMID: 34890619 DOI: 10.1016/j.chemosphere.2021.133207] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/13/2023]
Abstract
Crude oil contamination greatly influence soil bacterial community. Proliferative microbes in the crude oil-contaminated soil are closely related to the living conditions. Oil wells in the Yellow River Delta Natural Reserve (YRDNR) region is an ideal site for investigating the bacterial community of crude oil-contaminated saline soil. In the present study, 18 soil samples were collected from the depths of 0-20 cm and 20-40 cm around the oil wells in the YRDNR. The bacterial community profile was analyzed through high-throughput sequencing to trace the oil-degrading aerobic and anaerobic bacteria. The results indicated that C15-C28 and C29-C38 were the main fractions of total petroleum hydrocarbon (TPH) in the sampled soil. These TPH fractions had a significant negative effect on bacterial biodiversity (Shannon, Simpson, and Chao1 indices), which led to the proliferation of hydrocarbon-degrading bacteria. A comprehensive analysis between the environmental factors and soil microbial community structure showed that Streptococcus, Bacillus, Sphingomonas, and Arthrobacter were the aerobic hydrocarbon-degrading bacteria; unidentified Rhodobacteraceae and Porticoccus were considered to be the possible facultative anaerobic bacteria with hydrocarbon biodegradation ability; Acidithiobacillus, SAR324 clade, and Nitrosarchaeum were predicted to be the anaerobic hydrocarbon-degrading bacteria in the sub-surface soil. Furthermore, large amount of carbon sources derived from TPH was found to cause depletion of bioavailable nitrogen in the soil. The bacteria associated with nitrogen transformation, such as Solirubrobacter, Candidatus Udaeobacter, Lysinibacillus, Bradyrhizobium, Sphingomonas, Mycobacterium, and Acidithiobacillus, were highly abundant; these bacteria may possess the ability to increase nitrogen availability in the crude oil-contaminated soil. The bacterial community functions were significantly different between the surface and the sub-surface soil, and the dissolved oxygen concentration in soil was considered to be potential influencing factor. Our results could provide useful information for the bioremediation of crude oil-contaminated saline soil.
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Affiliation(s)
- Yongchao Gao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China.
| | - Liyuan Yuan
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Jianhua Du
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Hui Wang
- School of Resources and Environment, University of Jinan, Jinan, 250022, China
| | - Xiaodong Yang
- Department of Geography & Spatial Information Technology, Ningbo University, Ningbo, 315211, China.
| | - Luchun Duan
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Liwen Zheng
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Md Mezbaul Bahar
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wen Zhang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Yanju Liu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Zhaoyang Fu
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Wei Wang
- Qilu University of Technology (Shandong Academy of Sciences), Ecology Institute, Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan, 250103, China
| | - Ravi Naidu
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, Callaghan, NSW, 2308, Australia
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10
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Jia W, Ye Q, Shen D, Yu K, Zheng Y, Liu M, Jiang J, Wang W. Enhanced mineralization of chlorpyrifos bound residues in soil through inoculation of two synergistic degrading strains. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125116. [PMID: 33540267 DOI: 10.1016/j.jhazmat.2021.125116] [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: 09/25/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Bioaugmentation methods are frequently employed for pesticide pollution remediation; however, it is not clear whether the introduced bacteria affect the pesticide bound residue (BRs) composition and whether the BRs can be catabolized by the introduced strains. This study aimed at answering these questions by using 14C-chlorpyrifos (14C-CPF) and two CPF-degrading strains (Pseudomonas sp. DSP-1 and Cupriavidus sp. P2). The results showed that the BRs can be up to 83.0%, and that the CPF-BRs formed can be further transformed into 14CO2 by the strains. Indeed, the microbial inoculation can increase the CPF mineralization by 1.0-22.1 times and can decrease the BRs by up to ~50% of the control (on day 20). Compared with the control without bioaugmentation, microbial inoculation enhanced the release of BRs by 2.2-18.0 times. Adding biochar to the soil can greatly inhibit CPF mineralization and maintain the BR content at a relatively stable level. The CPF residue can affect the composition of the indigenous soil microbial community, but the introduction of bacteria for remediation did not have a significant effect. The results indicate that Pseudomonas sp. DSP-1 and Cupriavidus sp. P2 are useful for remediating both CPF extractable and bound residues.
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Affiliation(s)
- Weibin Jia
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China; Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingfu Ye
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Dahang Shen
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Kaixiang Yu
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Yaoying Zheng
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Mengdi Liu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Wei Wang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture of PRC and Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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11
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Xu S, He C, Song S, Li C. Spatiotemporal dynamics of marine microbial communities following a Phaeocystis bloom: biogeography and co-occurrence patterns. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:294-308. [PMID: 33527743 DOI: 10.1111/1758-2229.12929] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
Marine microbes play important roles in the development of phytoplankton blooms. The diversity and composition of free living (FL) and particle attached (PA) microbial communities have been well studied, while little is known about their geographic and co-occurrence patterns, especially during the subsiding process of Phaeocystis globosa blooms. Herein, the beta-diversity of FL and PA microbial communities in both the surface and bottom layers of different habitats were comprehensively examined during succession of a P. globosa bloom event. The results showed that microbial communities from bloom and non-bloom sites exhibited distinct community compositions. Among the different sampling sites, the community similarities decreased with spatial distance, in which the FL communities' similarity in bottom waters was more influenced by spatial variation. The variation of microbial communities was mostly attributed to environmental selection, spatial distance, and the abundance of P. globosa successively. The co-occurrence networks of microbial communities in bloom and non-bloom waters differed in terms of structure and composition, and the bloom network had more links and closer relationships between genera than the non-bloom network. The correlation among genera and modules suggested that the bloom microbes were likely driven by high environmental selection and low competitive effect between each other.
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Affiliation(s)
- Sha Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuqun Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Caiwen Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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12
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Zhen L, Hu T, Lv R, Wu Y, Chang F, Jia F, Gu J. Succession of microbial communities and synergetic effects during bioremediation of petroleum hydrocarbon-contaminated soil enhanced by chemical oxidation. JOURNAL OF HAZARDOUS MATERIALS 2021; 410:124869. [PMID: 33422735 DOI: 10.1016/j.jhazmat.2020.124869] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/19/2020] [Accepted: 12/12/2020] [Indexed: 06/12/2023]
Abstract
Biotechnologies integrated with chemical techniques are promising in treating the soils contaminated by petroleum hydrocarbons. Experiments by applying the degrading consortium and the modified Fenton (MF) with the chelator sodium citrate simultaneously were carried out to investigate the effects of the MF reagents on the degradation of total petroleum hydrocarbons (TPHs), changes in enzyme activities and the succession of microbial communities at the 0, 20, 100 and 500 mmol/kg hydrogen peroxide concentration levels. The ratio between hydrogen peroxide, ferrous sulfate and sodium citrate in the MF reagents was 100:1:1. The results indicated that the degradation of TPHs conformed to first-order kinetics and MF treatments increased the total removal rates of TPHs (4.73-24.26%) and activated dehydrogenase and polyphenol oxidase activities. A shift in microbial communities from Proteobacteria to Bacteroidetes was observed during the enhanced bioremediation, and the predominant genus shifted from Pseudomonas with an average relative abundance (ARAs) of 76.61% at the beginning to Sphingobacterium with ARAs of 52.06% at the later stage. The MF reagents at the proper level could simplify the relationship among the community populations, alleviate their competition and strengthen their associations, which would optimize the removal efficiency.
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Affiliation(s)
- Lisha Zhen
- Shaanxi Province Institute of Microbiology, Xi'an, Shaanxi 710043, China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A & Forestry University, Yangling, Shaanxi 712100, China
| | - Rui Lv
- Shaanxi Province Institute of Microbiology, Xi'an, Shaanxi 710043, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fan Chang
- Shaanxi Province Institute of Microbiology, Xi'an, Shaanxi 710043, China
| | - Feng'an Jia
- Shaanxi Province Institute of Microbiology, Xi'an, Shaanxi 710043, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A & Forestry University, Yangling, Shaanxi 712100, China.
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13
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Wan W, Gadd GM, Yang Y, Yuan W, Gu J, Ye L, Liu W. Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:2390-2403. [PMID: 33714213 DOI: 10.1111/mec.15882] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 01/03/2023]
Abstract
Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.
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Affiliation(s)
- Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, UK.,State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, China University of Petroleum, Beijing, China
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenke Yuan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jidong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Environmental Engineering, Guangdong Technion Israel Institute of Technology, Guangdong, China
| | - Luping Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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14
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Sheng Y, Li G, Dong H, Liu Y, Ma L, Yang M, Liu Y, Liu J, Deng S, Zhang D. Distinct assembly processes shape bacterial communities along unsaturated, groundwater fluctuated, and saturated zones. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143303. [PMID: 33187706 DOI: 10.1016/j.scitotenv.2020.143303] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/02/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
The subsurface soil environment through the unsaturated (vadose) zone and saturated (below groundwater table) zone is one of the most active layers in the Earth's surface with biogeochemical interactions. Geochemical variables and geographic distance are key driving forces shaping the distribution of soil microbial communities, but our understandings are mainly limited to surface soil or shallow unsaturated zone (1-3 m beneath the ground). In this study, soil and sediment samples were collected from the unsaturated zone, through groundwater fluctuated zone, to saturated zone (up to 20 m) to unravel the assembly processes mediating vertical bacterial community succession across these three zones. Our results suggested both geochemical niches and bacterial diversity had different vertical patterns in each zone. With increased depth, pH increased and nutrient levels (C, N, P, K) and bacterial diversity declined in the unsaturated zone, and nutrients and bacterial diversity remained low levels after reaching the fluctuated and saturated zones. Nutrients were the key drivers shaping bacterial variation in the unsaturated zone, but limited nutrients and only 'depth' significantly explained the variations in the fluctuated zone and saturated zone, respectively. The co-occurrence network supported a more species co-existence pattern in the unsaturated zone than that in the other two zones. Due to the geochemical variations across three zones, the assembly of phylogenetically more clustered communities was observed through deterministic processes (e.g., 55% homogenizing selection) in the unsaturated zone, but the stochastic process (e.g., 50%-70% dispersal limitation) was more important in the fluctuated and saturated zones. These findings together suggested that the vertical distribution of soil bacterial community assembly was zone-specific and shaped by the degree of deterministic vs. stochastic processes. Our results provide a novel insight into the microbial community assembly across three different ecosystems in the Earth's critical zone and shed a light on subsurface biogeochemical processes.
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Affiliation(s)
- Yizhi Sheng
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA
| | - Guanghe Li
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Yifei Liu
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Lin Ma
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Mengqing Yang
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Ying Liu
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Jun Liu
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 45056, USA; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
| | - Songqiang Deng
- Research Institute for Environmental Innovation (Suzhou), Tsinghua, Suzhou 215163, China
| | - Dayi Zhang
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China; Research Institute for Environmental Innovation (Suzhou), Tsinghua, Suzhou 215163, China.
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15
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Sheng Y, Liu Y, Yang J, Dong H, Liu B, Zhang H, Li A, Wei Y, Li G, Zhang D. History of petroleum disturbance triggering the depth-resolved assembly process of microbial communities in the vadose zone. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:124060. [PMID: 33254835 DOI: 10.1016/j.jhazmat.2020.124060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/12/2020] [Accepted: 09/20/2020] [Indexed: 06/12/2023]
Abstract
Biogeochemical gradient forms in vadose zone, yet little is known about the assembly processes of microbial communities in this zone under petroleum disturbance. This study collected vadose zone soils at three sites with 0, 5, and 30 years of petroleum contamination to unravel the vertical microbial community successions and their assembly mechanisms. The results showed that petroleum hydrocarbons exhibited higher concentrations at the long-term contaminated site, showing negative impacts on some soil properties, retarding in the surface soils and decreasing along soil depth. Cultivable fraction of heterotrophic bacteria and microbial α-diversity decreased along depth in vadose zones with short-term/no contamination history, but exhibited an opposite trend with long-term contamination history. Petroleum contamination intensified the vertical heterogeneity of microbial communities based on the contamination time. Microbial co-occurrence network revealed the lowest species co-occurrence pattern at the long-term contaminated site. The distance-decay patterns and null model analysis together suggested distinct assembly mechanisms at three sites, where dispersal limitation (42-45%) was higher and variable and homogenizing selections were lower (37-38%) in vadose zones under petroleum disturbance than those in the uncontaminated vadose zone. Our findings help to better understand the subsurface biogeochemical cycles and bioremediation of petroleum-contaminated vadose zones.
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Affiliation(s)
- Yizhi Sheng
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; Department of Geology and Environmental Earth Science, Miami University, Oxford OH 45056, USA
| | - Ying Liu
- The Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Juejie Yang
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Hailiang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford OH 45056, USA
| | - Bo Liu
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Hao Zhang
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Aiyang Li
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Yuquan Wei
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guanghe Li
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China.
| | - Dayi Zhang
- School of Environment & State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou), Tsinghua, Suzhou 215163, China.
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16
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Shang Y, Wu X, Wei Q, Dou H, Wang X, Chen J, Zhang H, Ma S, Zhang H. Total Arsenic, pH, and Sulfate Are the Main Environmental Factors Affecting the Microbial Ecology of the Water and Sediments in Hulun Lake, China. Front Microbiol 2020; 11:548607. [PMID: 33072010 PMCID: PMC7541820 DOI: 10.3389/fmicb.2020.548607] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/24/2020] [Indexed: 01/29/2023] Open
Abstract
Bacteria have the metabolic potential to produce a diverse array of secondary metabolites, which have important roles in biogeochemical cycling processes. However, for Hulun Lake and the rivers that enter into it, the bacterial community structures and their effects have not previously been widely studied, limiting our ecological understanding of this habitat. To address this, we have analyzed the bacterial communities in the water ecosystem of the Hulun Lake Basin. 16S rRNA high-throughput sequencing identified 64 phyla, 165 classes, 218 orders, 386 families, and 740 genera of bacteria across all samples. The dominant phyla in the central area of the lake were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, while in all other areas, Proteobacteria, Actinobacteria, and Bacteroidetes were dominant. The microbial community structures were significantly affected by environmental factors [arsenic (As), pH, and sulfate (SO4 2-)] and their location in the lake. The species richness in the sediments of Hulun Lake was higher than in the water, and this ecosystem harbored the highest proportion of unclassified sequences, representing unclassified bacteria. This study provides basic data for future investigations into the Hulun lake ecosystem and for water microbial monitoring and protection measures.
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Affiliation(s)
- Yongquan Shang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Xiaoyang Wu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Xibao Wang
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shengchao Ma
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, China
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17
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Zhou L, Liu L, Chen WY, Sun JJ, Hou SW, Kuang TX, Wang WX, Huang XD. Stochastic determination of the spatial variation of potentially pathogenic bacteria communities in a large subtropical river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114683. [PMID: 32388300 DOI: 10.1016/j.envpol.2020.114683] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/01/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
Understanding the composition and assembly mechanism of waterborne pathogen is essential for preventing the pathogenic infection and protecting the human health. Here, based on 16S rRNA sequencing, we investigated the composition and spatial variation of potentially pathogenic bacteria from different sections of the Pearl River, the most important source of water for human in Southern China. The results showed that the potential pathogen communities consisted of 6 phyla and 64 genera, covering 11 categories of potential pathogens mainly involving animal parasites or symbionts (AniP), human pathogens all (HumPA), and intracellular parasites (IntCelP). Proteobacteria (75.87%) and Chlamydiae (20.56%) were dominant at the phylum level, and Acinetobacter (35.01%) and Roseomonas (8.24%) were dominant at the genus level. Multivariate analysis showed that the potential pathogenic bacterial community was significantly different among the four sections in the Pearl River. Both physicochemical factors (e.g., NO3-N, and suspended solids) and land use (e.g., urban land and forest) significantly shaped the pathogen community structure. However, spatial effects contributed more to the variation of pathogen community based on variation partitioning and path analysis. Null model based normalized stochasticity ratio analysis further indicated that the stochastic process rather than deterministic process dominated the assembly mechanisms by controlling the spatial patterns of potential pathogens. In conclusion, high-throughput sequencing shows great potential for monitoring the potential pathogens, and provided more comprehensive information on the potentially pathogenic community. Our study highlighted the importance of considering the influences of dispersal-related processes in future risk assessments for the prevention and control of pathogenic bacteria.
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Affiliation(s)
- Lei Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wei-Yuan Chen
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Ji-Jia Sun
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Shi-Wei Hou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Tian-Xu Kuang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Xiong Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China; School of Energy and Environment, State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | - Xian-De Huang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, China.
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18
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Tai X, Li R, Zhang B, Yu H, Kong X, Bai Z, Deng Y, Jia L, Jin D. Pollution Gradients Altered the Bacterial Community Composition and Stochastic Process of Rural Polluted Ponds. Microorganisms 2020; 8:microorganisms8020311. [PMID: 32102406 PMCID: PMC7074964 DOI: 10.3390/microorganisms8020311] [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: 01/27/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 11/29/2022] Open
Abstract
Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the succession of microbial communities in different pollution levels rural ponds. Also, the processes that govern bacterial communities in polluted ponds are poorly understood. In this study, the microbial communities in water and sediment from the ponds were investigated by using the 16S rRNA gene high-throughput sequencing technology. Meanwhile, we used null model analyses based on a taxonomic and phylogenetic metrics approach to test the microbial community assembly processes. Pollution levels were found to significantly alter the community composition and diversity of bacteria. In the sediment samples, the bacterial diversity indices decreased with increasing pollutant levels. Between-community analysis revealed that community assembly processes among water and sediment samples stochastic ratio both gradually decreased with the increased pollution levels, indicating a potential deterministic environmental filtering that is elicited by pollution. Our results identified assemblage drivers of bacterial community is important for improving the efficacies of ecological evaluation and remediation for contaminated freshwater systems.
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Affiliation(s)
- Xin Tai
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China;
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
| | - Rui Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bao Zhang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- School of Civil Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Hao Yu
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China;
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- Correspondence: (H.Y.); (D.J.); Tel.: +86-183-4184-9989 (H.Y.); +86-152-1009-8966 (D.J.)
| | - Xiao Kong
- School of Health and Public, Qingdao University, Qingdao 266071, China;
| | - Zhihui Bai
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lan Jia
- Research Institute of Mineral Resources Development and Utilization Technology and Equipment, Liaoning Technical University, Fuxin 123000, China;
| | - Decai Jin
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (R.L.); (B.Z.); (Z.B.); (Y.D.)
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (H.Y.); (D.J.); Tel.: +86-183-4184-9989 (H.Y.); +86-152-1009-8966 (D.J.)
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19
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Zhu Q, Wu Y, Zeng J, Wang X, Zhang T, Lin X. Influence of bacterial community composition and soil factors on the fate of phenanthrene and benzo[a]pyrene in three contrasting farmland soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:229-237. [PMID: 30677667 DOI: 10.1016/j.envpol.2018.12.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/24/2018] [Accepted: 12/25/2018] [Indexed: 06/09/2023]
Abstract
The fate of polycyclic aromatic hydrocarbons (PAHs) determines their potential risk in soil, which may be directly affected by abiotic conditions and indirectly through the changes in decomposer communities. In comparison, the indirect effects on the fate remain largely elusive. In this study, the fate of phenanthrene and benzo[a]pyrene and the corresponding bacterial changes were investigated in three contaminated farmland soils using a 14C tracer method and Miseq sequencing. The results showed that most benzo[a]pyrene was consistently extractable with dichloromethane (DCM) after the 60-day incubation (60.4%-78.2%), while phenanthrene was mainly mineralized to CO2 during the 30-day incubation (40.4%-58.7%). Soils from Guangzhou (GZ) showed a different distribution pattern of 14C-PAHs exemplified by low mineralization and disparate bound residue formation. The PAH fate in the Shenyang (SY) and Nanjing (NJ) soils were similar to each other than to that in the GZ soil. The fate in the GZ soil seemed to be linked to the distinct edaphic properties, such as organic matter content, however soil microbial community could have influenced the distribution pattern of PAHs. This potential role of microorganisms was reflected by the unique changes in the copy numbers of Gram positive RHDα gene, and by the distinct shifts in bacterial community composition during the incubation. A quite different shift in bacterial communities was found in the GZ microcosms which may influence PAH mineralization and non-extractable residue (NER) formation.
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Affiliation(s)
- Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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20
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Feng Y, Chen R, Stegen JC, Guo Z, Zhang J, Li Z, Lin X. Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions. Mol Ecol 2018; 27:5238-5251. [DOI: 10.1111/mec.14914] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/03/2018] [Accepted: 10/09/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - James C. Stegen
- Earth and Biological Sciences Directorate Ecosystem Sciences Team Pacific Northwest National Laboratory Richland Washington
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences Nanjing China
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21
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Hu A, Li S, Zhang L, Wang H, Yang J, Luo Z, Rashid A, Chen S, Huang W, Yu CP. Prokaryotic footprints in urban water ecosystems: A case study of urban landscape ponds in a coastal city, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1729-1739. [PMID: 30064876 DOI: 10.1016/j.envpol.2018.07.097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/19/2018] [Accepted: 07/22/2018] [Indexed: 06/08/2023]
Abstract
The urban water ecosystems, such as the landscape ponds are commonly considered under the influence of anthropogenic disturbances, which can lead to the deterioration of the water quality. The prokaryotic communities are considered as one of the best indicators of the water quality. However, there are significant gaps in understanding the ecological processes that shape the composition and function of prokaryotic communities in the urban water ecosystems. Here, we investigated the biogeographic distribution of prokaryotic assemblages in water environments including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city (Xiamen), China, by using 16S rDNA amplicon sequencing. Our results indicated that the ponds had higher α-diversity of prokaryotic communities than those in the reservoirs, while there were significant variations in the community compositions among ponds, reservoirs, IFs and EFs. Moreover, ponds harbored a significantly higher proportion of sewage- and fecal-indicator taxa than those in the reservoirs, suggesting the occurrence of exogenous pollution in the urban ponds. Null model analysis revealed that dispersal limitation was the main ecological processes resulting in the divergence of prokaryotic community compositions between ponds and other environments, while dispersal limitation and variable selection played an essential role in the formation of unique prokaryotic assemblages in the reservoirs. Function predication analysis demonstrated that the ponds shared more similar functional profiles with IFs or EFs (e.g., chemoheterotrophy, fermentation, chlorate reducers, nitrate reduction and respiration) than the reservoirs, whereas dominance of photoautotrophy was observed in the reservoirs. Overall, this study provides a profound insight of the ecological mechanisms underlying the responses of prokaryotic communities in the urban landscape ponds to the anthropogenic disturbances.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Shuang Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanping Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhuanxi Luo
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Shaoqing Chen
- Village Planning and Construction Management Station of Jimei District, Xiamen 361022, China
| | - Weixiong Huang
- Xinglin Construction and Development Co. LTD., Xiamen 361022, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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22
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Zeng J, Zhu Q, Wu Y, Shan J, Ji R, Lin X. Oxidation of benzo[a]pyrene by laccase in soil enhances bound residue formation and reduces disturbance to soil bacterial community composition. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:462-469. [PMID: 30005258 DOI: 10.1016/j.envpol.2018.06.075] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 05/09/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Laccases are capable of rapidly oxidizing benzo[a]pyrene. It is thought that the metabolites with an increase in water solubility caused by the oxidation of benzo[a]pyrene may stimulate the subsequent mineralization. However, to date, there has been no experimental evidence to support this. In this study, the fate of benzo[a]pyrene in soil affected by laccase amendment and the resulting soil bacterial responses were investigated. Laccase amendment promoted benzo[a]pyrene dissipation (15.6%) from soil, accompanied by trace mineralization (<0.58 ± 0.02%) and substantial bound residue formation (∼80%). An increase of ∼15% in the bound residue fraction was observed by laccase amendment, which mainly resulted from covalent binding of the residues to humin fraction. During the incubation, the abundance of bacterial 16S rRNA and polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes did not change markedly. In contrast, benzo[a]pyrene treated with laccase resulted in a smaller shift in the bacterial community composition, indicating a reduced disturbance to the soil microbial communities. These results here suggest that benzo[a]pyrene contaminated soil can be detoxified by laccase amendment mainly due to the enhanced bound residue formation to soil organic matter via covalent binding.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71 Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71 Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71 Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jun Shan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71 Nanjing 210008, PR China
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Xianlin Avenue, 163 Nanjing 210023, PR China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71 Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong Baptist University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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23
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Dai W, Zhang J, Tu Q, Deng Y, Qiu Q, Xiong J. Bacterioplankton assembly and interspecies interaction indicating increasing coastal eutrophication. CHEMOSPHERE 2017; 177:317-325. [PMID: 28319885 DOI: 10.1016/j.chemosphere.2017.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/26/2017] [Accepted: 03/09/2017] [Indexed: 06/06/2023]
Abstract
Anthropogenic perturbations impose negative effects on coastal ecosystems, such as increasing levels of eutrophication. Given the biogeochemical significance of microorganisms, understanding the processes and mechanisms underlying their spatial distribution under changing environmental conditions is critical. To address this question, we examined how coastal bacterioplankton communities respond to increasing eutrophication levels created by anthropogenic perturbations. The results showed that the magnitude of changes in the bacterioplankton community compositions (BCCs) and the importance of deterministic processes that constrained bacterial assembly were closely associated with eutrophication levels. Moreover, increasing eutrophication significantly (P < 0.001) attenuated the distance decay rate, with a random spatial distribution of BCCs in the undisturbed location. In contrast, the complexity of interspecies interaction was enhanced under moderate eutrophication levels but declined under heavy eutrophication. Changes in the relative abundances of 27 bacterial families were significantly correlated with eutrophication levels. Notably, the pattern of enrichment or decrease for a given bacterial family was consistent with its known ecological functions. Our findings demonstrate that the magnitude of changes in BCCs and underlying determinism are dependent on eutrophication levels. However, the buffer capacity of bacterioplankton community is limited, with disrupted interspecies interaction occurring under heavy eutrophication. As such, bacterial assemblages are sensitive to changes in environmental conditions and could thus potentially serve as bio-indicators for increasing eutrophication.
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Affiliation(s)
- Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, 310058, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, CAS, Beijing, 100085, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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24
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Wang X, Zhao X, Li H, Jia J, Liu Y, Ejenavi O, Ding A, Sun Y, Zhang D. Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation. Res Microbiol 2016; 167:731-744. [PMID: 27475037 DOI: 10.1016/j.resmic.2016.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 11/18/2022]
Abstract
Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.
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Affiliation(s)
- Xinzi Wang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Xiaohui Zhao
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Hanbing Li
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Jianli Jia
- School of Chemical and Environmental Engineering, China University of Mining & Technology (Beijing), Beijing 100083, PR China
| | - Yueqiao Liu
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Odafe Ejenavi
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK
| | - Aizhong Ding
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yujiao Sun
- College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Dayi Zhang
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK.
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25
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Liang Y, Zhao H, Deng Y, Zhou J, Li G, Sun B. Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes. Front Microbiol 2016; 7:60. [PMID: 26870020 PMCID: PMC4737900 DOI: 10.3389/fmicb.2016.00060] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/13/2016] [Indexed: 12/11/2022] Open
Abstract
With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential "keystone" genes, defined as either "hubs" or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Huihui Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Ye Deng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Jizhong Zhou
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
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26
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Xiong J, Chen H, Hu C, Ye X, Kong D, Zhang D. Evidence of bacterioplankton community adaptation in response to long-term mariculture disturbance. Sci Rep 2015; 5:15274. [PMID: 26471739 PMCID: PMC4607939 DOI: 10.1038/srep15274] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/21/2015] [Indexed: 11/21/2022] Open
Abstract
Understanding the underlying mechanisms that shape the temporal dynamics of a microbial community has important implications for predicting the trajectory of an ecosystem’s response to anthropogenic disturbances. Here, we evaluated the seasonal dynamics of bacterioplankton community composition (BCC) following more than three decades of mariculture disturbance in Xiangshan Bay. Clear seasonal succession and site (fish farm and control site) separation of the BCC were observed, which were primarily shaped by temperature, dissolved oxygen and sampling time. However, the sensitive bacterial families consistently changed in relative abundance in response to mariculture disturbance, regardless of the season. Temporal changes in the BCC followed the time-decay for similarity relationship at both sites. Notably, mariculture disturbance significantly (P < 0.001) flattened the temporal turnover but intensified bacterial species-to-species interactions. The decrease in bacterial temporal turnover under long-term mariculture disturbance was coupled with a consistent increase in the percentage of deterministic processes that constrained bacterial assembly based on a null model analysis. The results demonstrate that the BCC is sensitive to mariculture disturbance; however, a bacterioplankton community could adapt to a long-term disturbance via attenuating temporal turnover and intensifying species-species interactions. These findings expand our current understanding of microbial assembly in response to long-term anthropogenic disturbances.
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Affiliation(s)
- Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Heping Chen
- Faculty of Architectural and Civil Engineering and Environment, Ningbo University, Ningbo, 315211, China
| | - Changju Hu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, State Oceanic Administration (SOA), Ningbo, 315040, China
| | - Dingjiang Kong
- Marine Environmental Monitoring Center of Ningbo, State Oceanic Administration (SOA), Ningbo, 315040, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
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