1
|
Wang H, Ren W, Xu Y, Wang X, Ma J, Sun Y, Hu W, Chen S, Dai S, Song J, Jia J, Teng Y. Long-term herbicide residues affect soil multifunctionality and the soil microbial community. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116783. [PMID: 39067076 DOI: 10.1016/j.ecoenv.2024.116783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/22/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Residues of herbicides with the extensive applications may impact the soil ecosystem and ultimately threaten agricultural sustainability. However, the effects of long-term herbicide residues on soil multifunctionality and the soil microbial community remain poorly understood. Here, we evaluated relationships between soil multifunctionality and soil microbial communities with residual herbicide concentrations by surveying and analyzing 62 black soil samples collected from an agricultural area in northeastern China. Total residual herbicide concentrations varied from 35 to 568 μg/kg in the soil samples. The response of soil multifunctionality to increasing residual herbicide concentrations exhibited an inverted U-shaped relationship with a peak at approximately 310 μg/kg, with net mineralized organic nitrogen (Nm) and total nitrogen (TN) exhibiting the same trend. Microbial community richness was significantly lower in soil samples with high residual herbicide concentrations (> 310 μg/kg, HG) compared to low residual herbicide concentrations (< 310 μg/kg, LG). In addition, the relative abundances of specific keystone microbial genera differed significantly between LG and HG: norank_f_Acetobacteraceae, norank_f_Caldilineaceae, Candidatus_Alysiosphaera, and Gonytrichum. The relative abundances of these genera were also significantly correlated with soil multifunctionality. Structural equation models (SEMs) further showed that herbicide residues influenced soil multifunctionality by affecting these specific keystone genera. Our study demonstrates that long-term herbicide residues significantly impact the multifunctionality of agricultural black soil, where low concentrations stimulate while high concentrations inhibit, underscoring the need for reasonable application of herbicides to maintain soil ecosystem health.
Collapse
Affiliation(s)
- Hongzhe Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Ren
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongfeng Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xia Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Sensen Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shixiang Dai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiayin Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Junfeng Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
2
|
Li Y, Zhang K, Chen J, Zhang L, Feng F, Cheng J, Ma L, Li M, Wang Y, Jiang W, Yu X. Rhizosphere Bacteria Help to Compensate for Pesticide-Induced Stress in Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12542-12553. [PMID: 38967661 DOI: 10.1021/acs.est.4c04196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Although exogenous chemicals frequently exhibit a biphasic response in regulating plant growth, characterized by low-dose stimulation and high-dose inhibition, the underlying mechanisms remain elusive. This study demonstrates, for the first time, the compensatory function of rhizosphere microbiota in assisting plants to withstand pesticide stress. It was observed that pak choi plants, in response to foliar-spraying imidacloprid at both low and high doses, could increase the total number of rhizosphere bacteria and enrich numerous beneficial bacteria. These bacteria have capabilities for promoting plant growth and degrading the pesticide, such as Nocardioides, Brevundimonas, and Sphingomonas. The beneficial bacterial communities were recruited by stressed plants through increasing the release of primary metabolites in root exudates, such as amino acids, fatty acids, and lysophosphatidylcholines. At low doses of pesticide application, the microbial compensatory effect overcame pesticide stress, leading to plant growth promotion. However, with high doses of pesticide application, the microbial compensatory effect was insufficient to counteract pesticide stress, resulting in plant growth inhibition. These findings pave the way for designing improved pesticide application strategies and contribute to a better understanding of how rhizosphere microbiota can be used as an eco-friendly approach to mitigate chemical-induced stress in crops.
Collapse
Affiliation(s)
- Yong Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Kaiwei Zhang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Jian Chen
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Leigang Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Fayun Feng
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Jinjin Cheng
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Liya Ma
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Mei Li
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Ya Wang
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Wayne Jiang
- Department of Entomology, Michigan State University, 288 Farm Lane, Room 243, East Lansing, Michigan 48824, United States
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, 50 Kaifang Avenue, Yancheng 224000, China
| |
Collapse
|
3
|
Harindintwali JD, He C, Wen X, Liu Y, Wang M, Fu Y, Xiang L, Jiang J, Jiang X, Wang F. A comparative evaluation of biochar and Paenarthrobacter sp. AT5 for reducing atrazine risks to soybeans and bacterial communities in black soil. ENVIRONMENTAL RESEARCH 2024; 252:119055. [PMID: 38710429 DOI: 10.1016/j.envres.2024.119055] [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: 02/19/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
Application of biochar and inoculation with specific microbial strains offer promising approaches for addressing atrazine contamination in agricultural soils. However, determining the optimal method necessitates a comprehensive understanding of their effects under similar conditions. This study aimed to evaluate the effectiveness of biochar and Paenarthrobacter sp. AT5, a bacterial strain known for its ability to degrade atrazine, in reducing atrazine-related risks to soybean crops and influencing bacterial communities. Both biochar and strain AT5 significantly improved atrazine degradation in both planted and unplanted soils, with the most substantial reduction observed in soils treated with strain AT5. Furthermore, bioaugmentation with strain AT5 outperformed biochar in enhancing soybean growth, photosynthetic pigments, and antioxidant defenses. While biochar promoted higher soil bacterial diversity compared to strain AT5, the latter selectively enriched specific bacterial populations. Additionally, soil inoculated with strain AT5 displayed a notable increase in the abundance of key genes associated with atrazine degradation (trzN, atzB, and atzC), surpassing the effects observed with biochar addition, thus highlighting its effectiveness in mitigating atrazine risks in soil.
Collapse
Affiliation(s)
- Jean Damascene Harindintwali
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin Wen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingyi Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; College of Geographical Sciences, Nantong University, Nantong, 226001, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; RWTH Aachen University, Institute for Environmental Research, WorringerWeg 1, 52074, Aachen, Germany.
| |
Collapse
|
4
|
Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
Collapse
Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
5
|
Ruan Z, Chen K, Cao W, Meng L, Yang B, Xu M, Xing Y, Li P, Freilich S, Chen C, Gao Y, Jiang J, Xu X. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat Commun 2024; 15:4694. [PMID: 38824157 PMCID: PMC11144243 DOI: 10.1038/s41467-024-49098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
Collapse
Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Lei Meng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Chen Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| |
Collapse
|
6
|
Cusaro CM, Capelli E, Picco AM, Brusoni M. Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy. Sci Rep 2024; 14:10544. [PMID: 38719860 PMCID: PMC11078947 DOI: 10.1038/s41598-024-59856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
The increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.
Collapse
Affiliation(s)
- Carlo Maria Cusaro
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Enrica Capelli
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Anna Maria Picco
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy
| | - Maura Brusoni
- Department of Earth and Environmental Sciences, University of Pavia, 27100, Pavia, Italy.
| |
Collapse
|
7
|
Zhou X, Sun Y, Wang T, Tang L, Ling W, Mosa A, Wang J, Gao Y. Remediation potential of an immobilized microbial consortium with corn straw as a carrier in polycyclic aromatic hydrocarbons contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134091. [PMID: 38513440 DOI: 10.1016/j.jhazmat.2024.134091] [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: 12/26/2023] [Revised: 02/27/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in soils and threaten human health seriously. The immobilized microorganisms (IM) technique is an effective and environmentally sound approach for remediating PAH-contaminated soil. However, the knowledge of the remedial efficiency and the way IM operates using natural organic materials as carriers in complex soil environments is limited. In this study, we loaded a functional microbial consortium on corn straw to analyze the effect of IM on PAH concentration and explore the potential remediation mechanisms of IM in PAH-contaminated soil. The findings revealed that the removal rate of total PAHs in the soil was 88.25% with the application of IM after 20 days, which was 39.25% higher than the control treatment, suggesting that IM could more easily degrade PAHs in soil. The findings from high-throughput sequencing and quantitative PCR revealed that the addition of IM altered the bacterial community structure and key components of the bacterial network, enhanced cooperative relationships among bacteria, and increased the abundance of bacteria and functional gene copies such as nidA and nahAc in the soil, ultimately facilitating the degradation of PAHs in the soil. This study enhances our understanding of the potential applications of IM for the treatment of PAH-contaminated soil.
Collapse
Affiliation(s)
- Xian Zhou
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yuhao Sun
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Tingting Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Lei Tang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wanting Ling
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ahmed Mosa
- Soils Department, Faculty of Agriculture, Mansoura University, 35516 Mansoura, Egypt
| | - Jian Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| |
Collapse
|
8
|
Harindintwali JD, Wen X, He C, Zhao M, Wang J, Dou Q, Xiang L, Fu Y, Alessi DS, Jiang X, Jiang J, Wang F. Synergistic mitigation of atrazine-induced oxidative stress on soybeans in black soil using biochar and Paenarthrobacter sp. AT5. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120951. [PMID: 38669877 DOI: 10.1016/j.jenvman.2024.120951] [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: 02/28/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Atrazine, a widely used herbicide in modern agriculture, can lead to soil contamination and adverse effects on specific crops. To address this, we investigated the efficacy of biochar loaded with Paenarthrobacter sp. AT5 (an atrazine-degrading bacterial strain) in mitigating atrazine's impact on soybeans in black soil. Bacterially loaded biochar (BBC) significantly enhanced atrazine removal rates in both unplanted and planted soil systems. Moreover, BBC application improved soybean biomass, photosynthetic pigments, and antioxidant systems while mitigating alterations in metabolite pathways induced by atrazine exposure. These findings demonstrate the effectiveness of BBC in reducing atrazine-induced oxidative stress on soybeans in black soil, highlighting its potential for sustainable agriculture.
Collapse
Affiliation(s)
- Jean Damascene Harindintwali
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Wen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao He
- Institute of Environment Pollution Control and Treatment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mingxu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jianhao Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qingyuan Dou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; RWTH Aachen University, Institute for Environmental Research, WorringerWeg 1, 52074, Aachen, Germany.
| |
Collapse
|
9
|
Vandermaesen J, Daly AJ, Mawarda PC, Baetens JM, De Baets B, Boon N, Springael D. Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship. Ecol Lett 2024; 27:e14433. [PMID: 38712704 DOI: 10.1111/ele.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Abstract
The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.
Collapse
Affiliation(s)
| | - Aisling J Daly
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Panji Cahya Mawarda
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
- Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, Indonesia
| | - Jan M Baetens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
| |
Collapse
|
10
|
Hu S, Xu C, Xie Y, Ma L, Niu Q, Han G, Huang J. Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168723. [PMID: 38008322 DOI: 10.1016/j.scitotenv.2023.168723] [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: 09/15/2023] [Revised: 11/15/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.
Collapse
Affiliation(s)
- Shunli Hu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Chuangchuang Xu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Lu Ma
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Qingfeng Niu
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China
| | - Guomin Han
- School of Life Sciences, Anhui Agricultural University, 230036 Hefei, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China.
| | - Junwei Huang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China.
| |
Collapse
|
11
|
Zhao J, Duan G, Zhu D, Li J, Zhu Y. Microbial-influenced pesticide removal co-occurs with antibiotic resistance gene variation in soil-earthworm-maize system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123010. [PMID: 38012967 DOI: 10.1016/j.envpol.2023.123010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/01/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Within human-influenced landscapes, pesticides cooccur with a variety of antibiotic stressors. However, the relationship between pesticides removal process and antibiotic resistance gene variation are not well understood. This study explored pesticide (topramezone, TPZ) and antibiotic (polymyxin E, PME) co-contamination using liquid chromatography-tandem mass spectrometry (LC-MS/MS), bacterial-16 S rRNA sequencing and high-throughput quantitative polymerase chain reaction (HT-qPCR) in a soil-earthworm-maize system. After incubating soil for 28 days with TPZ and PME (10 mg kg-1 dry weight), earthworm weight-gain, mortality rates, and maize plant weight-gain only differed slightly, but height-gain significantly decreased. PME significantly increased TPZ-removal in the soil. Accumulation of TPZ in earthworm's tissues may pose potential risks in the food chain. Combined pollution altered the microbial community structure and increased the abundance of functional microorganisms involved in aromatic compound degradation. Furthermore, maize rhizosphere can raise resistance genes, however earthworms can reduce resistance genes. Co-contamination increased absolute abundance of mobile genetic elements (MGEs) in bulk-soil samples, antibiotic resistance genes (ARGs) in skin samples and number of ARGs in bulk-soil samples, while decreased absolute abundance of transposase gene in bulk-soil samples and number of ARGs in rhizosphere-soil samples. Potential hosts harbouring ARGs may be associated with the antagonistic effect during resistance and detoxification of TPZ and PMB co-occurrence. These findings provide insights into the mechanism underlining pesticide removal regarding occurrence of ARGs in maize agroecosystem.
Collapse
Affiliation(s)
- Jun Zhao
- Laboratory for Chemical Environmental Risk Assessment, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guilan Duan
- University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Dong Zhu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jianzhong Li
- Laboratory for Chemical Environmental Risk Assessment, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongguan Zhu
- University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| |
Collapse
|
12
|
Harindintwali JD, Dou Q, Wen X, Xiang L, Fu Y, Xia L, Jia Z, Jiang X, Jiang J, Wang F. Physiological and transcriptomic changes drive robust responses in Paenarthrobacter sp. AT5 to co-exposure of sulfamethoxazole and atrazine. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132795. [PMID: 37865076 DOI: 10.1016/j.jhazmat.2023.132795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/23/2023]
Abstract
Agricultural waterways are often contaminated with herbicide and antibiotic residues due to the widespread use of these chemicals in modern agriculture. The search for resistant bacterial strains that can adapt to and degrade these mixed contaminants is essential for effective in situ bioremediation. Herein, by integrating chemical and transcriptomic analyses, we shed light on mechanisms through which Paenarthrobacter sp. AT5, a well-known atrazine-degrading bacterial strain, can adapt to sulfamethoxazole (SMX) while degrading atrazine. When exposed to SMX and/or atrazine, strain AT5 increased the production of extracellular polymeric substances and reactive oxygen species, as well as the rate of activity of antioxidant enzymes. Atrazine and SMX, either alone or combined, increased the expression of genes involved in antioxidant responses, multidrug resistance, DNA repair, and membrane transport of lipopolysaccharides. Unlike atrazine alone, co-exposure with SMX reduced the expression of genes encoding enzymes involved in the lower part of the atrazine degradation pathway. Overall, these findings emphasize the complexity of bacterial adaptation to mixed herbicide and antibiotic residues and highlight the potential of strain AT5 in bioremediation efforts.
Collapse
Affiliation(s)
- Jean Damascene Harindintwali
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyuan Dou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leilei Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Xia
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Jülich 52428, Germany; RWTH Aachen University, Institute for Environmental Research, WorringerWeg 1, 52074 Aachen, Germany.
| |
Collapse
|
13
|
Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
Collapse
Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
14
|
Han S, Tao Y, Zhao L, Cui Y, Zhang Y. Metabolic insights into how multifunctional microbial consortium enhances atrazine removal and phosphorus uptake at low temperature. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132539. [PMID: 37717445 DOI: 10.1016/j.jhazmat.2023.132539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Agricultural soils in the black soil region of northeast China often face negative stress due to low temperatures, pesticide contamination, and inadequate nutrient supply. In this study, a new cold-tolerant strain of Peribacillus simplex C1 (C1) was selectively isolated from atrazine contaminated soil. The artificially constructed microbial consortium (CPD) [C1, phosphorus-solubilizing bacterium Enterobacter sp. P1, and atrazine-degrading bacterium Acinetobacter lwoffii DNS32] demonstrated the most effective performance in enhancing atrazine degradation and phosphorus-solubilizing capacity when the initial inoculation ratio of 5:1:2 at 15 °C. CPD enhanced energy-related metabolic pathways and increased choline production to regulate bacterial adaptation to temperature decrease. Additionally, the strains could selectively utilize carbon sources (low molecular weight organic acids) or nitrogen sources (some metabolites of atrazine) provided by each other to enhance growth. Furthermore, strain C1 enhanced membrane fluidity through increased expression of the unsaturated fatty acids. Pot experiments demonstrated that CPD assisted soybean seedlings in resisting dual stresses of low temperature and atrazine contamination by inducing the expression of genes related to photosynthesis, membrane permeability, phosphorus response, and cold tolerance.
Collapse
Affiliation(s)
- Siyue Han
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yue Tao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Longwei Zhao
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Yunhe Cui
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China
| | - Ying Zhang
- School of Resources and Environment, Northeast Agricultural University, Harbin 150030, PR China.
| |
Collapse
|
15
|
Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
Collapse
Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
16
|
Cao L, Garcia SL, Wurzbacher C. Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research. Microb Cell Fact 2023; 22:245. [PMID: 38042813 PMCID: PMC10693053 DOI: 10.1186/s12934-023-02252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction. RESULTS Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities. CONCLUSIONS This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.
Collapse
Affiliation(s)
- Lijia Cao
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany.
| |
Collapse
|
17
|
Wang X, Teng Y, Wang X, Xu Y, Li R, Sun Y, Dai S, Hu W, Wang H, Li Y, Fang Y, Luo Y. Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation. THE ISME JOURNAL 2023; 17:2169-2181. [PMID: 37775536 PMCID: PMC10689768 DOI: 10.1038/s41396-023-01522-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.
Collapse
Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of the Chinese Academy of Sciences, 100049, Beijing, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Shixiang Dai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenbo Hu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Hongzhe Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanning Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| | - Yan Fang
- University of the Chinese Academy of Sciences, 100049, Beijing, China
- Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of the Chinese Academy of Sciences, 100049, Beijing, China
| |
Collapse
|
18
|
Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023; 18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.
Collapse
Affiliation(s)
- Osiel S Gonçalves
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Mateus F Santana
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
19
|
Satapute P, De Britto S, Hadimani S, Abdelrahman M, Alarifi S, Govind SR, Jogaiah S. Bacterial chemotaxis of herbicide atrazine provides an insight into the degradation mechanism through intermediates hydroxyatrazine, N-N-isopropylammelide, and cyanuric acid compounds. ENVIRONMENTAL RESEARCH 2023; 237:117017. [PMID: 37652220 DOI: 10.1016/j.envres.2023.117017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
In recent times, the herbicide atrazine (ATZ) has been commonly used before and after the cultivation of crop plants to manage grassy weeds. Despite its effect, the toxic residues of ATZ affect soil fertility and crop yield. Hence, the current study is focused on providing insight into the degradation mechanism of the herbicide atrazine through bacterial chemotaxis involving intermediates responsive to degradation. A bacterium was isolated from ATZ-contaminated soil and identified as Pseudomonas stutzeri based on its morphology, biochemical and molecular characterization. Upon ultra-performance liquid chromatography analysis, the free cells of isolated bacterium strain was found to utilize 174 μg/L of ATZ after 3-days of incubation on a mineral salt medium containing 200 μg/L of ATZ as a sole carbon source. It was observed that immobilized based degradation of ATZ yielded 198 μg/L and 190 μg/L by the cells entrapped with silica beads and sponge, respectively. Furthermore, the liquid chromatography-mass spectroscopy revealed that the secretion of three significant metabolites, namely, cyanuric acid, hydroxyatrazine and N- N-Isopropylammelide is responsive to the biodegradation of ATZ by the bacterium. Collectively, this research demonstrated that bacterium strains are the most potent agent for removing toxic pollutants from the environment, thereby enhancing crop yield and soil fertility with long-term environmental benefits.
Collapse
Affiliation(s)
- Praveen Satapute
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, 580003, Karnataka, India
| | - Savitha De Britto
- Division of Biological Sciences, School of Science and Technology, University of Goroka, Goroka, 441, Papua New Guinea
| | - Shiva Hadimani
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, 580003, Karnataka, India
| | | | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
| | | | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, P.G. Department of Biotechnology and Microbiology, Karnatak University, Dharwad, 580003, Karnataka, India; Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periye (PO), 671316, Kasaragod (DT), Kerala, India.
| |
Collapse
|
20
|
Chang X, Fu F, Sun Y, Zhao L, Li X, Li Y. Coupling multifactor dominated the biochemical response and the alterations of intestinal microflora of earthworm Pheretima guillelmi due to typical herbicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:94126-94137. [PMID: 37526832 DOI: 10.1007/s11356-023-29032-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
The excessive application of herbicides on farmlands can substantially reduce labor costs and increase crop yields, but can also have undesirable effects on terrestrial ecosystems. To evaluate the ecological toxicity of herbicides, metolachlor and fomesafen, two typical herbicides that are extensively used worldwide were chosen as target pollutants, and the endogeic earthworm Pheretima guillelmi, which is widely distributed in China, was selected as the test organism. A laboratory-scale microcosmic experiment was set, and energy resources, enzymes, and the composition and connections of intestinal microorganisms in earthworms were determined. Both herbicides depleted the energy resources of the earthworms, especially glycogen contents; increased the levels of antioxidant enzymes; and inhibited acetylcholinesterase. Moreover, the richness and diversity of the intestinal bacterial community of the earthworms were suppressed. Additionally, the bacterial composition at the genus level changed greatly and the connections between dominant bacteria increased dramatically. Most interactions among the bacterial genera belonging to the same and different phyla showed mutualism and competition, respectively. Importantly, metolachlor with higher toxicity had a transitory effect on these indicators in earthworms, whereas fomesafen, with lower toxicity but stronger bioaccumulation potential, exerted a sustaining impact on earthworms. Collectively, these results indicate that the toxic effects of herbicides on terrestrial organisms should be comprehensively considered in combination with biological toxicity, persistence, bioaccumulation potential, and other factors.
Collapse
Affiliation(s)
- Xingping Chang
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Furong Fu
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Yang Sun
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China.
| | - Lixia Zhao
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Xiaojing Li
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Agro-Environmental Protection Institute, MARA/Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin, 300191, China
| | - Yongtao Li
- College of Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| |
Collapse
|
21
|
Peng Q, Lin L, Tu Q, Wang X, Zhou Y, Chen J, Jiao N, Zhou J. Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates. mSystems 2023; 8:e0128322. [PMID: 37417747 PMCID: PMC10469889 DOI: 10.1128/msystems.01283-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/12/2023] [Indexed: 07/08/2023] Open
Abstract
Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
Collapse
Affiliation(s)
- Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Yueyue Zhou
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Joint Lab for Ocean Research and Education at Shandong University, Xiamen University and Dalhousie University, Qingdao, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
| |
Collapse
|
22
|
Zhou M, Guan X, Deng T, Hu R, Qian L, Yang X, Wu B, Li J, He Q, Shu L, Yan Q, He Z. Synthetic phylogenetically diverse communities promote denitrification and stability. ENVIRONMENTAL RESEARCH 2023; 231:116184. [PMID: 37207729 DOI: 10.1016/j.envres.2023.116184] [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: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.
Collapse
Affiliation(s)
- Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
23
|
Xu C, Cui D, Lv X, Zhong G, Liu J. Heterogeneous distribution of carbofuran shaped by Pseudomonas stutzeri biofilms enhances biodegradation of agrochemicals. ENVIRONMENTAL RESEARCH 2023; 229:115894. [PMID: 37068725 DOI: 10.1016/j.envres.2023.115894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023]
Abstract
Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but overlooking the dominant lifestyle of microorganisms is to form biofilms, which compromises the efficiency of biodegradation in natural environment. Here, we employed a carbofuran-degrading bacterium Pseudomonas stutzeri PS21 to investigate how the bacterial biofilms formed and responded to agrochemicals. First, the PS21 biofilms formed with a core of bacterial cells enclosing with extracellular polymeric substances (EPSs), and the biofilms were active and resilient when exposed to carbofuran (up to 50 mg L-1). The formation was regulated by the second messenger bis-(3'-5')-cyclic di-guanosine monophosphate signaling, which strengthened the structural resistance and metabolic basis of biofilms to remain the degrading efficiency as comparable as the planktonic cells. Second, carbofuran distributed heterogeneously in the near-biofilm microenvironment via the covalent adsorption of biofilms, which provided a spontaneous force that enhanced the combination of carbofuran with biofilms to maintain high degrading activity. Additionally, we elucidated the biodegradation was driven by the integrated metabolic system of biofilms involving the extracellular enzymes located in the EPSs. This study exhibited the structural and metabolic advantages of microbial biofilms, highlighting the attractive potentials of exploring biofilm-based strategies to facilitate the in-situ bioremediation of organic contaminations.
Collapse
Affiliation(s)
- Chunyuan Xu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, PR China
| | - Dongming Cui
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xuejuan Lv
- Instrumental Analysis and Research Center of South China Agricultural University, Guangzhou, 510642, PR China
| | - Guohua Zhong
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, PR China
| | - Jie Liu
- National Key Laboratory of Green Pesticide, South China Agricultural University, Guangzhou, 510642, PR China.
| |
Collapse
|
24
|
Huang H, Wu H, Qi M, Wang H, Lu Z. Thiamine-Mediated Microbial Interaction between Auxotrophic Rhodococcus ruber ZM07 and Prototrophic Cooperators in the Tetrahydrofuran-Degrading Microbial Community H-1. Microbiol Spectr 2023; 11:e0454122. [PMID: 37125924 PMCID: PMC10269752 DOI: 10.1128/spectrum.04541-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
As a crucial growth factor, thiamine can regulate functional microbial communities; however, our current understanding of its effect on bioremediation is lacking. Using metatranscriptome and 16S rRNA gene sequencing, we explored the mechanism of response of an efficient tetrahydrofuran (THF)-degrading microbial culture, designated H-1, to exogenous thiamine. Rhodococcus ruber ZM07, a strain performing the THF degradation function in H-1, is a thiamine-auxotrophic bacterium. Furthermore, thiamine affected the microbial community structure of H-1 by altering resource and niche distributions. A microbial co-occurrence network was constructed to help us identify and isolate the cooperators of strain ZM07 in the microbial community. Based on the prediction of the network, two non-THF-degrading bacteria, Hydrogenophaga intermedia ZM11 and Pigmentiphaga daeguensis ZM12, were isolated. Our results suggest that strain ZM11 is a good cooperator of ZM07, and it might be more competitive than other cooperators (e.g., ZM12) in cocultured systems. Additionally, two dominant strains in our microbial culture displayed a "seesaw" pattern, and they showed completely different responses to exogenous thiamine. The growth of the THF degrader ZM07 was spurred by additional thiamine (with an increased relative abundance and significant upregulation of most metabolic pathways), while the growth of the cooperator ZM11 was obviously suppressed under the same circumstances. This relationship was the opposite without thiamine addition. Our study reveals that exogenous thiamine can affect the interaction patterns between THF- and non-THF-degrading microorganisms and provides new insight into the effects of micronutrients on the environmental microbial community. IMPORTANCE Auxotrophic microorganisms play important roles in the biodegradation of pollutants in nature. Exploring the interspecies relationship between auxotrophic THF-degrading bacteria and other microbes is helpful for the efficient utilization of auxotrophic functional microorganisms. Herein, the thiamine-auxotrophic THF-degrading bacterium ZM07 was isolated from the microbial culture H-1, and the effect of thiamine on the structure of H-1 during THF bioremediation was studied. Thiamine may help ZM07 occupy more niches and utilize more resources, thus improving THF degradation efficiency. This research provides a new strategy to improve the THF or other xenobiotic compound biodegradation performance of auxotrophic functional microorganisms/microbial communities by artificially adding special micronutrients. Additionally, the "seesaw" relationship between the thiamine-auxotrophic strain ZM07 and its prototrophic cooperator ZM11 during THF bioremediation could be changed by exogenous thiamine. This study reveals the effect of micronutrients on microbial interactions and provides an effective way to regulate the pollutant biodegradation efficiency of microbial communities.
Collapse
Affiliation(s)
- Hui Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Minbo Qi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haixia Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
25
|
Zhang L, Yao G, Mao Z, Song M, Zhao R, Zhang X, Chen C, Zhang H, Liu Y, Wang G, Li F, Wu X. Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131155. [PMID: 36893600 DOI: 10.1016/j.jhazmat.2023.131155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had kcat and Km values of 5.7 s-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.
Collapse
Affiliation(s)
- Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaochun Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Chun Chen
- Institute of Biomedicine, Jinan University, Guangzhou, 510632, PR China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| |
Collapse
|
26
|
Gao T, Tian H, Wang Z, Shi J, Yang R, Wang F, Xiang L, Dai Y, Megharaj M, He W. Effects of atrazine on microbial metabolic limitations in black soils: Evidence from enzyme stoichiometry. CHEMOSPHERE 2023:139045. [PMID: 37244552 DOI: 10.1016/j.chemosphere.2023.139045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
Long-term input of agricultural chemicals such as pesticides into the soil can increase soil pollution, thereby affecting the productivity and quality of black soil. Triazine herbicide atrazine has been shown to have long-lasting residual effects in black soil. The atrazine residues affected soil biochemical properties, further leading to microbial metabolism restriction. It is necessary to explore the strategies to mitigate the limitations on microbial metabolism in atrazine-contaminated soils. Here, we evaluated the effect of the atrazine on microbial nutrient acquisition strategies as indicated by extracellular enzyme stoichiometry (EES) in four black soils. Atrazine degradation in soil followed the first-order kinetics model across various concentrations ranging from 10 to 100 mg kg-1. We found that the atrazine was negatively correlated with the EES for C-, N-, and P-acquisition. Vector lengths and angles decreased and increased significantly with an increase of atrazine concentration in tested black soils except for Lishu soils. Moreover, the vector angles were >45° for tested four black soils, indicating that atrazine residue had the greatest P-limitation on soil microorganisms. Interestingly, microbial C- and P-limitations with different atrazine concentrations showed a strong linear relationship, especially in Qiqihar and Nongan soils. Atrazine treatment significantly negatively affected microbial metabolic limitation. Soil properties and EES interaction explained up to 88.2% for microbial C-/P-limitation. In conclusion, this study confirms the EES as a useful method in evaluating the effects of pesticides on microbial metabolic limitations.
Collapse
Affiliation(s)
- Tiancong Gao
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Ziqi Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Jing Shi
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Rui Yang
- Hainan Academy of Environmental Sciences, Haikou, 571126, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leilei Xiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunchao Dai
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
27
|
Ji C, Liang Z, Cao H, Chen Z, Kong X, Xin Z, He M, Wang J, Wei Z, Xing J, Li C, Zhang Y, Zhang H, Sun F, Li J, Li K. Transcriptome-based analysis of the effects of compound microbial agents on gene expression in wheat roots and leaves under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1109077. [PMID: 37235031 PMCID: PMC10206238 DOI: 10.3389/fpls.2023.1109077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/17/2023] [Indexed: 05/28/2023]
Abstract
Introduction Salt stress inhibits the beneficial effects of most plant growth-promoting rhizobacteria. The synergistic relationship between beneficial rhizosphere microorganisms and plants helps achieve more stable growth-promoting effects. This study aimed 1) to elucidate changes in gene expression profiles in the roots and leaves of wheat after inoculation with compound microbial agents and 2) to determine the mechanisms by which plant growth-promoting rhizobacteria mediate plant responses to microorganisms. Methods Following inoculation with compound bacteria, transcriptome characteristics of gene expression profiles of wheat, roots, and leaves at the flowering stage were investigated using Illumina high-throughput sequencing technology. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the genes that were significantly differentially expressed. Results The expression of 231 genes in the roots of bacterial preparations (BIO) -inoculated wheat changed significantly (including 35 upregulated and 196 downregulated genes) compared with that of non-inoculated wheat. The expression of 16,321 genes in leaves changed significantly, including 9651 upregulated genes and 6670 downregulated genes. The differentially expressed genes were involved in the metabolism of carbohydrates, amino acids, and secondary compounds as well as signal transduction pathways. The ethylene receptor 1 gene in wheat leaves was significantly downregulated, and genes related to ethylene-responsive transcription factor were significantly upregulated. GO enrichment analysis showed that metabolic and cellular processes were the main functions affected in the roots and leaves. The main molecular functions altered were binding and catalytic activities, among which the cellular oxidant detoxification enrichment rate was highly expressed in the roots. The expression of peroxisome size regulation was the highest in the leaves. KEGG enrichment analysis showed that linoleic acid metabolism expression was highest in the roots, and the expression of photosynthesis-antenna proteins was the highest in leaves. After inoculation with a complex biosynthesis agent, the phenylalanine ammonia lyase (PAL) gene of the phenylpropanoid biosynthesis pathway was upregulated in wheat leaf cells while 4CL, CCR, and CYP73A were downregulated. Additionally, CYP98A and REF1 genes involved in the flavonoid biosynthesis pathway were upregulated, while F5H, HCT, CCR, E2.1.1.104, and TOGT1-related genes were downregulated. Discussion Differentially expressed genes may play key roles in improving salt tolerance in wheat. Compound microbial inoculants promoted the growth of wheat under salt stress and improved disease resistance by regulating the expression of metabolism-related genes in wheat roots and leaves and activating immune pathway-related genes.
Collapse
Affiliation(s)
- Chao Ji
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
- Taishan Forest Ecosystem Research Station, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, Shandong, China
| | - Zengwen Liang
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
- Shandong Yongsheng Agricultural Development Co., Ltd., Yongsheng (Shouguang) Vegetable Technology Research Institute Co., Ltd, Weifang, China
| | - Hui Cao
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Zhizhang Chen
- College of Foreign Languages, Weifang University, Weifang, Shandong, China
| | - Xuehua Kong
- Weifang Hanting Vestibule School, Weifang Education Bureau, Weifang, Shandong, China
| | - Zhiwen Xin
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Mingchao He
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Jie Wang
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Zichao Wei
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Jiahao Xing
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Chunyu Li
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Yingxiang Zhang
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Hua Zhang
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Fujin Sun
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Runxin Fruit and Vegetable Cultivation Cooperative of Weifang Economic Development Zone, Weifang Agricultural Bureau, Weifang, Shandong, China
| | - Jianlin Li
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Weifang Nuode Biotechnology Co., LTD, Weifang Agricultural Bureau, Weifang, Shandong, China
| | - Kun Li
- Taishan Forest Ecosystem Research Station, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, Shandong, China
- College of Forestry, Shandong Agriculture University, Taian, Shandong, China
| |
Collapse
|
28
|
Li X, Wu S, Fan H, Dong Y, Wang Y, Bai Z, Jing C, Zhuang X. Phylogenetic distance affects the artificial microbial consortia's effectiveness and colonization during the bioremediation of polluted soil with Cr(VI) and atrazine. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131460. [PMID: 37141777 DOI: 10.1016/j.jhazmat.2023.131460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Soils co-contaminated with heavy metals and organic pollutants are common and threaten the natural environment and human health. Although artificial microbial consortia have advantages over single strains, the mechanism affecting their effectiveness and colonization in polluted soils still requires determination. Here, we constructed two kinds of artificial microbial consortia from the same or different phylogenetic groups and inoculated them into soil co-contaminated with Cr(VI) and atrazine to study the effects of phylogenetic distance on consortia effectiveness and colonization. The residual concentrations of pollutants demonstrated that the artificial microbial consortium from different phylogenetic groups achieved the highest removal rates of Cr(VI) and atrazine. The removal rate of 400 mg/kg atrazine was 100%, while that of 40 mg/kg Cr(VI) was 57.7%. High-throughput sequence analysis showed that the soil bacterial negative correlations, core genera, and potential metabolic interactions differed among treatments. Furthermore, artificial microbial consortia from different phylogenetic groups had better colonization and a more significant effect on the abundance of native core bacteria than consortia from the same phylogenetic group. Our study highlights the importance of phylogenetic distance on consortium effectiveness and colonization and offers insight into the bioremediation of combined pollutants.
Collapse
Affiliation(s)
- Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanyong Jing
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
29
|
van der Zalm J, Zeng L, Chen A. Experimental and computational studies of photoelectrochemical degradation of atrazine by modified nanoporous titanium dioxide. CHEMOSPHERE 2023; 318:137985. [PMID: 36716933 DOI: 10.1016/j.chemosphere.2023.137985] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The presence of herbicides like Atrazine (ATZ) in groundwater from non-target runoff of the agriculture industry becomes a big concern due to its potential negative impacts on the environment and human health. The use of advanced oxidative processes (AOP) to remove harmful contaminants has been shown to be effective for wastewater treatment. Herein, we report on an advanced photoelectrochemical (PEC) approach based on electrochemically modified nanoporous TiO2 electrode for efficient degradation of ATZ. The electrochemical treated TiO2 electrodes were shown to have a six-fold increase in the photo-current density over the untreated ones. This increase in PEC activity was attributed to the increase in Ti3+ sites after the electrochemical modification, which was corroborated by low-temperature electron paramagnetic resonance (EPR) studies. The removal of ATZ by the PEC process resulted in a rate constant of 1.91 × 10-3 s-1, compared to 3.12 × 10-4 s-1 obtained by a strictly photocatalytic process. Liquid-Chromatography Mass-Spectrometric measurements showed the modified TiO2 electrodes highly effective at removing ATZ, with 96.1% removed after 10 h. Monitoring of the common degradation products desethyl atrazine (DEA), desisopropyl atrazine (DIA) and desethyl desisopropyl atrazine (DDA) revealed very low concentrations throughout the degradation process, indicating that further degradation was achieved. Quantum mechanical-based test for overall free radical scavenging activity (QM-ORSA) computational studies were performed and a mechanism for the N-dealkylation processes of ATZ has been proposed.
Collapse
Affiliation(s)
- Joshua van der Zalm
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Libin Zeng
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Aicheng Chen
- Electrochemical Technology Center, Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| |
Collapse
|
30
|
Dhakar K, Medina S, Ziadna H, Igbaria K, Achdari G, Lati R, Zarecki R, Ronen Z, Dovrat G, Eizenberg H, Freilich S. Comparative study of bacterial community dynamics in different soils following application of the herbicide atrazine. ENVIRONMENTAL RESEARCH 2023; 220:115189. [PMID: 36587716 DOI: 10.1016/j.envres.2022.115189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities in cultivated soils control the fate of pollutants associated with agricultural practice. The present study was designed to explore the response of bacterial communities to the application of the widely-used herbicide atrazine in three different crop fields that differ significantly in their physicochemical structure and nutritional content: the nutrient-rich (with relatively high carbon and nitrogen content) Newe Yaar (NY) and Ha-Ogen (HO) soils and the nutrient-poor, sandy Sde-Eliyahu (SE) soil. The 16 S rRNA gene amplicon sequencing revealed the nutrient poor HO soil differs in its response to atrazine in comparison to the two nutrient-rich soils both in the shortest persistence of atrazine and its effect on community structure and composition. Potential reported bacterial degraders of atrazine such as Pseudomonas, Clostridium and Bacillus were more abundant in contaminated sandy/poor soils (HO) whereas bacteria known for nitrogen cycling such as Azospirillum, Sinorhizobium, Nitrospira and Azohydromonas were significantly more abundant in the nutrient rich contaminated SE soils. No significant increase of potential indigenous degrader Arthrobacter was detected in SE and NY soils whereas a significant increase was recorded with HO soils. An overall shift in bacterial community composition following atrazine application was observed only in the nutrient poor soil. Understanding atrazine persistence and microbiome response to its application of in dependence with soil types serve the design of precision application strategies.
Collapse
Affiliation(s)
- Kusum Dhakar
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
| | - Shlomit Medina
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Hamam Ziadna
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Karam Igbaria
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Guy Achdari
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ran Lati
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Raphy Zarecki
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel; Department of Environmental Hydrology & Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | - Zeev Ronen
- Department of Environmental Hydrology & Microbiology, Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | - Guy Dovrat
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Hanan Eizenberg
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| |
Collapse
|
31
|
Wu S, Li X, Fan H, Dong Y, Wang Y, Bai Z, Zhuang X. Engineering artificial microbial consortia based on division of labor promoted simultaneous removal of Cr(VI)-atrazine combined pollution. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130221. [PMID: 36367470 DOI: 10.1016/j.jhazmat.2022.130221] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/04/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Combined pollution caused by organic pollutants and heavy metals is common in polluted sites and wastewater. Engineering artificial microbial consortia offers a promising approach to address this complex issue. However, the mutualistic interactions and the critical function of specific microbe within microbial consortia remain unclear. In this study, based on division of labor, we respectively co-cultured two Cr(VI)-reducing strains, Paenarthrobacter nitroguajacolicus C1 and Pseudomonas putida C2, with an atrazine-degrading strain, Paenarthrobacter ureafaciens AT. After 5 days, up to 95 % Cr(VI) and 100 % atrazine were removed from the cocultures. Strain AT degraded nearly all atrazine and contributed only to a fraction of Cr(VI) reduction, whereas C1 promoted 41 % Cr(VI) transformation to Cr(III) fixed in cells, and C2 promoted 91 % Cr(VI) transformation to soluble Cr(III). Metabolic analyses of the cocultures and monocultures demonstrated that AT provided C1 with isopropylamine by passive diffusion and C2 with other effective nitrogen resources by cell-cell surface contact to promote their growth. Soil experiments also showed that treatments with AT and C2 achieved the highest Cr(VI) reduction and no atrazine residue. Our results indicate that engineering artificial microbial consortia based on division of labor and metabolic interactions is effective in promoting highly efficient bioremediation of combined pollution.
Collapse
Affiliation(s)
- Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaxin Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
32
|
Pan Z, Wu Y, Zhai Q, Tang Y, Liu X, Xu X, Liang S, Zhang H. Immobilization of bacterial mixture of Klebsiella variicola FH-1 and Arthrobacter sp. NJ-1 enhances the bioremediation of atrazine-polluted soil environments. Front Microbiol 2023; 14:1056264. [PMID: 36819060 PMCID: PMC9937183 DOI: 10.3389/fmicb.2023.1056264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
In this study, the effects of the immobilized bacterial mixture (IM-FN) of Arthrobacter sp. NJ-1 and Klebsiella variicola strain FH-1 using sodium alginate-CaCl2 on the degradation of atrazine were investigated. The results showed that the optimal ratio of three types of carrier materials (i.e., rice straw powder, rice husk, and wheat bran) was 1:1:1 with the highest adsorption capacity for atrazine (i.e., 3774.47 mg/kg) obtained at 30°C. On day 9, the degradation efficiency of atrazine (50 mg/L) reached 98.23% with cell concentration of 1.6 × 108 cfu/ml at pH 9 and 30°C. The Box-Behnken method was used to further optimize the culture conditions for the degradation of atrazine by the immobilized bacterial mixture. The IM-FN could be reused for 2-3 times with the degradation efficiency of atrazine maintained at 73.0% after being stored for 80 days at 25°C. The population dynamics of IM-FN was explored with the total soil DNA samples specifically analyzed by real-time PCR. In 7 days, the copy numbers of both PydC and estD genes in the IM-FN were significantly higher than those of bacterial suspensions in the soil. Compared with bacterial suspensions, the IM-FN significantly accelerated the degradation of atrazine (20 mg/kg) in soil with the half-life shortened from 19.80 to 7.96 days. The plant heights of two atrazine-sensitive crops (wheat and soybean) were increased by 14.99 and 64.74%, respectively, in the soil restored by immobilized bacterial mixture, indicating that the IM-FN significantly reduced the phytotoxicity of atrazine on the plants. Our study evidently demonstrated that the IM-FN could significantly increase the degradation of atrazine, providing a potentially effective bioremediation technique for the treatment of atrazine-polluted soil environment and providing experimental support for the wide application of immobilized microorganism technology in agriculture.
Collapse
Affiliation(s)
- Zequn Pan
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Yulin Wu
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Qianhang Zhai
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Yanan Tang
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xuewei Liu
- College of Plant Protection, Jilin Agricultural University, Changchun, China
| | - Xuanwei Xu
- Ginseng and Antler Products Testing Center of the Ministry of Agricultural PRC, Jilin Agricultural University, Changchun, China
| | - Shuang Liang
- College of Plant Protection, Jilin Agricultural University, Changchun, China,*Correspondence: Shuang Liang, ✉
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, China,Hao Zhang, ✉
| |
Collapse
|
33
|
Kong X, Lv N, Liu S, Xu H, Huang J, Xie X, Tao Q, Wang B, Ji R, Zhang Q, Jiang J. Phytoremediation of isoproturon-contaminated sites by transgenic soybean. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:342-353. [PMID: 36278914 PMCID: PMC9884020 DOI: 10.1111/pbi.13951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/11/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
The widespread application of isoproturon (IPU) can cause serious pollution to the environment and threaten ecological functions. In this study, the IPU bacterial N-demethylase gene pdmAB was transferred and expressed in the chloroplast of soybean (Glycine max L. 'Zhonghuang13'). The transgenic soybeans exhibited significant tolerance to IPU and demethylated IPU to a less phytotoxic metabolite 3-(4-isopropylphenyl)-1-methylurea (MDIPU) in vivo. The transgenic soybeans removed 98% and 84% IPU from water and soil within 5 and 14 days, respectively, while accumulating less IPU in plant tissues compared with the wild-type (WT). Under IPU stress, transgenic soybeans showed a higher symbiotic nitrogen fixation performance (with higher total nodule biomass and nitrogenase activity) and a more stable rhizosphere bacterial community than the WT. This study developed a transgenic (TS) soybean capable of efficiently removing IPU from its growing environment and recovering a high-symbiotic nitrogen fixation capacity under IPU stress, and provides new insights into the interactions between rhizosphere microorganisms and TS legumes under herbicide stress.
Collapse
Affiliation(s)
- Xiangkun Kong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Na Lv
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Songmeng Liu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Hui Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Junwei Huang
- College of Resources and Environment, Key Laboratory of Agri‐food Safety of Anhui ProvinceAnhui Agricultural UniversityHefeiChina
| | | | - Qing Tao
- Beijing DaBeiNong Technology Co., Ltd.BeijingChina
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| | - Rong Ji
- State Key Laboratory of Pollution Control and Resource Reuse, School of the EnvironmentNanjing UniversityNanjingChina
| | - Qun Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental MicrobiologyMinistry of Agriculture and Rural AffairsNanjingChina
| |
Collapse
|
34
|
Berihu M, Somera TS, Malik A, Medina S, Piombo E, Tal O, Cohen M, Ginatt A, Ofek-Lalzar M, Doron-Faigenboim A, Mazzola M, Freilich S. A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data. MICROBIOME 2023; 11:8. [PMID: 36635724 PMCID: PMC9835355 DOI: 10.1186/s40168-022-01438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment. RESULTS This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 . CONCLUSIONS This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.
Collapse
Affiliation(s)
- Maria Berihu
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Tracey S. Somera
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
| | | | - Shlomit Medina
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
- Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden
| | - Ofir Tal
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), P.O. Box 447, 49500 Migdal, Israel
| | - Matan Cohen
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Alon Ginatt
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | | | - Adi Doron-Faigenboim
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Mark Mazzola
- United States Department of Agriculture-Agricultural Research Service Tree Fruit Research Lab, 1104 N. Western Ave, Wenatchee, WA 98801 USA
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7600 South Africa
| | - Shiri Freilich
- Agricultural Research Organization (ARO), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| |
Collapse
|
35
|
Nanetti E, Palladino G, Scicchitano D, Trapella G, Cinti N, Fabbrini M, Cozzi A, Accetta G, Tassini C, Iannaccone L, Candela M, Rampelli S. Composition and biodiversity of soil and root-associated microbiome in Vitis vinifera cultivar Lambrusco distinguish the microbial terroir of the Lambrusco DOC protected designation of origin area on a local scale. Front Microbiol 2023; 14:1108036. [PMID: 36910169 PMCID: PMC9992870 DOI: 10.3389/fmicb.2023.1108036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Wines produced from the same grape cultivars but in different locations possess distinctive qualities leading to different consumer's appreciation, preferences, and thus purchase choices. Here, we explore the possible importance of microbiomes at the soil-plant interface as a determinant of the terroir properties in grapevine production, which confer specific growth performances and wine chemo-sensory properties at the local scale. Methods In particular, we investigated the variation in microbial communities associated with the roots of Vitis vinifera cultivar Lambrusco, as well as with surrounding bulk soils, in different vineyards across the "Consorzio Tutela Lambrusco DOC" protected designation of origin area (PDO, Emilia Romagna, Italy), considering viticultural sites located both inside and outside the consortium in two different seasons (June and November 2021). Results According to our findings, rhizospheric and soil microbiomes show significant structural differences in relation to the sampling site, regardless of seasonality, while endophytic microbiomes seem to be completely unaffected by such variables. Furthermore, a deeper insight into the microbial terroir of PDO areas highlighted the presence of some rhizospheric microorganisms enriched inside the consortium and characterizing the PDO regardless of both sampling season and farming strategy. These include Bacillus, Paenibacillus, and Azospirillum, which are all well-known plant growth-promoting bacteria. Discussion Taken together, our results suggest a connection between soil and root microbiomes of V. vinifera cultivar Lambrusco and the local designation of origin, emphasizing the potential role of PDO-enriched plant growth-promoting bacteria in vine growing and final quality of the Lambrusco DOC wine.
Collapse
Affiliation(s)
- Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Giulia Trapella
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Nicolò Cinti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Microbiomics Unit, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Alice Cozzi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | - Carlo Tassini
- Istituto Tecnico Statale "Ignazio Calvi", Finale Emilia, Italy
| | | | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy.,Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum-University of Bologna, Bologna, Italy
| |
Collapse
|
36
|
Biodegradation of Crystalline and Nonaqueous Phase Liquid-Dissolved ATRAZINE by Arthrobacter sp. ST11 with Cd2+ Resistance. Catalysts 2022. [DOI: 10.3390/catal12121653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A newly isolated cadmium (Cd)-resistant bacterial strain from herbicides-polluted soil in China could use atrazine as the sole carbon, nitrogen, and energy source for growth in a mineral salt medium (MSM). Based on 16S rRNA gene sequence analysis and physiochemical tests, the bacterium was identified as Arthrobacter sp. and named ST11. The biodegradation of atrazine by ST11 was investigated in experiments, with the compound present either as crystals or dissolved in di(2-ethylhexyl) phthalate (DEHP) as a non-aqueous phase liquid (NAPL). After 48 h, ST11 consumed 68% of the crystalline atrazine in MSM. After being dissolved in DEHP, the degradation ratio of atrazine was reduced to 55% under the same conditions. Obviously, the NAPL-dissolved atrazine has lower bioavailability than the crystalline atrazine. Cd2+ at concentrations of 0.05–1.5 mmol/L either had no effect (<0.3 mmol/L), slight effects (0.5–1.0 mmol/L), or significantly (1.5 mmol/L) inhibited the growth of ST11 in Luria-Bertani medium. Correspondingly, in the whole concentration range (0.05–1.5 mmol/L), Cd2+ promoted ST11 to degrade atrazine, whether crystalline or dissolved in DEHP. Refusal to adsorb Cd2+ may be the main mechanism of high Cd resistance in ST11 cells. These results may provide valuable insights for the microbial treatment of arable soil co-polluted by atrazine and Cd.
Collapse
|
37
|
Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y, Tang H. Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. MLIFE 2022; 1:382-398. [PMID: 38818482 PMCID: PMC10989833 DOI: 10.1002/mlf2.12043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/01/2024]
Abstract
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
Collapse
Affiliation(s)
- Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Miaoxiao Wang
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyETH ZürichEawagSwitzerland
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yong Nie
- College of EngineeringPeking UniversityBeijingChina
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| |
Collapse
|
38
|
Chang J, Fang W, Chen L, Zhang P, Zhang G, Zhang H, Liang J, Wang Q, Ma W. Toxicological effects, environmental behaviors and remediation technologies of herbicide atrazine in soil and sediment: A comprehensive review. CHEMOSPHERE 2022; 307:136006. [PMID: 35973488 DOI: 10.1016/j.chemosphere.2022.136006] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/18/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Atrazine has become one of the most popular applied triazine herbicides in the world due to its high herbicidal efficiency and low price. With its large-dosage and long-term use on a global scale, atrazine can cause widespread and persistent contamination of soil and sediment. This review systematically evaluates the toxicological effects, environmental risks, environmental behaviors (adsorption, transport and transformation, and bioaccumulation) of atrazine, and the remediation technologies of atrazine-contaminated soil and sediment. For the adsorption behavior of atrazine on soil and sediment, the organic matter content plays an extremely important role in the adsorption process. Various models and equations such as the multi-media fugacity model and solute transport model are used to analyze the migration and transformation process of atrazine in soil and sediment. It is worth noting that certain transformation products of atrazine in the environment even have stronger toxicity and mobility than its parent. Among various remediation technologies, the combination of microbial remediation and phytoremediation for atrazine-contaminated soil and sediment has wide application prospects. Although other remediation technologies such as advanced oxidation processes (AOPs) can also efficiently remove atrazine from soil, some potential problems still need to be further clarified. Finally, some related challenges and prospects are proposed.
Collapse
Affiliation(s)
- Jianning Chang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Wei Fang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Le Chen
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Panyue Zhang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China.
| | - Guangming Zhang
- School of Energy & Environmental Engineering, Hebei University of Technology, Tianjin, 300130, China.
| | - Haibo Zhang
- College of Resources and Environment, Shanxi Agricultural University, Taigu, 030801, China
| | - Jinsong Liang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Qingyan Wang
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| | - Weifang Ma
- Beijing Key Lab for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China; Engineering Research Center for Water Pollution Source Control & Eco-remediation, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
39
|
Ruan Z, Xu M, Xing Y, Jiang Q, Yang B, Jiang J, Xu X. Interspecies Metabolic Interactions in a Synergistic Consortium Drive Efficient Degradation of the Herbicide Bromoxynil Octanoate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11613-11622. [PMID: 36089742 DOI: 10.1021/acs.jafc.2c03057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microbial communities play vital roles in biogeochemical cycles, allowing biodegradation of a wide range of pollutants. Although many studies have shown the importance of interspecies interactions on activities of communities, fully elucidating the complex interactions in microbial communities is still challenging. Here, we isolated a consortium containing two bacterial strains (Acinetobacter sp. AG3 and Bacillus sp. R45), which could mineralize bromoxynil octanoate (BO) with higher efficiency than either strain individually. The BO degradation pathway by the synergistic consortium was elucidated, and interspecies interactions in the consortium were explored using genome-scale metabolic models (GSMMs). Modeling showed that growth and degradation enhancements were driven by metabolic interactions, such as syntrophic exchanges of small metabolites in the consortium. Besides, nutritional enhancers were predicted to improve BO degradation, which were tested experimentally. Overall, our results will enhance our understanding of microbial mineralization of BO by consortia and promote the application of microbial communities for bioremediation.
Collapse
Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Qi Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| |
Collapse
|
40
|
Ke M, Xu N, Zhang Z, Qiu D, Kang J, Lu T, Wang T, Peijnenburg WJGM, Sun L, Hu B, Qian H. Development of a machine‐learning model to identify the impacts of pesticides characteristics on soil microbial communities from high‐throughput sequencing data. Environ Microbiol 2022; 24:5561-5573. [DOI: 10.1111/1462-2920.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022]
Affiliation(s)
- Mingjing Ke
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Nuohan Xu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Zhenyan Zhang
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Danyan Qiu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Jian Kang
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Tao Lu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Tingzhang Wang
- Key laboratory of microbial technology and bioinformatics of Zhejiang Province Hangzhou P.R. of China
| | - W. J. G. M. Peijnenburg
- Institute of Environmental Sciences (CML) Leiden University RA Leiden the Netherlands
- National Institute of Public Health and the Environment (RIVM) , Center for Safety of Substances and Products, P.O. Box 1 Bilthoven the Netherlands
| | - Liwei Sun
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Baolan Hu
- Department of Environmental Science Zhejiang University Hangzhou P.R. of China
| | - Haifeng Qian
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| |
Collapse
|
41
|
Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil. mSystems 2022; 7:e0016922. [PMID: 35913191 PMCID: PMC9426591 DOI: 10.1128/msystems.00169-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extensive use of agrochemicals is emerging as a serious environmental issue coming at the cost of the pollution of soil and water resources. Bioremediation techniques such as biostimulation are promising strategies used to remove pollutants from agricultural soils by supporting the indigenous microbial degraders. Though considered cost-effective and eco-friendly, the success rate of these strategies typically varies, and consequently, they are rarely integrated into commercial agricultural practices. In the current study, we applied metabolic-based community-modeling approaches for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Efficacy of biostimulants as enhancers of the indigenous degrader Paenarthrobacter was ranked through simulation and validated in pot experiments. A two-dimensional simulation matrix predicting the effect of different biostimulants on additional potential indigenous degraders (Pseudomonas, Clostridium, and Geobacter) was crossed with experimental observations. The overall ability of the models to predict the compounds that act as taxa-selective stimulants indicates that computational algorithms can guide the manipulation of the soil microbiome in situ and provides an additional step toward the educated design of biostimulation strategies. IMPORTANCE Providing the food requirements of a growing population comes at the cost of intensive use of agrochemicals, including pesticides. Native microbial soil communities are considered key players in the degradation of such exogenous substances. Manipulating microbial activity toward an optimized outcome in efficient biodegradation processes conveys a promise of maintaining intensive yet sustainable agriculture. Efficient strategies for harnessing the native microbiome require the development of approaches for processing big genomic data. Here, we pursued metabolic modeling for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Our genomic-based predictions point at strategies for optimizing biodegradation by the native community. Developing a systematic, data-guided understanding of metabolite-driven targeted enhancement of selected microorganisms lays the foundation for the design of ecologically sound methods for optimizing microbiome functioning.
Collapse
|
42
|
Vasileiadis S, Perruchon C, Scheer B, Adrian L, Steinbach N, Trevisan M, Plaza-Bolaños P, Agüera A, Chatzinotas A, Karpouzas DG. Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole. Environ Microbiol 2022; 24:5105-5122. [PMID: 35799498 DOI: 10.1111/1462-2920.16116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13 C-labelled versus 12 C-TBZ showed that 66% of the 13 C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.
Collapse
Affiliation(s)
- Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Chiara Perruchon
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| | - Benjamin Scheer
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Nicole Steinbach
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Marco Trevisan
- Department of Sustainable Food Process, Universitá Cattolica del Sacro Cuore, Piacenza, Italy
| | - Patricia Plaza-Bolaños
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Ana Agüera
- Solar Energy Research Centre (CIESOL), Joint Center University of Almería-CIEMAT, Almeria, Spain
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Viopolis, Greece
| |
Collapse
|
43
|
Li X, Lu C, Dai Y, Yu Z, Gu W, Li T, Li X, Li X, Wang X, Su Z, Xu M, Zhang H. Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing. Front Microbiol 2022; 13:912312. [PMID: 35814706 PMCID: PMC9260513 DOI: 10.3389/fmicb.2022.912312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a “top-down” synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L−1 CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only “functional bacteria” with degradation capacity but also “auxiliary bacteria” without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of “auxiliary bacteria” should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.
Collapse
Affiliation(s)
- Xiang Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changming Lu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yumeng Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixiong Yu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wu Gu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Li
- Shenyang Research Institute of Chemical Industry, Shenyang, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Xiujuan Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Mingkai Xu
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Mingkai Xu
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- *Correspondence: Huiwen Zhang
| |
Collapse
|
44
|
Li B, Hu K, Lysenko V, Khan KY, Wang Y, Jiang Y, Guo Y. A scientometric analysis of agricultural pollution by using bibliometric software VoSViewer and Histcite™. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:37882-37893. [PMID: 35067891 DOI: 10.1007/s11356-022-18491-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
While modern agriculture brings more food to people, it causes environmental pollution as well. Agricultural pollution has attracted extensive public attention. A lot of reviews on agricultural research were conducted from different research aspects, but there is a lack of work on analyzing the research trend from large volumes of publications in the field of agricultural pollution. In the present work, a scientometric analysis of agricultural pollution was conducted to fill the gap by using the software of VoSviewer and HistCite™. The datasets are collected from the core database of Web of Science from 1991 to 2019, totally 1338 records on the topic of agricultural pollutions. In most years (1996, 1999, 2002, 2006, 2009, 2011, and 2013), the total local citation score (TLCS) and total global citation score (TGCS) have coincident peaks. Zhang, Ju, and Zhu have the highest TLCS and TGCS. In terms of institutes, Chinese Acad Sci and China Agr Univ are the leading institutes in this field. The Univ Calif Davis, INRA, and USDA ARS have very high global impacts. From the research hot topics, the representative words include "soil," "agriculture," "contamination," "environment," "lead," and "balance." Representative words like "heavy-metals," "groundwater," "land-use," and "water" are emerging in the latter time period. Five leading research co-cited reference clusters are identified, including environment management, underground water, monitoring and alarming for the agriculture-environment standards, intrinsic mechanism to the circulatory system, and ecology system and land use. The recent trend is revealed from the bibliographical-coupling network, focusing on classical and old-fashion research, like pollution chemicals including N management, pesticides, and heavy metal. This work provides a holistic picture on the research in the field of agriculture pollution.
Collapse
Affiliation(s)
- Bin Li
- Intelligent Equipment Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Kai Hu
- Key Laboratory of Advanced Process Control for Light Industry, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Vladimir Lysenko
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don , 344041, Russia
| | - Kiran Yasmin Khan
- Key Laboratory of Advanced Process Control for Light Industry, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yingkuan Wang
- Chinese Academy of Agricultural Engineering, Beijing, 100125, China.
| | - Yongnian Jiang
- Jiangsu Zhongnong IoT Technology Co., LTD, Yixing, 214200, China
| | - Ya Guo
- Key Laboratory of Advanced Process Control for Light Industry, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
45
|
The relevance of hormesis at higher levels of biological organization: Hormesis in microorganisms. CURRENT OPINION IN TOXICOLOGY 2022. [DOI: 10.1016/j.cotox.2021.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
46
|
Zhao X, Li J, Zhang D, Huang Z, Luo C, Jiang L, Huang D, Zhang G. Mechanism of salicylic acid in promoting the rhizosphere benzo[a]pyrene biodegradation as revealed by DNA-stable isotope probing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152202. [PMID: 34890682 DOI: 10.1016/j.scitotenv.2021.152202] [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: 10/13/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
Benzo[a]pyrene (BaP) is a typical high-molecular-weight PAH with carcinogenicity. Rhizoremediation is commonly applied to remove soil BaP, but its mechanism remains unclear. The role of inducers in root exudates in BaP rhizoremediation is rarely studied. Here, to address this problem, we firstly investigated the effect of the inducer salicylic acid on BaP rhizoremediation, rhizosphere BaP degraders, and PAH degradation-related genes by combining DNA-stable-isotope-probing, high-throughput sequencing, and gene function prediction. BaP removal in the rhizosphere was significantly increased by stimulation with salicylic acid, and the rhizosphere BaP-degrading microbial community structure was significantly changed. Fourteen microbes were responsible for the BaP metabolism, and most degraders, e.g. Aeromicrobium and Myceligenerans, were firstly linked with BaP biodegradation. The enrichment of the PAH-ring hydroxylating dioxygenase (PAH-RHD) gene in the heavy fractions of all 13C-treatments further indicated their involvement in the BaP biodegradation, which was also confirmed by the enrichment of dominant PAH degradation-related genes (e.g. PAH dioxygenase and protocatechuate 3,4-dioxygenase genes) based on gene function prediction. Overall, our study demonstrates that salicylic acid can enhance the rhizosphere BaP biodegradation by altering the community structure of rhizosphere BaP-degrading bacteria and the abundance of PAH degradation-related genes, which provides new insights into BaP rhizoremediation mechanisms in petroleum-contaminated sites.
Collapse
Affiliation(s)
- Xuan Zhao
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Zilin Huang
- Joint Institute of Environmental Research & Education, South China Agricultural University, Guangzhou 510642, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China; Joint Institute of Environmental Research & Education, South China Agricultural University, Guangzhou 510642, China.
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Deyin Huang
- Guangdong Institute of Eco-environmental and Soil sciences, Guangdong Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| |
Collapse
|
47
|
Chen C, Wang M, Zhu J, Tang Y, Zhang H, Zhao Q, Jing M, Chen Y, Xu X, Jiang J, Shen Z. Long-term effect of epigenetic modification in plant-microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process. MICROBIOME 2022; 10:36. [PMID: 35209943 PMCID: PMC8876431 DOI: 10.1186/s40168-022-01236-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 01/23/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Soil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms from discovery to agricultural application remains challenging, as the mechanisms underlying the interactions between beneficial strains and plants in native soils are still largely unknown. Increasing numbers of studies have indicated that strains introduced to manipulate microbiomes are usually eliminated in soils, while others have reported that application of PGPB as inocula significantly improves plant growth. This contradiction suggests the need for a deeper understanding of the mechanisms underlying microbe-induced growth promotion. RESULTS We showed PGPB-induced long-term plant growth promotion after elimination of the PGPB inoculum in soils and explored the three-way interactions among the exogenous inoculum, indigenous microbiome, and plant, which were key elements of the plant growth-promoting process. We found the rhizosphere microbiome assembly was mainly driven by plant development and root recruitments greatly attenuated the influence of inocula on the rhizosphere microbiome. Neither changes in the rhizosphere microbiome nor colonization of inocula in roots was necessary for plant growth promotion. In roots, modification of DNA methylation in response to inoculation affects gene expression related to PGPB-induced growth promotion, and disruptions of the inoculation-induced DNA methylation patterns greatly weakened the plant growth promotion. Together, our results showed PGPB-induced DNA methylation modifications in roots mediated the promotion process and these modifications remained functional after elimination of the inoculum from the microbiome. CONCLUSION This study suggests a new mechanism in which PGPB affect DNA methylation in roots to promote plant growth, which provides important insights into microbiome-plant interactions and offers new strategies for plant microbiome engineering beyond the perspective of maintaining inoculum persistence in soils. Video abstract.
Collapse
Affiliation(s)
- Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Miao Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jingzhi Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qiming Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Minyu Jing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| |
Collapse
|
48
|
Vandermaesen J, Du S, Daly AJ, Baetens JM, Horemans B, De Baets B, Boon N, Springael D. Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1352-1364. [PMID: 34982540 DOI: 10.1021/acs.est.1c06653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.
Collapse
Affiliation(s)
- Johanna Vandermaesen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Siyao Du
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Aisling J Daly
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Jan M Baetens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| |
Collapse
|
49
|
Jia W, Li N, Yang T, Dai W, Jiang J, Chen K, Xu X. Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome. Front Microbiol 2021; 12:771463. [PMID: 34956132 PMCID: PMC8692732 DOI: 10.3389/fmicb.2021.771463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022] Open
Abstract
Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg−1 atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.
Collapse
Affiliation(s)
- Weibin Jia
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ning Li
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tunan Yang
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Weixian Dai
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Kai Chen
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Environmental Microbiology for Agriculture, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
50
|
Enrichment of Burkholderia in the Rhizosphere by Autotoxic Ginsenosides to Alleviate Negative Plant-Soil Feedback. Microbiol Spectr 2021; 9:e0140021. [PMID: 34756064 PMCID: PMC8579924 DOI: 10.1128/spectrum.01400-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The accumulation of autotoxins and soilborne pathogens in soil was shown to be the primary driver of negative plant-soil feedback (NPSF). There is a concerted understanding that plants could enhance their adaptability to biotic or abiotic stress by modifying the rhizosphere microbiome. However, it is not clear whether autotoxins could enrich microbes to degrade themselves or antagonize soilborne pathogens. Here, we found that the microbiome degraded autotoxic ginsenosides, belonging to triterpenoid glycosides, and antagonized pathogens in the rhizosphere soil of Panax notoginseng (sanqi). Deep analysis by 16S rRNA sequencing showed that the bacterial community was obviously changed in the rhizosphere soil and identified the Burkholderia-Caballeronia-Paraburkholderia (BCP) group as the main ginsenoside-enriched bacteria in the rhizosphere soil. Eight strains belonging to the BCP group were isolated, and Burkholderia isolate B36 showed a high ability to simultaneously degrade autotoxic ginsenosides (Rb1, Rg1, and Rd) and antagonize the soilborne pathogen Ilyonectria destructans. Interestingly, ginsenosides could stimulate the growth and biofilm formation of B36, eventually enhancing the antagonistic ability of B36 to I. destructans and the colonization ability in the rhizosphere soil. In summary, autotoxic ginsenosides secreted by P. notoginseng could enrich beneficial microbes in the rhizosphere to simultaneously degrade autotoxins and antagonize pathogen, providing a novel ecological strategy to alleviate NPSF. IMPORTANCE Autotoxic ginsenosides, secreted by sanqi into soil, could enrich Burkholderia sp. to alleviate negative plant-soil feedback (NPSF) by degrading autotoxins and antagonizing the root rot pathogen. In detail, ginsenosides could stimulate the growth and biofilm formation of Burkholderia sp. B36, eventually enhancing the antagonistic ability of Burkholderia sp. B36 to a soilborne pathogen and the colonization of B36 in soil. This ecological strategy could alleviate NPSF by manipulating the rhizosphere microbiome to simultaneously degrade autotoxins and antagonize pathogen.
Collapse
|