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Hu JP, He YY, Li JH, Lü ZL, Zhang YW, Li YH, Li JL, Zhang MX, Cao YH, Zhang JL. Planting halophytes increases the rhizosphere ecosystem multifunctionality via reducing soil salinity. ENVIRONMENTAL RESEARCH 2024; 261:119707. [PMID: 39084507 DOI: 10.1016/j.envres.2024.119707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/25/2024] [Accepted: 07/28/2024] [Indexed: 08/02/2024]
Abstract
Soil salinization poses a significant global challenge, exerting adverse effects on both agriculture and ecosystems. Planting halophytes has the potential ability to improve saline-alkali land and enhance ecosystem multifunctionality (EMF). However, it remains unclear which halophytes are effective in improving saline-alkali land and what impact they have on the rhizosphere microbial communities and EMF. In this study, we evaluated the Na+ absorption capability of five halophytes (Grubovia dasyphylla, Halogeton glomeratus, Suaeda salsa, Bassia scoparia, and Reaumuria songarica) and assessed their rhizosphere microbial communities and EMF. The results showed that S. salsa possessed the highest shoot (3.13 mmol g-1) and root (0.92 mmol g-1) Na+ content, and its soil Na+ absorption, along with B. scoparia, was significantly higher than that of other plants. The soil pH, salinity, and Na+ content of the halophyte rhizospheres decreased by 6.21%, 23.49%, and 64.29%, respectively, when compared to the bulk soil. Extracellular enzymes in the halophyte rhizosphere soil, including α-glucosidase, β-glucosidase, β-1,4-N-acetyl-glucosaminidase, neutral phosphatase, and alkaline phosphatase, increased by 70.1%, 78.4%, 38.5%, 79.1%, and 64.9%, respectively. Furthermore, the halophyte rhizosphere exhibited higher network complexity of bacteria and fungi and EMF than bulk soil. The relative abundance of the dominant phyla Proteobacteria, Firmicutes, and Ascomycota in the halophyte rhizosphere soil increased by 9.4%, 8.3%, and 22.25%, respectively, and showed higher microbial network complexity compared to the bulk soil. Additionally, keystone taxa, including Muricauda, Nocardioides, and Pontibacter, were identified with notable effects on EMF. This study confirmed that euhalophytes are the best choice for saline-alkali land restoration. These findings provided a theoretical basis for the sustainable use of saline-alkali cultivated land.
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Affiliation(s)
- Jin-Peng Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yuan-Yuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Jian-Hong Li
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, 553004, PR China
| | - Zhao-Long Lü
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yue-Wei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yuan-Hong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Jia-Lü Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Ming-Xu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Yan-Hua Cao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, PR China.
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Asif M, Xie X, Zhao Z. Virulence regulation in plant-pathogenic bacteria by host-secreted signals. Microbiol Res 2024; 288:127883. [PMID: 39208525 DOI: 10.1016/j.micres.2024.127883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/07/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
Bacterial pathogens manipulate host signaling pathways and evade host defenses using effector molecules, coordinating their deployment to ensure successful infection. However, host-derived metabolites as signals, and their critical role in regulating bacterial virulence requires further insights. Effective regulation of virulence, which is essential for pathogenic bacteria, involves controlling factors that enable colonization, defense evasion, and tissue damage. This regulation is dynamic, influenced by environmental cues including signals from host plants like exudates. Plant exudates, comprising of diverse compounds released by roots and tissues, serve as rich chemical signals affecting the behavior and virulence of associated bacteria. Plant nutrients act as signaling molecules that are sensed through membrane-localized receptors and intracellular response mechanisms in bacteria. This review explains how different bacteria detect and answer to secreted chemical signals, regulating virulence gene expression. Our main emphasis is exploring the recognition process of host-originated signaling molecules through molecular sensors on cellular membranes and intracellular signaling pathways. This review encompasses insights into how bacterial strains individually coordinate their virulence in response to various distinct host-derived signals that can positively or negatively regulate their virulence. Furthermore, we explained the interruption of plant defense with the perception of host metabolites to dampen pathogen virulence. The intricate interplay between pathogens and plant signals, particularly in how pathogens recognize host metabolic signals to regulate virulence genes, portrays a crucial initial interaction leading to profound influences on infection outcomes. This work will greatly aid researchers in developing new strategies for preventing and treating infections.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xin Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China.
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Sun Z, Du M, Yao Z, Wang M, Gao P, Liu N, Liu Q, Kang S, Lai Q. Combined alkali-photocatalytic stimulation enables click microbial domestication for boosted ammonia nitrogen removal. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135417. [PMID: 39128151 DOI: 10.1016/j.jhazmat.2024.135417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/20/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024]
Abstract
Microbe-driven ammonia nitrogen removal plays a crucial role in the nitrogen cycle and wastewater treatment. However, the rational methods and mechanisms for boosting nitrogen conversion through microbial domestication are still limited. Herein, a combined alkali-photocatalytic stimulation strategy was developed to activate the Halomonas shizuishanensis DWK9 for efficient ammonia nitrogen removal. The strain DWK9 selected from saline-alkaline soil in Northwestern China possessed strong resistance to stress of saline-alkaline environment and free radicals, and was abundant in nitrogen conversion genes, thus is an ideal model for advanced microbial domestication. Bacterial in the combined alkali-photocatalytic stimulation group achieved a high ammonia nitrogen conversion rate of 67.5 %, 10 times outperforming the non-stimulated and single alkali/photocatalytic stimulation control groups. Morphology analysis revealed that the bacteria in the alkali-photocatalytic stimulated group formed a favorable structure for bioelectric transfer. Remarkably, the domesticated bacteria demonstrated improved electrochemical properties, including increased current capacity and lower overpotentials and impedance. Prokaryotic transcription genetic analysis together with qPCR analysis showed upregulation of denitrification-related metabolic pathway genes. A novel FAD dependent and NAD(P)H independent energy mode has been proposed. The universality and effectiveness of the as-developed combined alkali-photocatalytic microbial domestication strategy were further validated through indicator fish survival experiments. This work provides unprecedented degrees of freedom for the exploration of rational microbial engineering for optimized and controllable biogeochemical conversion.
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Affiliation(s)
- Zhen Sun
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai 200093, PR China
| | - Mingzhu Du
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China; Institute of Photochemistry and Photofunctional Materials (IPPM), University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Zongli Yao
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai 200093, PR China
| | - Ming Wang
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Pengcheng Gao
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai 200093, PR China
| | - Nian Liu
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China; Institute of Photochemistry and Photofunctional Materials (IPPM), University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Qinhong Liu
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Shifei Kang
- Department of Environmental Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China; Institute of Photochemistry and Photofunctional Materials (IPPM), University of Shanghai for Science and Technology, Shanghai 200093, PR China.
| | - Qifang Lai
- East China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Shanghai 200093, PR China.
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Liu D, Fei YH, Peng Y, Zhu S, Lu J, Luo Y, Chen Z, Jiang Y, Wang S, Tang YT, Qiu R, Chao Y. Genotype of pioneer plant Miscanthus is not a key factor in the structure of rhizosphere bacterial community in heavy metal polluted sites. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135242. [PMID: 39032184 DOI: 10.1016/j.jhazmat.2024.135242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/02/2024] [Accepted: 07/16/2024] [Indexed: 07/22/2024]
Abstract
Miscanthus is a common pioneer plant with abundant genetic variation in abandoned mines in southern China. However, the extent to which genetic differentiation among species modulates rhizosphere bacterial communities remains unclear. Miscanthus samples were collected from 26 typical abandoned heavy-metal mines with different soil types in southern China, tested using 14 pairs of simple sequence repeats (SSR) primers, and classified into two genotypes based on Nei's genetic distance. The structure and diversity of rhizosphere bacterial communities were examined using 16 S rRNA sequencing. The results showed that among the factors affecting the rhizosphere bacterial community structure of Miscanthus samples, the role of genotype was not significant, and geographical conditions were the most important factors, followed by pH and total organic carbon (TOC). The process of rhizospheric community assembly varied among different genotypes; however, the recruited species and their abundances were similar. Collectively, we provided an approach based on genetic differentiation to quantify the relative contribution of genotypes to the rhizosphere bacterial community, demonstrating that genotypes contribute less than soil conditions. Our findings provide new insights into the role of host genetics in the ecological processes of plant rhizosphere bacterial communities in abandoned mines and provide theoretical support for microbe-assisted phytoremediation.
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Affiliation(s)
- Danni Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yuxin Peng
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Shichen Zhu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Jianan Lu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Yang Luo
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziwu Chen
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuanyuan Jiang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; 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
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China.
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024; 32:858-873. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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Chen Y, Hua X, Li S, Zhao J, Yu H, Wang D, Yang J, Liu L. Aromatic compound 2-acetyl-1-pyrroline coordinates nitrogen assimilation and methane mitigation in fragrant rice. Curr Biol 2024; 34:3429-3438.e4. [PMID: 39047736 DOI: 10.1016/j.cub.2024.06.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/29/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Rice paddy has been the main source of anthropogenic methane (CH4) emissions, with significant variations among rice varieties. 2-Acetyl-1-pyrroline (2-AP) is the key component of the pleasant aroma in fragrant rice. Here, we show that fragrant rice is metabolically active in nitrogen assimilation and exhibits high levels of 2-AP and that CH4 fluxes at the booting stage and cumulative emissions are 25.5% and 14.8% lower, respectively, in fragrant rice paddies compared with nonfragrant rice paddies. Three precursors involved in 2-AP synthesis-proline, glutamic acid, and ornithine-are identified as crucial nitrogen compounds that significantly promote CH4 oxidation in the rhizosphere. Augmenting 2-AP synthesis, either through foliar spraying or by utilizing CRISPR-Cas9 technology to generate knockout lines of BETAINE ALDEHYDE DEHYDROGENASE 2 gene, effectively enhances CH4 oxidation and reduces CH4 fluxes. Our findings reveal that the 2-AP metabolic pathway coordinates the carbon/nitrogen cycle to improve nitrogen assimilation along with high 2-AP levels and mitigate CH4 emissions in paddy ecosystems.
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Affiliation(s)
- Yun Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Xia Hua
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Siyu Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jiamei Zhao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Huan Yu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Dongyao Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiqiang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Lijun Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Key Laboratory of Crop Cultivation and Physiology, Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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Han C, Cao H, Tan H, Li X, Yang W. Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:50952-50966. [PMID: 39103584 DOI: 10.1007/s11356-024-34590-2] [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: 03/19/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.
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Affiliation(s)
- Chang Han
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing, 210024, China
| | - Huiqun Cao
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Haoyue Tan
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Xiaomeng Li
- Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Wenjun Yang
- Changjiang River Scientific Research Institute, Wuhan, 430010, China.
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Dong Q, Su H, Sun Y, Zhao Y, Zhou D, Wang X, Jiang C, Liu X, Zhong C, Zhang H, Kang S, Zhao X, Yu H. Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39031093 DOI: 10.1111/pce.15034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/09/2024] [Accepted: 06/28/2024] [Indexed: 07/22/2024]
Abstract
The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.
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Affiliation(s)
- Qiqi Dong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Huijie Su
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuexin Sun
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yubiao Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Dongying Zhou
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xiaoguang Wang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chunji Jiang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xibo Liu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Chao Zhong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - He Zhang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Shuli Kang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xinhua Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Haiqiu Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, China
- School of Agriculture and Horticulture, Liaoning Agricultural Vocational and Technical College, Yingkou, Liaoning, China
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Mishra S, Zhang X, Yang X. Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition. Microbiol Res 2024; 284:127726. [PMID: 38643524 DOI: 10.1016/j.micres.2024.127726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.
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Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
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Wang C, Zhang Y, Wang S, Lv X, Xu J, Zhang X, Yang Q, Meng F, Xu B. Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil. Front Microbiol 2024; 15:1383526. [PMID: 39040904 PMCID: PMC11261347 DOI: 10.3389/fmicb.2024.1383526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/20/2024] [Indexed: 07/24/2024] Open
Abstract
Objective Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process. Methods The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens. Results We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc. Conclusion This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.
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Affiliation(s)
- Can Wang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Yinghua Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shaoxiang Wang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Xia Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xueting Zhang
- Institute of Medicinal Biological Technique, Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, China
| | - Qing Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fanlai Meng
- College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, China
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11
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Mahadeo K, Taïbi A, Meile JC, Côme B, Gauvin-Bialecki A, Boubakri H, Herrera-Belaroussi A, Kodja H. Exploring endophytic bacteria communities of Vanilla planifolia. BMC Microbiol 2024; 24:218. [PMID: 38902615 PMCID: PMC11188167 DOI: 10.1186/s12866-024-03362-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Rhizosphere bacterial community and endophytes are now known to influence plant health and response to environmental stress. Very few studies have reported the diversity of endophytic bacterial communities of Vanilla planifolia and their potential roles in promoting plant growth or contributing to aromatic quality. RESULTS In this study, the composition and diversity of the Vanilla rhizosphere bacterial community were explored by analyzing rhizosphere soil and root tissue samples as well as green pods of three accessions of Vanilla planifolia grown on different types of substrates (compost and leaf litter). In addition, the endophytic bacterial diversity of roots and green pods as well as the evolution of endophytic bacteria after the curing process of vanilla green pods were analyzed based on a metabarcoding approach. The results showed that bacterial species richness and diversity were higher in the compost. The analysis of the soil bacterial composition displayed that Halomonas, Pseudoalteromonas, Enterobacter and Bradyrhizobium were the most abundant genera. Moreover, the results indicated that the soil bacterial community structure was linked to the host plant genotype. Regarding the roots endophytic bacteria composition, the genera Halomonas, Pseudoalteromonas, Bacillus and Carboxydocella genera were present in all samples, independently from the substrate nature. Several genera including Bacillus, Bradyrhizobium, Burkholderia and Halomonas were transmitted internally from the roots to the green pods. The curing process reduced the bacterial richness and bacterial diversity associated with the green pods. Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella are the dominant genera in the pods after the curing process. CONCLUSIONS This study provides an overview of changes of the bacterial communities dynamics especially endophytic in the roots and the green pods. It highlighted bacterial genera (Halomonas, Pseudoalteromonas, Bacillus, and Carboxydocella) potentially implicated in the formation of aroma compounds of vanilla beans.
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Affiliation(s)
- Keshika Mahadeo
- Laboratoire de Chimie et Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de la Réunion, 15 Avenue René Cassin, CS 92 003, 97 744 St Denis Cedex 9, La Réunion, France
| | - Ahmed Taïbi
- QualiSud, Université de La Réunion, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Montpellier, France
| | - Jean-Christophe Meile
- QualiSud, Université de La Réunion, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Montpellier, France
| | - Bertrand Côme
- La Vanilleraie, 2 ter Domaine du Grand Hazier, allée Chassagne, Sainte Suzanne, Réunion, 97441, France
| | - Anne Gauvin-Bialecki
- Laboratoire de Chimie et Biotechnologie des Produits Naturels, Faculté des Sciences et Technologies, Université de la Réunion, 15 Avenue René Cassin, CS 92 003, 97 744 St Denis Cedex 9, La Réunion, France
| | - Hasna Boubakri
- Laboratoire d'Ecologie Microbienne, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne, 69622, France
| | - Aude Herrera-Belaroussi
- Laboratoire d'Ecologie Microbienne, Université Claude Bernard Lyon 1, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, Villeurbanne, 69622, France
| | - Hippolyte Kodja
- QualiSud, Université de La Réunion, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, Montpellier, France.
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12
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Ji K, Wei Y, Lan G. Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:1565. [PMID: 38891373 PMCID: PMC11175100 DOI: 10.3390/plants13111565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/28/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024]
Abstract
Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees.
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Affiliation(s)
- Kepeng Ji
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- Hainan Danzhou Tropical Agro-Ecosystem National Observation and Research Station, Danzhou 571737, China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- Hainan Danzhou Tropical Agro-Ecosystem National Observation and Research Station, Danzhou 571737, China
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13
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Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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14
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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15
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Geng H, Wang F, Wu H, Qin Q, Ma S, Chen H, Zhou B, Yuan R, Luo S, Sun K. Biochar and nano-hydroxyapatite combined remediation of soil surrounding tailings area: Multi-metal(loid)s fixation and soybean rhizosphere soil microbial improvement. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133817. [PMID: 38422730 DOI: 10.1016/j.jhazmat.2024.133817] [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: 11/26/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
The soil near tailings areas is relatively barren and contaminated by multi-metal(loid)s, seriously threatening the safety of crop production. Here, biochar and nano-hydroxyapatite (nHAP) were combined to improve the sterilized and unsterilized polymetallic contaminated soil, and soil incubation and soybean pot experiments were designed. Results showed that biochar and nHAP not only increased soil C, N, and P but also effectively reduced multi-metal bioavailability, wherein the combined application of the two amendments had the best effect on metal immobilization. The synergistic effect of the two amendments decreased the acid-soluble contents of Co, Cu, Fe, and Pb in rhizosphere soils up to 86.75%, 80.69%, 89.09%, and 96.70%, respectively. The ameliorant reduced the accumulation of metal(loid)s in soybean plants, and rhizosphere microorganisms inhibited the migration of soil metals to plants. Additionally, biochar and nHAP regulated the rhizosphere soil microbial community. The rhizosphere soil of the sterilization group tended to prioritize the restoration of the original dominant bacteria. As, Pb, Fe, Urease, OM, TN, and TP were the critical environmental variables affecting rhizosphere soil bacterial communities. Therefore, combining biochar and nHAP is an environmentally friendly strategy to reduce polymetallic mobility in tailings soil and crops and improve soil microbial community structure.
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Affiliation(s)
- Huanhuan Geng
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China; School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Fei Wang
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China.
| | - Haoming Wu
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Qizheng Qin
- School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing), D11 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Ma
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Huilun Chen
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Beihai Zhou
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Rongfang Yuan
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Luo
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Ke Sun
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
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16
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Guo J, Zhao Y, Kang SG, Huang K, Tong T. Differential effects of four laboratory animal control diets on gut microbiota in mice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4438-4452. [PMID: 38323712 DOI: 10.1002/jsfa.13331] [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: 07/13/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND The gut microbiota is intricate and susceptible to multiple factors, with diet being a major contributor. The present study aimed to investigate the impact of four commonly used laboratory animal control diets, namely Keao Xieli's maintenance diet (KX), HFK's 1025 (HF), Research Diets' D12450B (RD), and Lab Diet's 5CC4 (LD), on the gut microbiota of mice. RESULTS A total of 40 mice were randomly assigned to four groups, and each group was fed one of the four diets for a duration of 8 weeks. The assessment of gut microbiota was conducted using 16S rRNA sequencing both at the beginning of the study (week 0) and the end (week 8), which served as the baseline and endpoint samples, respectively. Following the 8-week feeding period, no significant differences were observed in physiological parameters, including body weight, visceral weight, and blood biochemical indices, across the four groups. Nonetheless, relative to the baseline, discernible alterations in the gut microbiota were observed in all groups, encompassing shifts in beta-diversity, hierarchical clustering, and key genera. Among the four diets, HF diet exhibited a significant influence on alpha-diversity, RD diet brought about notable changes in microbial composition at the phylum level, and LD diet demonstrated an interconnected co-occurrence network. Mantel analysis indicated no significant correlation between physiological parameters and gut microbiota in the four groups. CONCLUSION Overall, our study demonstrated that the four control diets had a minimal impact on physiological parameters, while exerting a distinct influence on the gut microbiota after 8 weeks. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jingya Guo
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
| | - Yuhan Zhao
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
| | - Seong-Gook Kang
- Department of Food Engineering and Solar Salt Research Center, Mokpo National University, Muangun, Republic of Korea
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, P. R. China
- Beijing Laboratory for Food Quality and Safety, Beijing, P. R. China
| | - Tao Tong
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing, P. R. China
- Beijing Laboratory for Food Quality and Safety, Beijing, P. R. China
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17
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Zhu G, Luan L, Zhou S, Dini-Andreote F, Bahram M, Yang Y, Geisen S, Zheng J, Wang S, Jiang Y. Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates. Microbiol Res 2024; 282:127669. [PMID: 38442455 DOI: 10.1016/j.micres.2024.127669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.
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Affiliation(s)
- Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51005, Estonia
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen 6700 ES, Netherlands
| | - Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shaopeng Wang
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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18
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He X, Wang D, Jiang Y, Li M, Delgado-Baquerizo M, McLaughlin C, Marcon C, Guo L, Baer M, Moya YAT, von Wirén N, Deichmann M, Schaaf G, Piepho HP, Yang Z, Yang J, Yim B, Smalla K, Goormachtig S, de Vries FT, Hüging H, Baer M, Sawers RJH, Reif JC, Hochholdinger F, Chen X, Yu P. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. NATURE PLANTS 2024; 10:598-617. [PMID: 38514787 DOI: 10.1038/s41477-024-01654-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbiota interactions in the face of environmental stresses. Here we surveyed 3,168 root and rhizosphere microbiome samples from 129 accessions of locally adapted Zea, sourced from diverse habitats and grown under control and different stress conditions. We quantified stress treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome abundance. Genome-wide association analysis identified host genetic variants linked to both rhizosphere microbiome abundance and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone bacterium Massilia in our controlled experiments and total soil nitrogen in the source environment. Isolation and controlled inoculation of Massilia alone can contribute to root development, whole-plant biomass production and adaptation to low nitrogen availability. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.
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Affiliation(s)
- Xiaoming He
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Danning Wang
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yong Jiang
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Meng Li
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Chloee McLaughlin
- Department of Plant Science, Pennsylvania State University, State College, PA, USA
| | - Caroline Marcon
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Li Guo
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Marcel Baer
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Yudelsy A T Moya
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nicolaus von Wirén
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marion Deichmann
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Gabriel Schaaf
- Plant Nutrition, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | | | - Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bunlong Yim
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Hubert Hüging
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mareike Baer
- Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Ruairidh J H Sawers
- Department of Plant Science, Pennsylvania State University, State College, PA, USA.
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
| | - Xinping Chen
- College of Resources and Environment, and Academy of Agricultural Sciences, Southwest University (SWU), Chongqing, People's Republic of China.
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
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Ważny R, Jędrzejczyk RJ, Rozpądek P, Domka A, Tokarz KM, Janicka M, Turnau K. Bacteria Associated with Spores of Arbuscular Mycorrhizal Fungi Improve the Effectiveness of Fungal Inocula for Red Raspberry Biotization. MICROBIAL ECOLOGY 2024; 87:50. [PMID: 38466433 DOI: 10.1007/s00248-024-02364-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Intensive crop production leads to the disruption of the symbiosis between plants and their associated microorganisms, resulting in suboptimal plant productivity and lower yield quality. Therefore, it is necessary to improve existing methods and explore modern, environmentally friendly approaches to crop production. One of these methods is biotization, which involves the inoculation of plants with appropriately selected symbiotic microorganisms which play a beneficial role in plant adaptation to the environment. In this study, we tested the possibility of using a multi-microorganismal inoculum composed of arbuscular mycorrhizal fungi (AMF) and AMF spore-associated bacteria for biotization of the red raspberry. Bacteria were isolated from the spores of AMF, and their plant growth-promoting properties were tested. AMF inocula were supplemented with selected bacterial strains to investigate their effect on the growth and vitality of the raspberry. The investigations were carried out in the laboratory and on a semi-industrial scale in a polytunnel where commercial production of seedlings is carried out. In the semi-industrial experiment, we tested the growth parameters of plants and physiological response of the plant to temporary water shortage. We isolated over fifty strains of bacteria associated with spores of AMF. Only part of them showed plant growth-promoting properties, and six of these (belonging to the Paenibacillus genus) were used for the inoculum. AMF inoculation and co-inoculation of AMF and bacteria isolated from AMF spores improved plant growth and vitality in both experimental setups. Plant dry weight was improved by 70%, and selected chlorophyll fluorescence parameters (the contribution of light to primary photochemistry and fraction of reaction centre chlorophyll per chlorophyll of the antennae) were increased. The inoculum improved carbon assimilation, photosynthetic rate, stomatal conductance and transpiration after temporary water shortage. Raspberry biotization with AMF and bacteria associated with spores has potential applications in horticulture where ecological methods based on plant microorganism interaction are in demand.
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Affiliation(s)
- Rafał Ważny
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland.
| | - Roman J Jędrzejczyk
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Piotr Rozpądek
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Agnieszka Domka
- Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7a, 30-387, Kraków, Poland
- W. Szafer Institute of Botany Polish Academy of Sciences, Lubicz 46, 31-512, Kraków, Poland
| | - Krzysztof M Tokarz
- Department of Botany, Physiology and Plant Protection, University of Agriculture in Krakow, Aleja Mickiewicza 21, 31-120, Kraków, Poland
| | - Martyna Janicka
- Department of Nanobiology and Biomaterials, Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163, Warsaw, Poland
- Division of Microbiology, Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Katarzyna Turnau
- Institute of Environmental Sciences, Jagiellonian University in Kraków, Gronostajowa 7, 30-387, Kraków, Poland
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20
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Hathurusinghe SHK, Azizoglu U, Shin JH. Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health. PLANTS (BASEL, SWITZERLAND) 2024; 13:695. [PMID: 38475541 DOI: 10.3390/plants13050695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.
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Affiliation(s)
| | - Ugur Azizoglu
- Department of Crop and Animal Production, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri 38039, Turkey
- Genome and Stem Cell Research Center, Erciyes University, Kayseri 38039, Turkey
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Republic of Korea
- NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
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21
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Wu QY, Ma R, Wang X, Ma YN, Wang ZS, Wei HL, Zhang XX. Effects of the invasion of Ralstonia solanacearum on soil microbial community structure in Wuhan, China. mSphere 2024; 9:e0066523. [PMID: 38231250 PMCID: PMC10900898 DOI: 10.1128/msphere.00665-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
This study investigated the change in the microbiome of tomato rhizosphere soils after the invasion of Ralstonia solanacearum and analyzed the correlation between microbes and soil physicochemical properties. Diversity analyses of the bacteria in healthy and diseased rhizosphere soil samples (HRS and DRS) revealed that HRS had a higher species diversity and were compositionally different from DRS (P ≤ 0.05). Substantial differences in the relative abundance of Actinobacteria (37.52% vs 28.96%, P ≤ 0.05) and Proteobacteria (29.20% vs 35.59%, P ≤ 0.05) were identified in HRS and DRS, respectively. Taxonomic composition analysis showed ten differentially abundant genera, and seven of them (Gaiella, Roseisolibacter, Solirubrobacter, Kribbella, Acidibacter, Actinomarinicola, and Marmoricola) are more abundant in HRS. Soil pH and enzyme activities were negatively correlated with the abundance of R. solanacearum. The contents of total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkaline nitrogen (alkaline N), available phosphorus (AP), available potassium (AK), NO3-N(NN), NH4+-N (AN), and organic matter (OM) were all significantly increased in DRS. The composition and richness of protozoa in the samples show significant differences. Cephalobus, Acrobeles, Heteromita, norank_Tylenchida, and Rotylenchulus were enriched in DRS. Microbial interaction networks revealed that the HRS networks were more complex than the DRS networks. Overall, the results of this study demonstrate that healthy soil has a more complex microbial community structure and higher enzyme activity, and the invasion of R. solanacearum damages the soil microbial system.IMPORTANCEHow does the invasion of Ralstonia solanacearum affect tomato rhizosphere bacteria and protozoa? Which microbial changes can affect the growth of R. solanacearum? To date, most research studies focus on bacteria, with little research on protozoa, and even less on the synergistic effects between protozoa and bacteria. Here, we analyzed the correlation between tomato rhizosphere bacterial and protozoan communities and soil physicochemical properties during the invasion of R. solanacearum. We found that the diversity and abundance of rhizosphere microorganisms in healthy rhizosphere soil samples (HRS) were significantly higher than those in diseased rhizosphere soil samples (DRS), and there were significant changes in soil pH and enzyme activity. Overall, in this study, the analysis of microbial changes during the invasion of R. solanacearum provides a theoretical basis for the prevention and control of bacterial wilt.
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Affiliation(s)
- Qian-Yu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi-Nan Ma
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Shan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Hai-Lei Wei
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Xia Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Meshram S, Adhikari TB. Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:364. [PMID: 38337897 PMCID: PMC10856849 DOI: 10.3390/plants13030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.
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Affiliation(s)
- Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara 144402, India;
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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23
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Wang M, Sun H, Xu Z. Characterization of Rhizosphere Microbial Diversity and Selection of Plant-Growth-Promoting Bacteria at the Flowering and Fruiting Stages of Rapeseed. PLANTS (BASEL, SWITZERLAND) 2024; 13:329. [PMID: 38276786 PMCID: PMC10819753 DOI: 10.3390/plants13020329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Plant rhizosphere microorganisms play an important role in modulating plant growth and productivity. This study aimed to elucidate the diversity of rhizosphere microorganisms at the flowering and fruiting stages of rapeseed (Brassica napus). Microbial communities in rhizosphere soils were analyzed via high-throughput sequencing of 16S rRNA for bacteria and internal transcribed spacer (ITS) DNA regions for fungi. A total of 401 species of bacteria and 49 species of fungi in the rhizosphere soil samples were found in three different samples. The composition and diversity of rhizosphere microbial communities were significantly different at different stages of rapeseed growth. Plant-growth-promoting rhizobacteria (PGPRs) have been widely applied to improve plant growth, health, and production. Thirty-four and thirty-one PGPR strains were isolated from the rhizosphere soil samples collected at the flowering and fruiting stages of rapeseed, respectively. Different inorganic phosphorus- and silicate-solubilizing and auxin-producing capabilities were found in different strains, in addition to different heavy-metal resistances. This study deepens the understanding of the microbial diversity in the rapeseed rhizosphere and provides a microbial perspective of sustainable rapeseed cultivation.
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Affiliation(s)
- Mengjiao Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China;
- Collaborative Innovation Center for Comprehensive Development of Biological Resources in Qinling-Ba Mountains, Hanzhong 723000, China
- Shaanxi Key Laboratory Bioresources, Hanzhong 723000, China
| | - Haiyan Sun
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China;
- Shaanxi Key Laboratory Bioresources, Hanzhong 723000, China
| | - Zhimin Xu
- School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, LA 70809, USA;
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24
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Li D, Zhang X, Chen J, Li J. Toxicity factors to assess the ecological risk for soil microbial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115867. [PMID: 38142592 DOI: 10.1016/j.ecoenv.2023.115867] [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: 09/26/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
The toxicity factor (TF), a critical parameter within the potential ecological risk index (RI), is determined without accounting for microbial factors. It is considerable uncertainty exists concerning its validity for quantitatively assessing the influence of metal(loid)s on microorganisms. To evaluate the suitability of TF, we constructed microcosm experiments with varying RI levels (RI = 100, 200, 300, 500, and 700) by externally adding zinc (Zn), chromium (Cr), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd), and mercury (Hg) to uncontaminated soil (CK). Quantitative real-time PCR (qPCR) and high-throughput sequencing techniques were employed to measure the abundance and community of bacteria and fungi, and high-throughput qPCR was utilised to quantify functional genes associated with CNPS cycles. The results demonstrated that microbial diversity and function exhibited significant alterations (p < 0.05) in response to increasing RI levels, and the influences on microbial community structure, enzyme activity, and functional gene abundances were different due to the types of metal(loid)s treatments. At the same RI level, significant differences (p < 0.05) were discerned in microbial diversity and function across metal(loid) treatments, and these differences became more pronounced (p < 0.001) at higher levels. These findings suggest that TF may not be suitable for the quantitative assessment of microbial ecological risk. Therefore, we adjusted the TF by following three steps (1) determining the adjustment criteria, (2) deriving the initial TF, and (3) adjusting and optimizing the TF. Ultimately, the optimal adjusted TF was established as Zn = 1.5, Cr = 4.5, Cu = 6, Pb = 4.5, Ni = 5, Cd = 22, and Hg = 34. Our results provide a new reference for quantitatively assessing the ecological risks caused by metal(loid)s to microorganisms.
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Affiliation(s)
- Dale Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Xiujuan Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi 030006, China.
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25
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Reid TE, Kavamura VN, Torres-Ballesteros A, Smith ME, Abadie M, Pawlett M, Clark IM, Harris JA, Mauchline TH. Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat. THE ISME JOURNAL 2024; 18:wrae131. [PMID: 38990206 PMCID: PMC11292143 DOI: 10.1093/ismejo/wrae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/17/2024] [Accepted: 07/10/2024] [Indexed: 07/12/2024]
Abstract
The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root-soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.
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Affiliation(s)
- Tessa E Reid
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Vanessa N Kavamura
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | | | - Monique E Smith
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Maïder Abadie
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
- Present address: INRAE, UR1264 MycSA, CS2032, 33882 Villenave d’Ornon, France
| | - Mark Pawlett
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
| | - Jim A Harris
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom
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26
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Liu C, Geng HY, Li WX, Li YY, Lu YS, Xie KZ, Sun LL, Zhang JX, Peng HL, Shi CH, Li WL, Zhou CM, Gu WJ, Wang D. Innate Root Exudates Contributed to Contrasting Coping Strategies in Response to Ralstonia solanacearum in Resistant and Susceptible Tomato Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20092-20104. [PMID: 38051256 DOI: 10.1021/acs.jafc.3c06410] [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: 12/07/2023]
Abstract
Tomato cultivars with contrasting resistance to pathogens regulate root exudates differentially in response to Ralstonia solanacearum attacks. However, strategies using innate root exudates against infection remain unknown. This study analyzed the innate root exudates of two tomato cultivars and their functions in regulating R. solanacearum infection. The innate root exudates differed between the two cultivars. Astaxanthin released from resistant plants inhibited colonization by R. solanacearum but promoted motility, while neferine released from susceptible plants suppressed motility and colonization. The secretion of astaxanthin in resistant tomatoes promoted the growth of biocontrol fungi in soil and reduced the abundance of pathogenic fungi. Neferine secreted by the susceptible cultivar inhibited the relative abundance of the bacterial-biocontrol-related Bacillus genus, indirectly reducing the soil's immune capacity. This study revealed contrasting strategies using root exudates in resistant and susceptible tomato cultivars to cope with R. solanacearum infection, providing a basis for breeding disease-resistant cultivars.
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Affiliation(s)
- Chong Liu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Hao-Yang Geng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Wang-Xi Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Ya-Ying Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Yu-Sheng Lu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Kai-Zhi Xie
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Li Li Sun
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Jie-Xin Zhang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Huan-Long Peng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Chao-Hong Shi
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Wan-Ling Li
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Chang-Min Zhou
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
| | - Wen-Jie Gu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Dan Wang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Guangdong Engineering Research Center of Soil Microbes and Cultivated Land Conservation, Guangzhou 510640, China
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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Chen S, Wang Y, Gao J, Chen X, Qi J, Peng Z, Chen B, Pan H, Liang C, Liu J, Wang Y, Wei G, Jiao S. Agricultural tillage practice and rhizosphere selection interactively drive the improvement of soybean plant biomass. PLANT, CELL & ENVIRONMENT 2023; 46:3542-3557. [PMID: 37564021 DOI: 10.1111/pce.14694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/30/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Rhizosphere microbes play key roles in plant growth and productivity in agricultural systems. One of the critical issues is revealing the interaction of agricultural management (M) and rhizosphere selection effects (R) on soil microbial communities, root exudates and plant productivity. Through a field management experiment, we found that bacteria were more sensitive to the M × R interaction effect than fungi, and the positive effect of rhizosphere bacterial diversity on plant biomass existed in the bacterial three two-tillage system. In addition, inoculation experiments demonstrated that the nitrogen cycle-related isolate Stenotrophomonas could promote plant growth and alter the activities of extracellular enzymes N-acetyl- d-glucosaminidase and leucine aminopeptidase in rhizosphere soil. Microbe-metabolites network analysis revealed that hubnodes Burkholderia-Caballeronia-Paraburkholderia and Pseudomonas were recruited by specific root metabolites under the M × R interaction effect, and the inoculation of 10 rhizosphere-matched isolates further proved that these microbes could promote the growth of soybean seedlings. Kyoto Encyclopaedia of Genes and Genomes pathway analysis indicated that the growth-promoting mechanisms of these beneficial genera were closely related to metabolic pathways such as amino acid metabolism, melatonin biosynthesis, aerobactin biosynthesis and so on. This study provides field observation and experimental evidence to reveal the close relationship between beneficial rhizosphere microbes and plant productivity under the M × R interaction effect.
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Affiliation(s)
- Shi Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiamin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xingyu Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiejun Qi
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Beibei Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chunling Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jiai Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yihe Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Yang L, Wan X, Zhou R, Yuan Y. The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar. BIOLOGY 2023; 12:1363. [PMID: 37997962 PMCID: PMC10669795 DOI: 10.3390/biology12111363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora-a perennial herb species of the family Paeoniaceae-includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars "Sheng Tao Hua" and "Zi Lou Xian Jin" exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between "Lian Tai" and "Zi Hong Zheng Hui", as well as between "Sheng Tao Hua" and "Tao Hua Fei Xue", and the maximum similarity between "Duo Ye Zi" and "Xue Feng". Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.
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Affiliation(s)
- Liping Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (L.Y.); (R.Z.)
| | - Xin Wan
- Jiangsu Academy of Forestry, Nanjing 211153, China;
- Jiangsu Yangzhou Urban Forest Ecosystem National Observation and Research Station, Yangzhou 225006, China
| | - Runyang Zhou
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (L.Y.); (R.Z.)
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (L.Y.); (R.Z.)
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [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: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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31
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Wu L, Weston LA, Zhu S, Zhou X. Editorial: Rhizosphere interactions: root exudates and the rhizosphere microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1281010. [PMID: 37736613 PMCID: PMC10509041 DOI: 10.3389/fpls.2023.1281010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023]
Affiliation(s)
- Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Leslie A. Weston
- Gulbali Institute for Agriculture, Water and the Environment, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xingang Zhou
- College of Horticulture, Northeast Agricultural University, Xiangfang, Harbin, China
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Tie Z, Wang P, Chen W, Tang B, Yu Y, Liu Z, Zhao S, Khan FH, Zhang X, Xi H. Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars. Front Microbiol 2023; 14:1229454. [PMID: 37637103 PMCID: PMC10450913 DOI: 10.3389/fmicb.2023.1229454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.
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Affiliation(s)
- Zhanjiang Tie
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Peng Wang
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Weijian Chen
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Binghui Tang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, Xinjiang, China
| | - Yu Yu
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Zheng Liu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Sifeng Zhao
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Faisal Hayat Khan
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - XueKun Zhang
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Hui Xi
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Wang X, Li W. Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum. Microbiol Spectr 2023; 11:e0533322. [PMID: 37222589 PMCID: PMC10269492 DOI: 10.1128/spectrum.05333-22] [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: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
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Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Gu J, Guo F, Lin L, Zhang J, Sun W, Muhammad R, Liang H, Duan D, Deng X, Lin Z, Wang Y, Zhong Y, Xu Z. Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163896. [PMID: 37146825 DOI: 10.1016/j.scitotenv.2023.163896] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/07/2023]
Abstract
Security utilization measures (SUMs) for "production while remediating" in moderate and mild Cd-polluted paddy fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into FeMn oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aromatization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial microbes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore, SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to participate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.
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Affiliation(s)
- Jiguang Gu
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Fang Guo
- Department of Ecology, Jinan University, Guangzhou 510632, China
| | - Lihong Lin
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jiexiang Zhang
- GRG Metrology& Test Group Co., Ltd., Guangzhou 510656, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Riaz Muhammad
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Haojie Liang
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Dengle Duan
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xingying Deng
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zheng Lin
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yifan Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuming Zhong
- College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Zhimin Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300350, China; College of Resources and Environment, Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
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