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Xiao Y, Xiang W, Gao D, Zheng B, Wang Z, Rong D, Bayram H, Ghiladi RA, Lorimer GH, Xie Z, Wang J. hmuSTUV operon positively regulates the alginate gene cluster to mediate the pathogenicity of Pseudomonas donghuensis HYS. Int J Biol Macromol 2025; 306:141430. [PMID: 40010467 DOI: 10.1016/j.ijbiomac.2025.141430] [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: 11/19/2024] [Revised: 01/27/2025] [Accepted: 02/22/2025] [Indexed: 02/28/2025]
Abstract
Pseudomonas donghuensis HYS is highly virulent to Caenorhabditis elegans, but with mechanistic details that are not fully understood. The hmuSTUV operon was reported to participate in the synthesis of heme in Pseudomonas. However, the exact role of the hmuSTUV operon in Pseudomonas virulence has not been elucidated. In this study, we report for the first time that the hmuSTUV operon in P. donghuensis HYS causes host virulence, and that hmuS was a key gene for the toxicity of this operon. Furthermore, RNA-seq data showed that hmuS deletion inhibited alginate gene expression, thereby inhibiting biofilm formation. The hmuSTUV operon and alginate gene cluster are conserved in Pseudomonas. By constructing mutant strains carrying GFP, we found that the hmuS deletion reduced colonisation of HYS to the host gut. Moreover, the expression of the alginate gene cluster was controlled by the construction of a L-arabinose-inducible promoter. hmuS positively regulated alginate gene cluster expression, mediating bacterial virulence against C. elegans. In addition, HYS originating from the East Lake of Wuhan City was more pathogenic to zebrafish than any other pathogenic Pseudomonas, through impairment of zebrafish neurodevelopment and locomotor ability, by colonizing to the zebrafish brain. In conclusion, the hmuSTUV operon positively regulated the alg gene cluster, thereby disabling bacterial biofilm formation and colonisation to mediate bacterial pathogenicity to the host. These novel findings revealed the critical interaction between the hmuSTUV operon and the alg gene cluster in the bacterial virulence of Pseudomonas, providing new insights into Pseudomonas pathogenicity.
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Affiliation(s)
- Yaqian Xiao
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China; Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wang Xiang
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China
| | - Donghao Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Bowen Zheng
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China
| | - Zhiqian Wang
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China
| | - Dechang Rong
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China
| | - Hasan Bayram
- Department of Pulmonary Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - George H Lorimer
- Department of Chemistry, University of Maryland, College Park, MD, USA
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
| | - Jun Wang
- Hubei Key Laboratory of Industry Microbiology, International Center for Redox Biology & Precision Medicine of Hubei Province, Hubei University of Technology, Wuhan, Hubei, China.
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Lee SM, Kong HG, Lee B, Chang YK, Ryu CM. Management of Naturally Occurring Diseases by Supernatant from Chlorella Cultures in Pepper. J Microbiol Biotechnol 2025; 35:e2502004. [PMID: 40295202 PMCID: PMC12089950 DOI: 10.4014/jmb.2502.02004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 03/10/2025] [Accepted: 03/17/2025] [Indexed: 04/30/2025]
Abstract
The large-scale culture of Chlorella, a genus of microalgae, generates valuable products used to improve human health and produce biofuel. Such commercial applications utilized only the microalgal cells. However, the process produces tons of supernatant waste that require detoxification and disposal. A previous study demonstrated that cell-free supernatants from Chlorella fusca culture primes plant immunity in the model plant Arabidopsis thaliana, suggesting its potential for use as a bioprotectant. The current study investigated the effects of treatment with Chlorella supernatant on crop plants in an agricultural setting. Supernatants from Chlorella sp. strains HS2 and ABC001 were drench-applied to pepper (Capsicum annum L.) seedlings under greenhouse and field conditions. The disease control capacity and growth of plants were evaluated, as well as the diversity of the rhizosphere microbiota. Application of either supernatant reduced the severity of bacterial leaf spot disease caused by Xanthomonas axonopodis pv. vesicatoria and enhanced pepper seedling growth in the greenhouse. Under field conditions, cell-free supernatants of strains HS2 and ABC001 not only reduced the severity of natural-occurring viral and bacterial diseases and insect infestation but also increased fruit yield. Additionally, drenching with Chlorella supernatants improved species diversity in the rhizosphere microbiota. The application of Chlorella supernatant to pepper therefore offered protection against diverse field pathogens and promoted seedling growth and productivity. Our finding provides insight into novel methods of sustainable agriculture utilizing recycled cell-free waste supernatants from the industrial culture of Chlorella.
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Affiliation(s)
- Sang-Moo Lee
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Plant Medicine, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Bongsoo Lee
- Department of Microbial and Nano Materials, College of Science and Technology, Mokwon University, Daejeon 35349, Republic of Korea
| | - Yong-Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
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Li J, Qu K, Wei L, Chen H, Cai H, Zhang J, Mei L, Liu B, Han Y, Miao Y, Liu D. Artemisia argyi leaf powder improves soil properties and recruits Sphingobium bacteria to promote the growth and yield of Pinellia ternata. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 371:123322. [PMID: 39547026 DOI: 10.1016/j.jenvman.2024.123322] [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: 07/25/2024] [Revised: 11/09/2024] [Accepted: 11/09/2024] [Indexed: 11/17/2024]
Abstract
Recent research has reported the strong herbicidal activity of Artemisia argyi leaf powder (AALP), indicating its high potential for use as an environmentally friendly weed management solution for ecological agriculture. However, AALP's impacts on soil physicochemical properties and microbial communities have remained uninvestigated. This study explores these effects through pot experiments assessing the AALP's efficacy in weed suppression and its ability to promote the growth of Pinellia ternata, a plant utilized in traditional Chinese medicine. The results demonstrate that a 10% concentration of AALP suppressed nearly 100% of all weeds. Additionally, AALP treatments at 2.5%, 5%, 7.5%, and 10% concentrations increased P. ternata yields by 29.79%, 24.76%, 35.67%, and 31.00%, respectively. A soil analysis revealed that AALP enhanced soil fertility by increasing the contents of nutrients such as SOM, AN, AP, AK, Ca, Fe, Mn, and Zn, as well as the enzyme activity of CAT, ACP, UE, and SC, creating an optimal growth environment for P. ternata. In addition, AALP significantly increased the PA (phenolic acid) content in soil, which is a key factor in inhibiting weed germination and growth. Furthermore, a microbial community structure analysis indicated an enrichment of Actinobacteriota and Bacteroidota after AALP treatment, with notable increases in the growth-promoting bacteria Sphingobium and Flavobacterium. A permutational multivariate analysis of variance (PERMANOVA) based on the Bray-Curtis distance reaveled that all of the tested soil properties were significantly correlated with changes in bacterial community composition except for pH. Further two-factor correlation network analysis identified AN, Zn, SC, and PA as key environmental factors. Finally, the Sphingobium sp. strain AFR15, isolated from AALP-treated soil, exhibited significant growth-promoting effects on P. ternata. After inoculation with Sphingobium sp. strain AFR15 for one month, the heights of P. ternata were increased significantly. The leaf length and leaf width of P. ternata were also positively correlated with the treatment concentration of AFR15, and the chlorophyll contents of the leaves also increased. This results highlighted Sphingobium sp. strain AFR15's potential as a specialized microbial fertilizer in crop yield increased. In conclusion, AALP applications not only control weeds but also promote P. ternata growth by improving soil physiochemical properties and fostering beneficial bacterial allies. These findings lay the groundwork for future research and promote the use of AALP in ecological agriculture.
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Affiliation(s)
- Jinxin Li
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Kaili Qu
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Lu Wei
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Hong Chen
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Huixia Cai
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Jingyi Zhang
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Likun Mei
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Bingsen Liu
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yifan Han
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yuhuan Miao
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Dahui Liu
- Pharmacy Faculty, Hubei University of Chinese Medicine, Wuhan 430065, China; Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, 430065, China.
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Luo C, He Y, Chen Y. Rhizosphere microbiome regulation: Unlocking the potential for plant growth. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 8:100322. [PMID: 39678067 PMCID: PMC11638623 DOI: 10.1016/j.crmicr.2024.100322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2024] Open
Abstract
Rhizosphere microbial communities are essential for plant growth and health maintenance, but their recruitment and functions are affected by their interactions with host plants. Finding ways to use the interaction to achieve specific production purposes, so as to reduce the use of chemical fertilizers and pesticides, is an important research approach in the development of green agriculture. To demonstrate the importance of rhizosphere microbial communities and guide practical production applications, this review summarizes the outstanding performance of rhizosphere microbial communities in promoting plant growth and stress tolerance. We also discuss the effect of host plants on their rhizosphere microbes, especially emphasizing the important role of host plant species and genes in the specific recruitment of beneficial microorganisms to improve the plants' own traits. The aim of this review is to provide valuable insights into developing plant varieties that can consistently recruit specific beneficial microorganisms to improve crop adaptability and productivity, and thus can be applied to green and sustainable agriculture in the future.
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Affiliation(s)
- Chenghua Luo
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yijun He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaping Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
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Feng Z, Liang Q, Yao Q, Bai Y, Zhu H. The role of the rhizobiome recruited by root exudates in plant disease resistance: current status and future directions. ENVIRONMENTAL MICROBIOME 2024; 19:91. [PMID: 39550594 PMCID: PMC11569615 DOI: 10.1186/s40793-024-00638-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 11/08/2024] [Indexed: 11/18/2024]
Abstract
Root exudates serve as a bridge connecting plant roots and rhizosphere microbes, playing a key role in influencing the assembly and function of the rhizobiome. Recent studies have fully elucidated the role of root exudates in recruiting rhizosphere microbes to enhance plant performance, particularly in terms of plant resistance to soil-borne pathogens; however, it should be noted that the composition and amount of root exudates are primarily quantitative traits regulated by a large number of genes in plants. As a result, there are knowledge gaps in understanding the contribution of the rhizobiome to soil-borne plant disease resistance and the ternary link of plant genes, root exudates, and disease resistance-associated microbes. Advancements in technologies such as quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) offer opportunities for the identification of genes associated with quantitative traits. In the present review, we summarize recent studies on the interactions of plant and rhizosphere microbes through root exudates to enhance soil-borne plant disease resistance and also highlight methods for quantifying the contribution of the rhizobiome to plant disease resistance and identifying the genes responsible for recruiting disease resistance-associated microbes through root exudates.
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Affiliation(s)
- Zengwei Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qiuhong Liang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Yao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Bai
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
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Zheng W, Wang N, Qian G, Qian X, Liu W, Huang L. Cross-niche protection of kiwi plant against above-ground canker disease by beneficial rhizosphere Flavobacterium. Commun Biol 2024; 7:1458. [PMID: 39511396 PMCID: PMC11543660 DOI: 10.1038/s42003-024-07208-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 11/04/2024] [Indexed: 11/15/2024] Open
Abstract
Beneficial rhizosphere microorganisms are widely employed to shield crops from underground pathogen infections. In this study, we challenge this conventional idea by employing rhizosphere soil bacteria to safeguard kiwi plants against the above-ground canker, caused by Pseudomonas syringae pv. actinidiae (Psa). Microbiome comparisons were conducted in different resistant cultivars Actinidia chinensis var. deliciosa 'Hayward' and A. chinensis var. chinensis 'Hongyang'. Our findings reveal the most notable disparity in the rhizosphere soil microbiome, with the Flavobacterium significantly enriched in the rhizosphere soil of more resistant cultivar, 'Hayward'. We isolated Flavobacterium isolates and observed their efficacy in preventing Psa infection, which is further confirmed in field trial by using a representative strain Flavobacterium soyae F55. Furthermore, undescribed gene clusters responsible for antimicrobial metabolite biosynthesis were identified in F. soyae F55, and F. soyae F55 growth was evidently promoted by the root exudates of 'Hayward'. The results underscore the potential of beneficial rhizosphere soil bacteria in protection against above-ground disease.
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Affiliation(s)
- Wei Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Nana Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, China
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Guoliang Qian
- College of Plant Protection, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, China
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, China.
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
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Wang F, Zhang H, Liu H, Wu C, Wan Y, Zhu L, Yang J, Cai P, Chen J, Ge T. Combating wheat yellow mosaic virus through microbial interactions and hormone pathway modulations. MICROBIOME 2024; 12:200. [PMID: 39407339 PMCID: PMC11481568 DOI: 10.1186/s40168-024-01911-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 08/17/2024] [Indexed: 10/19/2024]
Abstract
BACKGROUND The rhizosphere microbiome is critical for promoting plant growth and mitigating soil-borne pathogens. However, its role in fighting soil-borne virus-induced diseases, such as wheat yellow mosaic virus (WYMV) transmitted by Polymyxa graminis zoospores, remains largely underexplored. In this study, we hypothesized that during viral infections, plant microbiomes engage in critical interactions with plants, with key microbes playing vital roles in maintaining plant health. Our research aimed to identify microbial taxa that not only suppress the disease but also boost wheat yield by using a blend of techniques, including field surveys, yield assessments, high-throughput sequencing of plant and soil microbiomes, microbial isolation, hydroponic experiments, and transcriptome sequencing. RESULTS We found that, compared with roots and leaves, the rhizosphere microbiome showed a better performance in predicting wheat yield and the prevalence of P. graminis and WYMV across the three WYMV-impacted regions in China. Using machine learning, we found that healthy rhizospheres were marked with potentially beneficial microorganisms, such as Sphingomonas and Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, whereas diseased rhizospheres were associated with a higher prevalence of potential pathogens, such as Bipolaris and Fusicolla. Structural equation modeling showed that these biomarkers both directly and indirectly impacted wheat yield by modulating the rhizosphere microbiome and P. graminis abundance. Upon re-introduction of two key healthy rhizosphere biomarkers, Sphingomonas azotifigens and Rhizobium deserti, into the rhizosphere, wheat growth and health were enhanced. This was attributed to the up-regulation of auxin and cytokinin signaling pathways and the regulation of jasmonic acid and salicylic acid pathways during infections. CONCLUSIONS Overall, our study revealed the critical role of the rhizosphere microbiome in combating soil-borne viral diseases, with specific rhizosphere microbes playing key roles in this process. Video Abstract.
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Affiliation(s)
- Fangyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
| | - Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yi Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lifei Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Ping X, Khan RAA, Chen S, Jiao Y, Zhuang X, Jiang L, Song L, Yang Y, Zhao J, Li Y, Mao Z, Xie B, Ling J. Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties. MICROBIOME 2024; 12:160. [PMID: 39215347 PMCID: PMC11363401 DOI: 10.1186/s40168-024-01883-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/27/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood. RESULTS Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray-Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots. CONCLUSIONS The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. Video Abstract.
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Affiliation(s)
- Xingxing Ping
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Raja Asad Ali Khan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, YaZhou, 572024, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Jiao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Zhuang
- School of Life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Lijun Jiang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liqun Song
- Microbial Research Institute of Liaoning Province, Liaoning Academy of Agricultural Sciences, Chaoyang, China
| | - Yuhong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bingyan Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jian Ling
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Jin X, Jia H, Ran L, Wu F, Liu J, Schlaeppi K, Dini-Andreote F, Wei Z, Zhou X. Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates. Nat Commun 2024; 15:5125. [PMID: 38879580 PMCID: PMC11180119 DOI: 10.1038/s41467-024-49218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.
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Affiliation(s)
- Xue Jin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Huiting Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Lingyi Ran
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China.
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10
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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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11
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Liu J, Deng S, Chang W, Yu D, Wang H. Development of a Multiplex PCR Assay for the Detection of Tomato Wilt Caused by Coinfection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum Based on Comparative Genomics. PLANT DISEASE 2024; 108:1128-1138. [PMID: 37953228 DOI: 10.1094/pdis-05-23-0962-sr] [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: 11/14/2023]
Abstract
Tomato is consumed worldwide as fresh or processed food products. However, soilborne diseases of tomato plants caused by coinfection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soilborne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by coinfection of Fusarium brachygibbosum, F. oxysporum, and Ralstonia solanacearum. Therefore, developing a method for simultaneous detection of DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum is of great importance to efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of F. brachygibbosum, F. oxysporum, and R. solanacearum and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity, and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100 pg/μl. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum in a single PCR system to accurately identify and diagnose the pathogen causing tomato wilt.
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Affiliation(s)
- Jun Liu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Siyi Deng
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Wei Chang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Dazhao Yu
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
| | - Hua Wang
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
- Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Wuhan 430064, China
- Key Laboratory of Integrated Pest Management on Crops in Central China, Ministry of Agriculture, Wuhan 430064, China
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12
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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13
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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14
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Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
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Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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15
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Bhatt S, Faridi N, Raj SMP, Agarwal A, Punetha M. Recent advances in immuno-based methods for the detection of Ralstonia solanacearum. J Microbiol Methods 2024; 217-218:106889. [PMID: 38211840 DOI: 10.1016/j.mimet.2024.106889] [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: 10/10/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
Ralstonia solanacearum (RS) is a widely recognized phytopathogenic bacterium which is responsible for causing devastating losses in a wide range of economically significant crops. Timely and accurate detection of this pathogen is pivotal to implementing effective disease management strategies and preventing crop losses. This review provides a comprehensive overview of recent advances in immuno-based detection methods for RS. The review begins by introducing RS, highlighting its destructive potential and the need for point-of-care detection techniques. Subsequently, it explores traditional detection methods and their limitations, emphasizing the need for innovative approaches. The main focus of this review is on immuno-based detection methods and it discusses recent advancements in serological detection techniques. Furthermore, the review sheds light on the challenges and prospects of immuno-based detection of RS. It emphasizes the importance of developing rapid, field-deployable assays that can be used by farmers and researchers alike. In conclusion, this review provides valuable insights into the recent advances in immuno-based detection methods for RS.
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Affiliation(s)
- Shalini Bhatt
- P P Savani University, Surat 394125, Gujarat, India; Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India.
| | - Neha Faridi
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
| | - S Merwyn P Raj
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
| | - Ankur Agarwal
- Defence Institute of Bio-Energy Research (DIBER), DRDO, Nainital, Haldwani 263139, Uttarakhand, India
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16
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Gong C, Wang Z, Li Z, Sun B, Luo W, Luo S, Chen S, Mai P, Li Z, Li Y, Wang Y, Li T. A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt. HORTICULTURE RESEARCH 2024; 11:uhad272. [PMID: 38333730 PMCID: PMC10852381 DOI: 10.1093/hr/uhad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.
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Affiliation(s)
- Chao Gong
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhiliang Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Baojuan Sun
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Wenlong Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shanwei Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shuting Chen
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Peiting Mai
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenxing Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Ye Li
- Harbin Academy of Agricultural Sciences, Harbin, Heilongjiang, 150029, China
| | - Yikui Wang
- Institute of Vegetable, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Tao Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
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Wei C, Liang J, Wang R, Chi L, Wang W, Tan J, Shi H, Song X, Cui Z, Xie Q, Cheng D, Wang X. Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis. FRONTIERS IN PLANT SCIENCE 2024; 14:1339478. [PMID: 38317834 PMCID: PMC10839043 DOI: 10.3389/fpls.2023.1339478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/28/2023] [Indexed: 02/07/2024]
Abstract
The soil microbial community plays a critical role in promoting robust plant growth and serves as an effective defence mechanism against root pathogens. Current research has focused on unravelling the compositions and functions of diverse microbial taxa in plant rhizospheres invaded by Ralstonia solanacearum, however, the specific mechanisms by which key microbial groups with distinct functions exert their effects remain unclear. In this study, we employed a combination of amplicon sequencing and metabolomics analysis to investigate the principal metabolic mechanisms of key microbial taxa in plant rhizosphere soil. Compared to the healthy tobacco rhizosphere samples, the bacterial diversity and co-occurrence network of the diseased tobacco rhizosphere soil were significantly reduced. Notably, certain genera, including Gaiella, Rhodoplanes, and MND1 (Nitrosomonadaceae), were found to be significantly more abundant in the rhizosphere of healthy plants than in that of diseased plants. Eight environmental factors, including exchangeable magnesium, available phosphorus, and pH, were found to be crucial factors influencing the composition of the microbial community. Ralstonia displayed negative correlations with pH, exchangeable magnesium, and cation exchange flux, but showed a positive correlation with available iron. Furthermore, metabolomic analysis revealed that the metabolic pathways related to the synthesis of various antibacterial compounds were significantly enriched in the healthy group. The correlation analysis results indicate that the bacterial genera Polycyclovorans, Lysobacter, Pseudomonas, and Nitrosospira may participate in the synthesis of antibacterial compounds. Collectively, our findings contribute to a more in-depth understanding of disease resistance mechanisms within healthy microbial communities and provide a theoretical foundation for the development of targeted strategies using beneficial microorganisms to suppress disease occurrence.
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Affiliation(s)
- Chengjian Wei
- College of Agriculture, Guangxi University, Nanning, China
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Luping Chi
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, Enshi, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, Yuxi, China
| | - Zhenzhen Cui
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qiang Xie
- Sichuan Tobacco Science and Technology Center, Chengdu, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, Nanning, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Xiao Z, Lu C, Wu Z, Li X, Ding K, Zhu Z, Han R, Zhao J, Ge T, Li G, Zhu YG. Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168558. [PMID: 37979870 DOI: 10.1016/j.scitotenv.2023.168558] [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: 07/13/2023] [Revised: 11/08/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
Abstract
Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.
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Affiliation(s)
- Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Zhiyong Wu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Xinyuan Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
| | - Zhe Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham, Ningbo 315100, PR China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Junyi Zhao
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
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Liang J, Wei C, Song X, Wang R, Shi H, Tan J, Cheng D, Wang W, Wang X. Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum. ENVIRONMENTAL MICROBIOME 2024; 19:6. [PMID: 38229154 PMCID: PMC10792853 DOI: 10.1186/s40793-024-00548-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.
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Affiliation(s)
- Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Chengjian Wei
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, 653100, Yuxi, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
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20
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Kashyap S, Sharma I, Dowarah B, Barman R, Gill SS, Agarwala N. Plant and soil-associated microbiome dynamics determine the fate of bacterial wilt pathogen Ralstonia solanacearum. PLANTA 2023; 258:57. [PMID: 37524889 DOI: 10.1007/s00425-023-04209-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
MAIN CONCLUSION Plant and the soil-associated microbiome is important for imparting bacterial wilt disease tolerance in plants. Plants are versatile organisms that are endowed with the capacity to withstand various biotic and abiotic stresses despite having no locomotory abilities. Being the agent for bacterial wilt (BW) disease, Ralstonia solanacearum (RS) colonizes the xylem vessels and limits the water supply to various plant parts, thereby causing wilting. The havoc caused by RS leads to heavy losses in crop productivity around the world, for which a sustainable mitigation strategy is urgently needed. As several factors can influence plant-microbe interactions, comprehensive understanding of plant and soil-associated microbiome under the influence of RS and various environmental/edaphic conditions is important to control this pathogen. This review mainly focuses on microbiome dynamics associated with BW disease and also provide update on microbial/non-microbial approaches employed to control BW disease in crop plants.
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Affiliation(s)
- Sampurna Kashyap
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Indrani Sharma
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Bhaskar Dowarah
- Department of Botany, Bahona College, Bahona, Jorhat, Assam, 785101, India
| | - Ramen Barman
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India.
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Liu L, Cheng L, Liu K, Yu T, Liu Q, Gong Z, Cai Z, Liu J, Zhao X, Nian H, Ma Q, Lian T. Transgenic soybean of GsMYB10 shapes rhizosphere microbes to promote resistance to aluminum (Al) toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131621. [PMID: 37187122 DOI: 10.1016/j.jhazmat.2023.131621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Plant resistance genes could affect rhizosphere microbiota, which in turn enhanced plant resistance to stresses. Our previous study found that overexpression of the GsMYB10 gene led to enhanced tolerance of soybean plants to aluminum (Al) toxicity. However, whether GsMYB10 gene could regulate rhizosphere microbiota to mitigate Al toxicity remains unclear. Here, we analyzed the rhizosphere microbiomes of HC6 soybean (WT) and transgenic soybean (trans-GsMYB10) at three Al concentrations, and constructed three different synthetic microbial communities (SynComs), including bacterial, fungal and cross-kingdom (bacteria and fungi) SynComs to verify their role in improving Al tolerance of soybean. Trans-GsMYB10 shaped the rhizosphere microbial communities and harbored some beneficial microbes, such as Bacillus, Aspergillus and Talaromyces under Al toxicity. Fungal and cross-kingdom SynComs showed a more effective role than the bacterial one in resistance to Al stress, and these SynComs helped soybean resist Al toxicity via affecting some functional genes that involved cell wall biosynthesis and organic acid transport etc. Overall, this study reveals the mechanism of soybean functional genes regulating the synergistic resistance of rhizosphere microbiota and plants to Al toxicity, and also highlights the possibility of focusing on the rhizobial microbial community as a potential molecular breeding target to produce crops.
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Affiliation(s)
- Lingrui Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kun Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihui Gong
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Junjie Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xueqiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
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Thomas P, Knox OGG, Powell JR, Sindel B, Winter G. The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised? Microorganisms 2023; 11:microorganisms11040835. [PMID: 37110258 PMCID: PMC10141029 DOI: 10.3390/microorganisms11040835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.
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Affiliation(s)
- Phil Thomas
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Oliver G. G. Knox
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Brian Sindel
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Gal Winter
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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