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Wang J, Ou Y, Li R, Tao C, Liu H, Li R, Shen Z, Shen Q. The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116982. [PMID: 39217893 DOI: 10.1016/j.ecoenv.2024.116982] [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: 05/30/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses,this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.
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Affiliation(s)
- Jiabao Wang
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yannan Ou
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ruochen Li
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chengyuan Tao
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hongjun Liu
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rong Li
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zongzhuan Shen
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Qirong Shen
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Lyng M, Þórisdóttir B, Sveinsdóttir SH, Hansen ML, Jelsbak L, Maróti G, Kovács ÁT. Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis. mSystems 2024:e0021224. [PMID: 39254334 DOI: 10.1128/msystems.00212-24] [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: 02/13/2024] [Accepted: 08/16/2024] [Indexed: 09/11/2024] Open
Abstract
Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence. IMPORTANCE There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Birta Þórisdóttir
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sigrún H Sveinsdóttir
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten L Hansen
- Microbiome Interactions and Engineering, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Jelsbak
- Microbiome Interactions and Engineering, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
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3
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Wang H, Zhang F, Zhang Y, Wang M, Zhang Y, Zhang J. Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles. MICROBIOME 2024; 12:169. [PMID: 39252132 PMCID: PMC11382411 DOI: 10.1186/s40168-024-01884-z] [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: 01/26/2024] [Accepted: 07/27/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Plants have evolved various defense mechanisms against insect herbivores, including the formation of physical barriers, the synthesis of toxic metabolites, and the activation of phytohormone responses. Although plant-associated microbiota influence plant growth and health, whether they play a role in plant defense against insect pests in natural ecosystems is unknown. RESULTS Here, we show that leaves of beetle-damaged weeping willow (Salix babylonica) trees are more resistant to the leaf beetle Plagiodera versicolora (Coleoptera) than those of undamaged leaves. Bacterial community transplantation experiments demonstrated that plant-associated microbiota from the beetle-damaged willow contribute to the resistance of the beetle-damaged willow to P. versicolora. Analysis of the composition and abundance of the microbiome revealed that Pseudomonas spp. is significantly enriched in the phyllosphere, roots, and rhizosphere soil of beetle-damaged willows relative to undamaged willows. From a total of 49 Pseudomonas strains isolated from willows and rhizosphere soil, we identified seven novel Pseudomonas strains that are toxic to P. versicolora. Moreover, re-inoculation of a synthetic microbial community (SynCom) with these Pseudomonas strains enhances willow resistance to P. versicolora. CONCLUSIONS Collectively, our data reveal that willows can exploit specific entomopathogenic bacteria to enhance defense against P. versicolora, suggesting that there is a complex interplay among plants, insects, and plant-associated microbiota in natural ecosystems.
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Affiliation(s)
- Haitao Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yali Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Mengnan Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Yiqiu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jiang Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Chaudhary P, Bhattacharjee A, Khatri S, Dalal RC, Kopittke PM, Sharma S. Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms. Microbiol Res 2024; 289:127880. [PMID: 39236602 DOI: 10.1016/j.micres.2024.127880] [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: 11/05/2023] [Revised: 05/23/2024] [Accepted: 08/14/2024] [Indexed: 09/07/2024]
Abstract
Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.
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Affiliation(s)
- Priya Chaudhary
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ram C Dalal
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Peter M Kopittke
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; School of Agriculture and Food Sustainability, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shilpi Sharma
- The University of Queensland and Indian Institute of Technology Delhi Research Academy, New Delhi 110016, India; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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Chen Y, Li X, Zhou D, Wei Y, Feng J, Cai B, Qi D, Zhang M, Zhao Y, Li K, Pan Z, Wang W, Xie J. Streptomyces-Secreted Fluvirucin B6 as a Potential Bio-Fungicide for Managing Banana Fusarium Wilt and Mycotoxins and Modulating the Soil Microbial Community Structure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17890-17902. [PMID: 39083645 DOI: 10.1021/acs.jafc.4c04077] [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: 08/02/2024]
Abstract
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc TR4) is the most destructive soil-borne fungal disease. Until now, there has been a lack of effective measures to control the disease. It is urgent to explore biocontrol agents to control Foc TR4 and the secretion of mycotoxin. In this study, fluvirucin B6 was screened from Streptomyces solisilvae using an activity-guided method. Fluvirucin B6 exhibited strong antifungal activity against Foc TR4 (0.084 mM of EC50 value) and significantly inhibited mycelial growth and spore germination. Further studies demonstrated that fluvirucin B6 could cause the functional loss of mitochondria, the disorder of metabolism of Foc TR4 cells, and the decrease of enzyme activities in the tricarboxylic acid cycle and electron transport chain, ultimately inhibiting mycotoxin metabolism. In a pot experiment, the application of fluvirucin B6 significantly decreased the incidence of banana Fusarium wilt and the amount of Foc TR4 and controlled fungal toxins in the soil. Additionally, fluvirucin B6 could positively regulate the changes in the structure of the banana rhizosphere microbial community, significantly enriching beneficial microbes associated with disease resistance. In summary, this study identifies fluvirucin B6, which plays versatile roles in managing fungal diseases and mycotoxins.
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Affiliation(s)
- Yufeng Chen
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - XiaoJuan Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengbo Zhou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongzan Wei
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Junting Feng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bingyu Cai
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengfeng Qi
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miaoyi Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yankun Zhao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kai Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiqiang Pan
- Agricultural Research Service, Natural Products Utilization Research Unit, U.S. Department of Agriculture, University of Mississippi, University, Mississippi 38677, United States
| | - Wei Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianghui Xie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Liu J, Xu W, Zhang Q, Liao W, Li L, Chen S, Yang J, Wang Z, Xu F. OsPHR2-mediated recruitment of Pseudomonadaceae enhances rice phosphorus uptake. PLANT COMMUNICATIONS 2024; 5:100930. [PMID: 38685708 PMCID: PMC11369732 DOI: 10.1016/j.xplc.2024.100930] [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: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Plants can shape their root microbiome to promote growth and nutrient uptake. PHOSPHATE STARVATION RESPONSE 2 (OsPHR2) is a central regulator of phosphate signaling in rice, but whether OsPHR2 can shape the root microbiome to promote phosphorus uptake is unclear. Here, we investigate the role of OsPHR2 in recruiting microbiota for phosphorus uptake using high-throughput sequencing and metabolite analysis. OsPHR2-overexpressing (OsPHR2 OE) rice showed 69.8% greater shoot P uptake in natural soil compared with sterilized soil under high-phosphorus (HP) conditions, but there was only a 54.8% increase in the wild-type (WT). The abundance of the family Pseudomonadaceae was significantly enriched in OsPHR2 OE roots relative to those of WT rice. Compared with the WT, OsPHR2 OE rice had a relatively higher abundance of succinic acid and methylmalonic acid, which could stimulate the growth of Pseudomonas sp. (P6). After inoculation with P6, phosphorus uptake in WT and OsPHR2 OE rice was higher than that in uninoculated rice under low-phosphorus (LP) conditions. Taken together, our results suggest that OsPHR2 can increase phosphorus use in rice through root exudate-mediated recruitment of Pseudomonas. This finding reveals a cooperative contribution of the OsPHR2-modulated root microbiome, which is important for improving phosphorus use in agriculture.
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Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wencheng Liao
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liang Li
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shu Chen
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinyong Yang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengrui Wang
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of JunCao Science and Ecology, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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7
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Zhou Y, Liu D, Li F, Dong Y, Jin Z, Liao Y, Li X, Peng S, Delgado-Baquerizo M, Li X. Superiority of native soil core microbiomes in supporting plant growth. Nat Commun 2024; 15:6599. [PMID: 39097606 PMCID: PMC11297980 DOI: 10.1038/s41467-024-50685-3] [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: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/05/2024] Open
Abstract
Native core microbiomes represent a unique opportunity to support food provision and plant-based industries. Yet, these microbiomes are often neglected when developing synthetic communities (SynComs) to support plant health and growth. Here, we study the contribution of native core, native non-core and non-native microorganisms to support plant production. We construct four alternative SynComs based on the excellent growth promoting ability of individual stain and paired non-antagonistic action. One of microbiome based SynCom (SC2) shows a high niche breadth and low average variation degree in-vitro interaction. The promoting-growth effect of SC2 can be transferred to non-sterile environment, attributing to the colonization of native core microorganisms and the improvement of rhizosphere promoting-growth function including nitrogen fixation, IAA production, and dissolved phosphorus. Further, microbial fertilizer based on SC2 and composite carrier (rapeseed cake fertilizer + rice husk carbon) increase the net biomass of plant by 129%. Our results highlight the fundamental importance of native core microorganisms to boost plant production.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Donghui Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Fengqiao Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili Jin
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Yangwenke Liao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaohui Li
- Yongzhou Company of Hunan Tobacco Company, Yongzhou, 425000, China
| | - Shuguang Peng
- Hunan Province Company of China Tobacco Corporation, Changsha, 410004, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, China.
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Zhao Z, Gao B, Yang C, Wu Y, Sun C, Jiménez N, Zheng L, Huang F, Ren Z, Yu Z, Yu C, Zhang J, Cai M. Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application. ENVIRONMENT INTERNATIONAL 2024; 190:108831. [PMID: 38936065 DOI: 10.1016/j.envint.2024.108831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".
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Affiliation(s)
- Zhengzheng Zhao
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Bingqi Gao
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chongrui Yang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Yushi Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chen Sun
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Núria Jiménez
- Department of Chemical Engineering, Vilanova i la Geltrú School of Engineering (EPSEVG), Universitat Politècnica de Catalunya BarcelonaTech, Vilanova i la Geltrú 08800, Spain
| | - Longyu Zheng
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Feng Huang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Zhuqing Ren
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China; Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ziniu Yu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China
| | - Chan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jibin Zhang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China.
| | - Minmin Cai
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, National Engineering Research Center of Microbial Pesticides, Huazhong Agricultural University, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, Hubei, China.
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9
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Liu Y, Lai J, Sun X, Huang L, Sheng Y, Zhang Q, Zeng H, Zhang Y, Ye P, Wei S. Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage. Microorganisms 2024; 12:1370. [PMID: 39065138 PMCID: PMC11278620 DOI: 10.3390/microorganisms12071370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pengsheng Ye
- Industrial Crops Research Institute, Sichuan Academy of Agricultural Sciences/The Key Laboratory of Vegetable Germplasm and Variety Innovation in Sichuan Province, Chengdu 610300, China; (Y.L.); (J.L.); (X.S.); (L.H.); (Y.S.); (Q.Z.); (H.Z.); (Y.Z.)
| | - Shugu Wei
- Industrial Crops Research Institute, Sichuan Academy of Agricultural Sciences/The Key Laboratory of Vegetable Germplasm and Variety Innovation in Sichuan Province, Chengdu 610300, China; (Y.L.); (J.L.); (X.S.); (L.H.); (Y.S.); (Q.Z.); (H.Z.); (Y.Z.)
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10
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Huang H, Li M, Guo Q, Zhang R, Zhang Y, Luo K, Chen Y. Influence of Drought Stress on the Rhizosphere Bacterial Community Structure of Cassava ( Manihot esculenta Crantz). Int J Mol Sci 2024; 25:7326. [PMID: 39000433 PMCID: PMC11242396 DOI: 10.3390/ijms25137326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Drought presents a significant abiotic stress that threatens crop productivity worldwide. Rhizosphere bacteria play pivotal roles in modulating plant growth and resilience to environmental stresses. Despite this, the extent to which rhizosphere bacteria are instrumental in plant responses to drought, and whether distinct cassava (Manihot esculenta Crantz) varieties harbor specific rhizosphere bacterial assemblages, remains unclear. In this study, we measured the growth and physiological characteristics, as well as the physical and chemical properties of the rhizosphere soil of drought-tolerant (SC124) and drought-sensitive (SC8) cassava varieties under conditions of both well-watered and drought stress. Employing 16S rDNA high-throughput sequencing, we analyzed the composition and dynamics of the rhizosphere bacterial community. Under drought stress, biomass, plant height, stem diameter, quantum efficiency of photosystem II (Fv/Fm), and soluble sugar of cassava decreased for both SC8 and SC124. The two varieties' rhizosphere bacterial communities' overall taxonomic structure was highly similar, but there were slight differences in relative abundance. SC124 mainly relied on Gamma-proteobacteria and Acidobacteriae in response to drought stress, and the abundance of this class was positively correlated with soil acid phosphatase. SC8 mainly relied on Actinobacteria in response to drought stress, and the abundance of this class was positively correlated with soil urease and soil saccharase. Overall, this study confirmed the key role of drought-induced rhizosphere bacteria in improving the adaptation of cassava to drought stress and clarified that this process is significantly related to variety.
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Affiliation(s)
- Huling Huang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
| | - Kai Luo
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication, Sanya Institute of Breeding and Multiplication, Hainan University, Sanya 572025, China; (H.H.); (M.L.); (Q.G.); (R.Z.)
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
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11
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Li C, Chen X, Jia Z, Zhai L, Zhang B, Grüters U, Ma S, Qian J, Liu X, Zhang J, Müller C. Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities. Nat Ecol Evol 2024; 8:1270-1284. [PMID: 38849504 DOI: 10.1038/s41559-024-02437-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/13/2024] [Indexed: 06/09/2024]
Abstract
Microbial inoculation involves transplanting microorganisms from their natural habitat to new plants or soils to improve plant performance, and it is being increasingly used in agriculture and ecological restoration. However, microbial inoculants can invade and alter the composition of native microbial communities; thus, a comprehensive analysis is urgently needed to understand the overall impact of microbial inoculants on the biomass, diversity, structure and network complexity of native communities. Here we provide a meta-analysis of 335 studies revealing a positive effect of microbial inoculants on soil microbial biomass. This positive effect was weakened by environmental stress and enhanced by the use of fertilizers and native inoculants. Although microbial inoculants did not alter microbial diversity, they induced major changes in the structure and bacterial composition of soil microbial communities, reducing the complexity of bacterial networks and increasing network stability. Finally, higher initial levels of soil nutrients amplified the positive impact of microbial inoculants on fungal biomass, actinobacterial biomass, microbial biomass carbon and microbial biomass nitrogen. Together, our results highlight the positive effects of microbial inoculants on soil microbial biomass, emphasizing the benefits of native inoculants and the important regulatory roles of soil nutrient levels and environmental stress.
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Affiliation(s)
- Chong Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Zhaohui Jia
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Lu Zhai
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, USA
| | - Bo Zhang
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | - Uwe Grüters
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
| | - Shilin Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China
| | - Jing Qian
- Yangzhou China Grand Canal Museum, Yangzhou, China
| | - Xin Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Jinchi Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Province Key Laboratory of Soil and Water Conservation and Ecological Restoration, Nanjing Forestry University, Nanjing, China.
| | - Christoph Müller
- Institute of Plant Ecology, Justus-Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
- Liebig Centre for Agroecology and Climate Impact Research, Justus-Liebig University, Giessen, Germany
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12
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Qiao Y, Wang Z, Sun H, Guo H, Song Y, Zhang H, Ruan Y, Xu Q, Huang Q, Shen Q, Ling N. Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects. MICROBIOME 2024; 12:101. [PMID: 38840214 DOI: 10.1186/s40168-024-01814-z] [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: 12/01/2023] [Accepted: 04/11/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Plant microbiota contributes to plant growth and health, including enhancing plant resistance to various diseases. Despite remarkable progress in understanding diseases resistance in plants, the precise role of rhizosphere microbiota in enhancing watermelon resistance against soil-borne diseases remains unclear. Here, we constructed a synthetic community (SynCom) of 16 core bacterial strains obtained from the rhizosphere of grafted watermelon plants. We further simplified SynCom and investigated the role of bacteria with synergistic interactions in promoting plant growth through a simple synthetic community. RESULTS Our results demonstrated that the SynCom significantly enhanced the growth and disease resistance of ungrafted watermelon grown in non-sterile soil. Furthermore, analysis of the amplicon and metagenome data revealed the pivotal role of Pseudomonas in enhancing plant health, as evidenced by a significant increase in the relative abundance and biofilm-forming pathways of Pseudomonas post-SynCom inoculation. Based on in vitro co-culture experiments and bacterial metabolomic analysis, we selected Pseudomonas along with seven other members of the SynCom that exhibited synergistic effects with Pseudomonas. It enabled us to further refine the initially constructed SynCom into a simplified SynCom comprising the eight selected bacterial species. Notably, the plant-promoting effects of simplified SynCom were similar to those of the initial SynCom. Furthermore, the simplified SynCom protected plants through synergistic effects of bacteria. CONCLUSIONS Our findings suggest that the SynCom proliferate in the rhizosphere and mitigate soil-borne diseases through microbial synergistic interactions, highlighting the potential of synergistic effects between microorganisms in enhancing plant health. This study provides a novel insight into using the functional SynCom as a promising solution for sustainable agriculture. Video Abstract.
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Affiliation(s)
- Yizhu Qiao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhendong Wang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Sun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hanyue Guo
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Song
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - He Zhang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Ruan
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qicheng Xu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qiwei Huang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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13
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Ruan YN, Nong C, Jintrawet A, Fan H, Fu L, Zheng SJ, Li S, Wang ZY. A smooth vetch ( Vicia villosa var.) strain endogenous to the broad-spectrum antagonist Bacillus siamensis JSZ06 alleviates banana wilt disease. FRONTIERS IN PLANT SCIENCE 2024; 15:1410197. [PMID: 38978518 PMCID: PMC11229777 DOI: 10.3389/fpls.2024.1410197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 05/13/2024] [Indexed: 07/10/2024]
Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), poses a significant threat to banana production globally, thereby necessitating effective biocontrol methods to manage this devastating disease. This study investigates the potential of Bacillus siamensis strain JSZ06, isolated from smooth vetch, as a biocontrol agent against Foc TR4. To this end, we conducted a series of in vitro and in vivo experiments to evaluate the antifungal activity of strain JSZ06 and its crude extracts. Additionally, genomic analyses were performed to identify antibiotic synthesis genes, while metabolomic profiling was conducted to characterize bioactive compounds. The results demonstrated that strain JSZ06 exhibited strong inhibitory activity against Foc TR4, significantly reducing mycelial growth and spore germination. Moreover, scanning and transmission electron microscopy revealed substantial ultrastructural damage to Foc TR4 mycelia treated with JSZ06 extracts. Genomic analysis identified several antibiotic synthesis genes, and metabolomic profiling revealed numerous antifungal metabolites. Furthermore, in pot trials, the application of JSZ06 fermentation broth significantly enhanced banana plant growth and reduced disease severity, achieving biocontrol efficiencies of 76.71% and 79.25% for leaves and pseudostems, respectively. In conclusion, Bacillus siamensis JSZ06 is a promising biocontrol agent against Fusarium wilt in bananas, with its dual action of direct antifungal activity and plant growth promotion underscoring its potential for integrated disease management strategies.
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Affiliation(s)
- Yan-Nan Ruan
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- College of Agronomy and Life Sciences, Kunming Universities, Kunming, Yunnan, China
| | - Caihong Nong
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- College of Agronomy and Life Sciences, Kunming Universities, Kunming, Yunnan, China
| | | | - Huacai Fan
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Libo Fu
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Si-Jun Zheng
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Shu Li
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Zhi-Yuan Wang
- Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
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14
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Li Y, Ding Z, Xu T, Wang Y, Wu Q, Song T, Wei X, Dong J, Lin Y. Synthetic consortia of four strains promote Schisandra chinensis growth by regulating soil microbial community and improving soil fertility. PLANTA 2024; 259:135. [PMID: 38678496 DOI: 10.1007/s00425-024-04410-5] [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: 12/08/2023] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
MAIN CONCLUSION Synthetic consortia performed better in promoting Schisandra chinensis growth than individual strains, and this result provides valuable information for the development of synthetic microbial fertilizers. Schisandra chinensis is an herbal medicine that can treat numerous diseases. However, the excessive reliance on chemical fertilizers during the plantation of S. chinensis has severely restricted the development of the S. chinensis planting industry. Plant growth-promoting rhizobacteria (PGPR) can promote the growth of a wide range of crops, and synthetic consortia of them are frequently superior to those of a single strain. In this study, we compared the effects of four PGPR and their synthetic consortia on S. chinensis growth. The pot experiment showed that compared with the control, synthetic consortia significantly increased the plant height, biomass, and total chlorophyll contents of S. chinensis, and their combined effects were better than those of individual strains. In addition, they improved the rhizosphere soil fertility (e.g., TC and TN contents) and enzyme activities (e.g., soil urease activity) and affected the composition and structure of soil microbial community significantly, including promoting the enrichment of beneficial microorganisms (e.g., Actinobacteria and Verrucomicrobiota) and increasing the relative abundance of Proteobacteria, a dominant bacterial phylum. They also enhanced the synergistic effect between the soil microorganisms. The correlation analysis between soil physicochemical properties and microbiome revealed that soil microorganisms participated in regulating soil fertility and promoting S. chinensis growth. This study may provide a theoretical basis for the development of synthetic microbial fertilizers for S. chinensis.
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Affiliation(s)
- Yan Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zanbo Ding
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tengqi Xu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yulong Wang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiaolu Wu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tianjiao Song
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaomin Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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15
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Feng G, Wu Y, Yang C, Zhang Q, Wang S, Dong M, Wang Y, Qi H, Guo L. Effects of coastal saline-alkali soil on rhizosphere microbial community and crop yield of cotton at different growth stages. Front Microbiol 2024; 15:1359698. [PMID: 38706969 PMCID: PMC11066693 DOI: 10.3389/fmicb.2024.1359698] [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: 12/21/2023] [Accepted: 03/21/2024] [Indexed: 05/07/2024] Open
Abstract
Soil salinization is a global constraint that significantly hampers agricultural production, with cotton being an important cash crop that is not immune to its detrimental effects. The rhizosphere microbiome plays a critical role in plant health and growth, which assists plants in resisting adverse abiotic stresses including soil salinization. This study explores the impact of soil salinization on cotton, including its effects on growth, yield, soil physical and chemical properties, as well as soil bacterial community structures. The results of β-diversity analysis showed that there were significant differences in bacterial communities in saline-alkali soil at different growth stages of cotton. Besides, the more severity of soil salinization, the more abundance of Proteobacteria, Bacteroidota enriched in rhizosphere bacterial composition where the abundance of Acidobacteriota exhibited the opposite trend. And the co-occurrence network analysis showed that soil salinization affected the complexity of soil bacterial co-occurrence network. These findings provide valuable insights into the mechanisms by which soil salinization affects soil microorganisms in cotton rhizosphere soil and offer guidance for improving soil salinization using beneficial microorganisms.
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Affiliation(s)
- Guoyi Feng
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Yajie Wu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
| | - Chuanzhen Yang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
| | - Qian Zhang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Shulin Wang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Ming Dong
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Yan Wang
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Hong Qi
- Hebei Branch of National Cotton Improvement Center/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Cotton Research Institute Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Lixue Guo
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang, China
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16
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Guo Z, Lu Z, Liu Z, Zhou W, Yang S, Lv J, Wei M. Difference in the Effect of Applying Bacillus to Control Tomato Verticillium Wilt in Black and Red Soil. Microorganisms 2024; 12:797. [PMID: 38674740 PMCID: PMC11052436 DOI: 10.3390/microorganisms12040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In practical applications, the effectiveness of biological control agents such as Bacillus is often unstable due to different soil environments. Herein, we aimed to explore the control effect and intrinsic mechanism of Bacillus in black soil and red soil in combination with tomato Verticillium wilt. Bacillus application effectively controlled the occurrence of Verticillium wilt in red soil, reducing the incidence by 19.83%, but played a limited role in black soil. Bacillus colonized red soil more efficiently. The Verticillium pathogen decreased by 71.13% and 76.09% after the application of Bacillus combinations in the rhizosphere and bulk of the red soil, respectively, while there was no significant difference in the black soil. Additionally, Bacillus application to red soil significantly promoted phosphorus absorption. Furthermore, it significantly altered the bacterial community in red soil and enriched genes related to pathogen antagonism and phosphorus activation, which jointly participated in soil nutrient activation and disease prevention, promoting tomato plant growth in red soil. This study revealed that the shaping of the bacterial community by native soil may be the key factor affecting the colonization and function of exogenous Bacillus.
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Affiliation(s)
| | | | | | | | | | | | - Mi Wei
- School of Agriculture, Shenzhen Campus, Sun Yat-Sen University, Shenzhen 518107, China; (Z.G.); (Z.L.); (Z.L.); (W.Z.); (S.Y.); (J.L.)
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17
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Batool M, Carvalhais LC, Fu B, Schenk PM. Customized plant microbiome engineering for food security. TRENDS IN PLANT SCIENCE 2024; 29:482-494. [PMID: 37977879 DOI: 10.1016/j.tplants.2023.10.012] [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: 05/10/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.
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Affiliation(s)
- Maria Batool
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brendan Fu
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peer M Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia; Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD 4105, Australia.
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18
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Xiao Y, Ma J, Chen R, Xiang S, Yang B, Chen L, Fang J, Liu S. Two microbes assisting Miscanthus floridulus in remediating multi-metal(loid)s-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28922-28938. [PMID: 38565816 DOI: 10.1007/s11356-024-33032-3] [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: 09/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Miscanthus has good tolerance to multi-metal(loid)s and has received increasing attention in remediated studies of metal(loid)s-contaminated soil. In this study, we conducted phytoextraction techniques to investigate the synergic effects of remediation of multi-metal(loid)s-contaminated soil by Miscanthus floridulus (Lab.) and two plant growth-promoting bacteria (PGPB), TS8 and MR2, affiliated to Enterobacteriaceae. The results exhibited a decrease of arsenic (15.27-21.50%), cadmium (8.64-15.52%), plumbum (5.92-12.76%), and zinc (12.84-24.20%) except for copper contents in the soil in bacterial inoculation groups, indicating that MR2 and TS8 could enhance the remediation of metal(loid)s. Moreover, increased fresh/dry weight and height indicated that inoculated bacteria could promote Miscanthus growth. Although the activities of antioxidant enzymes and the content of chlorophyll in the overground tissues showed no significant increase or even decrease, the activities of antioxidant enzymes in the underground tissues and soil were elevated by 48.95-354.17%, available P by 19.07-23.02%, and available K by 15.34-17.79% (p < 0.05). Bacterial inoculants could also decrease the soil pH. High-throughput sequencing analysis showed that the bacterial inoculant affected the rhizosphere bacterial community and reduced community diversity, but the relative abundance of some PGPB was found to increase. Phylogenetic molecular ecological networks indicated that bacterial inoculants reduced interactions between rhizosphere bacteria and thereby led to a simpler network structure but increased the proportion of positive-correlation links and enhanced the metabiosis and symbiosis of those bacteria. Spearman's test showed that OTUs affiliated with Enterobacteriaceae and soil nutrients were critical for metal(loid) remediation and Miscanthus growth. The results of this study provide a basis for the synergic remediation of multi-metal(loid)s-contaminated soils by Miscanthus and PGPB and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by the other PGPB or critical bacteria.
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Affiliation(s)
- Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Rui Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Sha Xiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Shuming Liu
- School of Resources and Environment, Yili Normal University, Yining, 835000, China.
- Key Laboratory of Pollutant Chemistry and Environmental Treatment, Yili Normal University, Yining, 835000, China.
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19
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Wang X, Chi Y, Song S. Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review. Front Microbiol 2024; 15:1347745. [PMID: 38591030 PMCID: PMC10999704 DOI: 10.3389/fmicb.2024.1347745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.
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Affiliation(s)
| | - Yongkuan Chi
- School of Karst Science, State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
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20
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Li X, Wu J, Cheng X, Cai Z, Wang Z, Zhou J. Biodegradable microplastics reduce the effectiveness of biofertilizers by altering rhizospheric microecological functions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 352:120071. [PMID: 38246103 DOI: 10.1016/j.jenvman.2024.120071] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/06/2024] [Indexed: 01/23/2024]
Abstract
The effectiveness of biofertilizers as a cost-effective crop yield enhancer can be compromised by residual soil pollutants. However, the impact of accumulated polyadipate/butylene terephthalate microplastics (PBAT-MPs) from biodegradable mulch films on biofertilizer application and the consequent growth of crop plants remains unclear. Here, the effects of different levels of PBAT-MPs in soil treated with Bacillus amyloliquefaciens biofertilizer were assessed in a four-week potted experiment. PBAT-MPs significantly decreased the growth-promoting effect of the biofertilizer on Brassica chinensis L., resulting in a notable reduction in both above- and belowground biomass (up to 52.91% and 57.53%, respectively), as well as nitrate and crude fiber contents (up to 12.18% and 13.64%, respectively). In the rhizosphere microenvironment, PBAT-MPs increased soil organic carbon by 2.63-fold and organic matter by 2.68-fold, while enhancing sucrase (from 67.55% to 108.89%) and cellulase (from 31.26% to 49.10%) activities. PBAT-MPs also altered the rhizospheric bacterial community composition/diversity, resulting in more complex microbial networks. With regard to microbial function, PBAT-MPs impacted carbon metabolic function by inhibiting the 3-hydroxypropionate/4-hydroxybutyrate fixation pathway and influencing chitin and lignin degradation processes. Overall, the rhizospheric microbial profiles (composition, function, and network interactions) were the main contributors to plant growth inhibition. This study provides a practical case and theoretical basis for rational use of biodegradable mulch films and indicates that the residue of biodegradable films needs pay attention.
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Affiliation(s)
- Xinyang Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Jialing Wu
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, PR China
| | - Xueyu Cheng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zhonghua Cai
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Zongkang Wang
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, PR China.
| | - Jin Zhou
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China.
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21
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Wei D, Zhu D, Zhang Y, Yang Z, Hu Y, Song C, Yang W, Chang X. Pseudomonas chlororaphis IRHB3 assemblies beneficial microbes and activates JA-mediated resistance to promote nutrient utilization and inhibit pathogen attack. Front Microbiol 2024; 15:1328863. [PMID: 38380096 PMCID: PMC10877055 DOI: 10.3389/fmicb.2024.1328863] [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: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction The rhizosphere microbiome is critical to plant health and resistance. PGPR are well known as plant-beneficial bacteria and generally regulate nutrient utilization as well as plant responses to environmental stimuli. In our previous work, one typical PGPR strain, Pseudomonas chlororaphis IRHB3, isolated from the soybean rhizosphere, had positive impacts on soil-borne disease suppression and growth promotion in the greenhouse, but its biocontrol mechanism and application in the field are not unclear. Methods In the current study, IRHB3 was introduced into field soil, and its effects on the local rhizosphere microbiome, disease resistance, and soybean growth were comprehensively analyzed through high-throughput sequencing and physiological and molecular methods. Results and discussion We found that IRHB3 significantly increased the richness of the bacterial community but not the structure of the soybean rhizosphere. Functional bacteria related to phosphorus solubilization and nitrogen fixation, such as Geobacter, Geomonas, Candidatus Solibacter, Occallatibacter, and Candidatus Koribacter, were recruited in rich abundance by IRHB3 to the soybean rhizosphere as compared to those without IRHB3. In addition, the IRHB3 supplement obviously maintained the homeostasis of the rhizosphere microbiome that was disturbed by F. oxysporum, resulting in a lower disease index of root rot when compared with F. oxysporum. Furthermore, JA-mediated induced resistance was rapidly activated by IRHB3 following PDF1.2 and LOX2 expression, and meanwhile, a set of nodulation genes, GmENOD40b, GmNIN-2b, and GmRIC1, were also considerably induced by IRHB3 to improve nitrogen fixation ability and promote soybean yield, even when plants were infected by F. oxysporum. Thus, IRHB3 tends to synergistically interact with local rhizosphere microbes to promote host growth and induce host resistance in the field.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiaoli Chang
- College of Agronomy, Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, Sichuan, China
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22
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Ji M, Xu J, Gao L, Li L, Liu H, Hao B. Effect of long-term in-row branch covering on soil microorganisms in pear orchards. Open Life Sci 2024; 19:20220807. [PMID: 38299010 PMCID: PMC10828664 DOI: 10.1515/biol-2022-0807] [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: 07/28/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 02/02/2024] Open
Abstract
Branches covering (BC) is a way to reuse the pruned branches and save the cost of ground cloth. This study investigated the effects of BC and ground-cloth covering on the soil microcosm environment by measuring the chemical properties and microbial communities at different soil depths for 6 years. The results revealed that BC significantly improved soil chemical properties, increased the abundance of bacterial microbial communities and the diversity and homogeneity of bacteria and fungi, while decreased the abundance of fungal microbial communities. There was a threshold value for the regulation of microbial communities by BC, which decreased the high-abundance communities (Proteobacteria, Ascomycota, etc.) and increased the low-abundance communities (Acidobacteriota, Basidiomycota, etc.). Fungi were more sensitive to BC than bacteria. The stability and homogeneity of microorganisms were stronger in the 15-25 cm soil layer. The bacterial phyla were dominated by Proteobacteria, with the top 10 phyla accounting for more than 80% of the relative abundance; the genera were dominated by MND1, with the top 10 genera accounting for about 10%. The fungal phyla were dominated by Ascomycota, with the top 10 phyla accounting for 50-90%; the genera were dominated by unidentified Pyronemataceae sp., with the top 10 genera accounting for 30-60%. The phyla that differed significantly between treatments were mainly Proteobacteria, Ascomycota, Acidobacteriota, and Basidiomycota. In addition, metabolism was the predominant function in bacteria, while Saprotroph was the predominant function in fungi. Bacteroidota correlated strongly with soil chemical properties and bacterial functions, while Chytridiomycota correlated strongly with soil chemical properties and Pathogen-Saprotroph-Symbiotroph. In conclusion, BC can improve soil nutrient content and optimize microbial community structure and function. Through initially assessing the effects of BC on soil nutrients and microorganisms in pear orchard rows, this study provides a reference for excavating key microorganisms and updating the soil row management model.
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Affiliation(s)
- Minghui Ji
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Jintao Xu
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Lijuan Gao
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Longfei Li
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Huan Liu
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
| | - Baofeng Hao
- Changli Institute of Pomology HAAFS, Qinhuangdao, Hebei, 066600, China
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23
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Guo S, Jiao Z, Yan Z, Yan X, Deng X, Xiong W, Tao C, Liu H, Li R, Shen Q, Kowalchuk GA, Geisen S. Predatory protists reduce bacteria wilt disease incidence in tomato plants. Nat Commun 2024; 15:829. [PMID: 38280866 PMCID: PMC10821857 DOI: 10.1038/s41467-024-45150-0] [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: 06/13/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhiguang Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xinyue Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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Li Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Biofilms formation in plant growth-promoting bacteria for alleviating agro-environmental stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167774. [PMID: 37848152 DOI: 10.1016/j.scitotenv.2023.167774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Biofilm formation represents a pivotal and adaptable trait among microorganisms within natural environments. This attribute plays a multifaceted role across diverse contexts, including environmental, aquatic, industrial, and medical systems. While previous research has primarily focused on the adverse impacts of biofilms, harnessing their potential effectively could confer substantial advantages to humanity. In the face of escalating environmental pressures (e.g., drought, salinity, extreme temperatures, and heavy metal pollution), which jeopardize global crop yields, enhancing crop stress tolerance becomes a paramount endeavor for restoring sufficient food production. Recently, biofilm-forming plant growth-promoting bacteria (PGPB) have emerged as promising candidates for agricultural application. These biofilms are evidence of microorganism colonization on plant roots. Their remarkable stress resilience empowers crops to thrive and yield even in harsh conditions. This is accomplished through increased root colonization, improved soil properties, and the synthesis of valuable secondary metabolites (e.g., ACC deaminase, acetin, 2,3-butanediol, proline, etc.). This article elucidates the mechanisms underpinning the role of biofilm-forming PGPB in bolstering plant growth amidst environmental challenges. Furthermore, it explores the tangible applications of these biofilms in agriculture and delves into strategies for manipulating biofilm formation to extract maximal benefits in practical crop production scenarios.
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Affiliation(s)
- Yujia Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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25
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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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26
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Kong L, Zhang L, Wang Y, Huang Z. Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils. Microorganisms 2023; 12:41. [PMID: 38257868 PMCID: PMC10818615 DOI: 10.3390/microorganisms12010041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.
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Affiliation(s)
| | | | | | - Zhanbin Huang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China; (L.K.); (L.Z.); (Y.W.)
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Zhou Y, Yang Z, Liu J, Li X, Wang X, Dai C, Zhang T, Carrión VJ, Wei Z, Cao F, Delgado-Baquerizo M, Li X. Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease. Nat Commun 2023; 14:8126. [PMID: 38065941 PMCID: PMC10709580 DOI: 10.1038/s41467-023-43926-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhen Yang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jinguang Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xudong Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Xingxiang Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Taolin Zhang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Víctor J Carrión
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Zhong Wei
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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28
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Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D. Microbial diversity in soils suppressive to Fusarium diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1228749. [PMID: 38111879 PMCID: PMC10726057 DOI: 10.3389/fpls.2023.1228749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.
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Affiliation(s)
- Irena Todorović
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Wang Z, Solanki MK, Kumar A, Solanki AC, Pang F, Ba ZX, Niu JQ, Ren ZX. Promoting plant resilience against stress by engineering root microenvironment with Streptomyces inoculants. Microbiol Res 2023; 277:127509. [PMID: 37788547 DOI: 10.1016/j.micres.2023.127509] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023]
Abstract
Plant growth is directly influenced by biotic and abiotic stress factors resulting from environmental changes. Plant growth-promoting rhizobacteria (PGPR) have become a crucial area of research aimed at addressing these challenges. However, a knowledge gap exists regarding how PGPR impacts the microenvironments surrounding plant roots. The purpose of this study is to elucidate the effects of two distinct PGPR strains, Streptomyces griseorubiginosus BTU6 (known for its resistance to smut disease) and S. chartreusis WZS021, on sugarcane roots. Additionally, we compare the resultant modifications in the physicochemical characteristics of the rhizospheric soil and root architecture. The results reveal that following the inoculation of S. chartreusis WZS021, there was a significant increase in the active chemicals associated with nitrogen metabolism in sugarcane roots. This enhancement led to a substantial enrichment of nitrogen-cycling microbes like Pseudomonas and Gemmatimona. This finding supports earlier research indicating that S. chartreusis WZS021 enhances sugarcane's capacity to utilize nitrogen effectively. Furthermore, after treatment with S. chartreusis, Aspergillus became the predominant strain among endophytic fungi, resulting in alterations to their community structure that conferred drought resistance. In contrast, the relative abundance of Xanthomonas in the root environment decreased following inoculation with S. griseorubiginosus. Instead, Gemmatimona became more prevalent, creating a favorable environment for plants to bolster their resistance against disease. Notably, inoculations with S. chartreusis WZS021 and S. griseorubiginosus BTU6 led to substantial changes in the chemical composition, enzymatic activity, and microbial community composition in the soil surrounding sugarcane roots. However, there were distinct differences in the specific alterations induced by each strain. These findings enhance plant resilience to stress by shedding light on PGPR-mediated modifications in root microenvironments.
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Affiliation(s)
- Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh 201313, India
| | - Anjali Chandrol Solanki
- Department of Agriculture, Mansarover Global University, Bhopal, Madhya Pradesh 462042, India
| | - Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Zi-Xuan Ba
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Jun-Qi Niu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China.
| | - Zhen-Xin Ren
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China.
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Zhang N, Wang Z, Shao J, Xu Z, Liu Y, Xun W, Miao Y, Shen Q, Zhang R. Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture. Microb Biotechnol 2023; 16:2250-2263. [PMID: 37837627 PMCID: PMC10686189 DOI: 10.1111/1751-7915.14348] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/16/2023] Open
Abstract
Species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development. New mechanisms underlying Bacillus biocontrol activity have been revealed with the development of microbiome and microbe-plant interaction research. In this review, we first briefly introduce the typical Bacillus biocontrol mechanisms, such as the production of antimicrobial compounds, competition for niches/nutrients, and induction of systemic resistance. Then, we discussed in detail the new mechanisms of pathogen quorum sensing interference and reshaping of the soil microbiota. The "cry for help" mechanism was also introduced, in which plants can release specific signals under pathogen attack to recruit biocontrol Bacillus for root colonization against invasion. Finally, two emerging strategies for enhancing the biocontrol efficacy of Bacillus agents, including the construction of synthetic microbial consortia and the application of rhizosphere-derived prebiotics, were proposed.
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Affiliation(s)
- Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijingChina
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
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Thompson MEH, Shrestha A, Rinne J, Limay-Rios V, Reid L, Raizada MN. The Cultured Microbiome of Pollinated Maize Silks Shifts after Infection with Fusarium graminearum and Varies by Distance from the Site of Pathogen Inoculation. Pathogens 2023; 12:1322. [PMID: 38003787 PMCID: PMC10675081 DOI: 10.3390/pathogens12111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Styles transmit pollen-derived sperm nuclei from pollen to ovules, but also transmit environmental pathogens. The microbiomes of styles are likely important for reproduction/disease, yet few studies exist. Whether style microbiome compositions are spatially responsive to pathogens is unknown. The maize pathogen Fusarium graminearum enters developing grain through the style (silk). We hypothesized that F. graminearum treatment shifts the cultured transmitting silk microbiome (TSM) compared to healthy silks in a distance-dependent manner. Another objective of the study was to culture microbes for future application. Bacteria were cultured from husk-covered silks of 14 F. graminearum-treated diverse maize genotypes, proximal (tip) and distal (base) to the F. graminearum inoculation site. Long-read 16S sequences from 398 isolates spanned 35 genera, 71 species, and 238 OTUs. More bacteria were cultured from F. graminearum-inoculated tips (271 isolates) versus base (127 isolates); healthy silks were balanced. F. graminearum caused a collapse in diversity of ~20-25% across multiple taxonomic levels. Some species were cultured exclusively or, more often, from F. graminearum-treated silks (e.g., Delftia acidovorans, Klebsiella aerogenes, K. grimontii, Pantoea ananatis, Stenotrophomonas pavanii). Overall, the results suggest that F. graminearum alters the TSM in a distance-dependent manner. Many isolates matched taxa that were previously identified using V4-MiSeq (core and F. graminearum-induced), but long-read sequencing clarified the taxonomy and uncovered greater diversity than was initially predicted (e.g., within Pantoea). These isolates represent the first comprehensive cultured collection from pathogen-treated maize silks to facilitate biocontrol efforts and microbial marker-assisted breeding.
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Affiliation(s)
- Michelle E. H. Thompson
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Jeffrey Rinne
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
| | - Victor Limay-Rios
- Department of Plant Agriculture, University of Guelph Ridgetown Campus, 120 Main Street E, Ridgetown, ON N0P 2C0, Canada
| | - Lana Reid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Central Experimental Farm, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.E.H.T.)
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Ma H, Li J, Luo A, Lv H, Ren Z, Yang H, Fang X, Shahzad MA, Qu H, Zhang K, Wang Q, Zheng S. Vanillin, a Newly Discovered Autotoxic Substance in Long-Term Potato Continuous Cropping Soil, Inhibits Plant Growth by Decreasing the Root Auxin Content and Reducing Adventitious Root Numbers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37905798 DOI: 10.1021/acs.jafc.3c05027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Phenolic acids are known to reduce root biomass and hinder plant development, but it is unclear how they affect potato root traits. Over a 10 year field experiment, we found a negative correlation between the potato yield and continuous cropping years. The substantial reduction in adventitious root (AR) numbers was found to be primarily inhibited by soil vanillin accumulation. The study also found that vanillin had a more pronounced inhibitory effect on the potato yield than commonly reported ferulic acid and p-hydroxybenzoic acid. The decrease in yield was attributed to the reduction of root indole-3-acetic acid (IAA) content, which impeded the formation of AR. Exogenous IAA was found to increase the root IAA content and stimulate AR formation under vanillin stress, ultimately leading to an increase in the potato yield. This study provides valuable insights into potential strategies for the degradation of autotoxic substances and breeding of potato cultivars with enhanced resistance to autotoxicity.
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Affiliation(s)
- Haiyan Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Junji Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Aihua Luo
- Potato Research Institute of Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, People's Republic of China
| | - Heping Lv
- Potato Research Institute of Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, People's Republic of China
| | - Zhitong Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Hongkun Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Xiaoting Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Muhammad Amir Shahzad
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Huijuan Qu
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Kaiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Qiang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
| | - Shunlin Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, People's Republic of China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu, Sichuan 611130, People's Republic of China
- Key Laboratory of Tuber Crop Genetics and Breeding, Ministry of Agriculture, Chengdu Joyson Agricultural Technology Company, Limited, Xindu, Sichuan 610500, People's Republic of China
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Jia F, Chang F, Guan M, Jia Q, Sun Y, Li Z. Effects of rotation and Bacillus on the changes of continuous cropping soil fungal communities in American ginseng. World J Microbiol Biotechnol 2023; 39:354. [PMID: 37874395 PMCID: PMC10598105 DOI: 10.1007/s11274-023-03807-w] [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: 08/03/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023]
Abstract
The continuous cropping obstacle is the main factor in leading to difficulty in American ginseng replanting. The dormant microbiota in the soil may be the cause of American ginseng disease and eventually caused continuous cropping obstacles, but there are few studies on the dynamic changes of soil microenvironment after American ginseng planting. In this study, we tracked short-term variation in physicochemical properties, enzyme activities, and fungal communities over time-series in soils with continuous cropping obstacle under crop rotation and probiotic Bacillus treatments. Furthermore, we examined the relationships between the important fungal compositions and the soil properties. The results showed that sucrase, cellulase, urease and acid phosphatase activities were significantly increased, while catalase and dehydrogenase were decreased with treatments time. Rotation treatment significantly affected the diversity, dissimilarity degree and species distribution of soil fungal community with continuous cropping obstacle over a short-term. Moreover, beneficial fungal biomarkers such as Cladorrhinum, Oidiodendron, and Mariannaea were accumulated at 48 h under rotation treatments. Almost all fungal biomarkers were negatively correlated with hydrolases and positively correlated with oxidoreductases and acid phosphatase under crop rotation treatments. This study suggested that compared to probiotic Bacillus, crop rotation can significantly affect soil fungal community structure, especially the enrichment of specific potentially beneficial fungal species. Our findings provide a scientific basis for understanding the dynamic changes of fungal communities and soil properties with continuous cropping obstacle of American ginseng in initial stage of soil improvement.
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Affiliation(s)
- Fengan Jia
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Fan Chang
- Shaanxi Institute of Microbiology, Xi'an, 710043, China
| | - Min Guan
- Shaanxi Agricultural Machinery Research Institute, Xianyang, 712000, China
| | - Qingan Jia
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yan Sun
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China
| | - Zhi Li
- College of Life Science, Shaanxi Normal University, Xi'an, 710062, China.
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Sun K, Jiang HJ, Pan YT, Lu F, Zhu Q, Ma CY, Zhang AY, Zhou JY, Zhang W, Dai CC. Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil. THE ISME JOURNAL 2023; 17:1626-1638. [PMID: 37443341 PMCID: PMC10504341 DOI: 10.1038/s41396-023-01476-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.
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Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Fan Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Qiang Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Jia-Yu Zhou
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China.
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China.
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Li Y, Lu D, Xia Y, Xu X, Huang H, Mei X, Yang M, Li J, Zhu S, Liu Y, Zhang Z. Effects of allyl isothiocyanate fumigation on medicinal plant root knot disease control, plant survival, and the soil bacterial community. BMC Microbiol 2023; 23:278. [PMID: 37775764 PMCID: PMC10542678 DOI: 10.1186/s12866-023-02992-w] [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: 12/29/2022] [Accepted: 08/22/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Allyl isothiocyanate (AITC) is a natural product with high volatility that is used as a biofumigant to alleviate soil-borne plant diseases, and problems such as root knot nematodes (RKNs) that necessitate continuous cropping. However, little research has assessed the effects of AITC fumigation on medicinal plants. RESULTS AITC significantly reduced the population of RKNs in soil (p < 0.0001) and showed an excellent RKN disease control effect within 6 months after sowing Panax notoginseng (p < 0.0001). The seedling survival rate of 2-year-old P. notoginseng was approximately 1.7-fold higher after soil treatment with AITC (p = 0.1008). 16S rRNA sequencing indicated that the AITC treatment affected bacterial richness rather than diversity in consecutively cultivated (CC) soil. Furthermore, biomarkers with statistical differences between AITC-treated and untreated CC soil showed that Pirellulales (order), Pirellulaceae (family), Pseudomonadaceae (family), and Pseudomonas (genus) played important roles in the AITC-treated group. In addition, the microbiome functional phenotypes predicted using the BugBase tool suggested that AITC treatment is more conducive to improving CC soil through changes in the bacterial community structure. Crucially, our research also suggested that AITC soil treatment significantly increases soil organic matter (p = 0.0055), total nitrogen (p = 0.0054), and available potassium (p = 0.0373), which promotes the survival of a succeeding medicinal plant (Polygonatum kingianum). CONCLUSION AITC is an ecologically friendly soil treatment that affects the top 10 bacterial richness but not diversity. It could also provide a basis for a useful agricultural soil management measure to alleviate soil sickness.
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Affiliation(s)
- Yingbin Li
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Daqing Lu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yan Xia
- Department of Pesticide Science, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinjing Xu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinyue Mei
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jianqiang Li
- Department of Plant Pathology, Beijing Key Laboratory of Seed Disease Testing and Control, China Agricultural University, Beijing, 100193, China
| | - Shusheng Zhu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Zhiping Zhang
- Department of Horticulture, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Li M, Chen C, Zhang H, Wang Z, Song N, Li J, Liang X, Yi K, Gu Y, Guo X. Effects of biochar amendment and organic fertilizer on microbial communities in the rhizosphere soil of wheat in Yellow River Delta saline-alkaline soil. Front Microbiol 2023; 14:1250453. [PMID: 37808323 PMCID: PMC10556502 DOI: 10.3389/fmicb.2023.1250453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
The biochar and organic fertilizer amendment have been used as an effective practice to increase soil fertility. Nevertheless, the mechanisms of microbial community response to organic fertilizer and biochar application on saline-alkali soil have not been clarified. This study investigated the effects at different concentrations of organic fertilizer and biochar on the microbial community of wheat rhizosphere soil under field experiment in the Yellow River Delta (China, YRD), using high-throughput sequencing technology. Biochar and organic fertilizer significantly influenced in most soil parameters (p < 0.05), apart from soil moisture content (M), pH, total nitrogen (TN) and soil total phosphorus (TP). Proteobacteria and Actinobacteriota were found in the rhizosphere soil as the main bacterial phyla, and the main fungal phyla were Ascomycota and Mortierellomycota. The soil bacterial and fungal communities under organic fertilizer were distinct from CK. Furthermore, redundancy analysis (RDA) directed that changes in bacterial communities were related to soil properties like pH, available phosphorus (AP), and total organic carbon (TOC), while pH, AP and TP, were crucial contributors in regulating fungal distribution. The correlation between soil parameters and bacteria or fungi varied with the application of biochar and organic fertilizers, and the interaction between the bacteria and fungi in organic fertilizer treatments formed more connections compared with biochar treatments. Our results indicated that biochar was superior to organic fertilizer under the contents set up in this study, and soil parameters increased with biochar and organic fertilizer application rate. The diversity and structure of soil bacteria and fungi differed with the application of biochar and organic fertilizer. The research provides a reference to rational application of organic fertilizer and biochar improvement in saline-alkali soil.
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Affiliation(s)
- Meng Li
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Chuanjie Chen
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Haiyang Zhang
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Zongshuai Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ningning Song
- School of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Junlin Li
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Xiaoyan Liang
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Kuihua Yi
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Yinyu Gu
- Shandong Institute of Sericulture, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Xiaohong Guo
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
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Wang D, Sarsaiya S, Qian X, Jin L, Shu F, Zhang C, Chen J. Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data. FRONTIERS IN PLANT SCIENCE 2023; 14:1227507. [PMID: 37771489 PMCID: PMC10522861 DOI: 10.3389/fpls.2023.1227507] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Pinellia ternata (Thunb.) Breit. (Araceae), a significant medicinal plant, has been used to treat various diseases for centuries. Terahertz radiation (THZ) is located between microwaves and infrared rays on the electromagnetic spectrum. THZ possesses low single-photon energy and a spectral fingerprint, but its effects on plant growth have not yet been investigated. The study's primary objective was to examine the transcriptome and metabolome databases of the SY line to provide a new perspective for identifying genes associated with resistance and growth promotion and comprehending the underlying molecular mechanism. Variations in the biological characteristics of P. ternata grown under control and experimental conditions were analyzed to determine the effect of THZ. Compared with the control group, phenotypic variables such as leaf length, petiole length, number of leaves, leaf petiole diameter, and proliferation coefficient exhibited significant differences. P. ternata response to THZ was analyzed regarding the effects of various coercions on root exudation. The experimental group contained considerably more sugar alcohol than the control group. The transcriptome analysis revealed 1,695 differentially expressed genes (DEGs), including 509 upregulated and 1,186 downregulated genes. In the KEGG-enriched plant hormone signaling pathway, there were 19 differentially expressed genes, 13 of which were downregulated and six of which were upregulated. In the metabolomic analysis, approximately 416 metabolites were uncovered. There were 112 DEMs that were downregulated, whereas 148 were upregulated. The P. ternata leaves displayed significant differences in phytohormone metabolites, specifically in brassinolide (BR) and abscisic acid (ABA). The rise in BR triggers alterations in internal plant hormones, resulting in faster growth and development of P. ternata. Our findings demonstrated a link between THZ and several metabolic pathway processes, which will enhance our understanding of P. ternata mechanisms.
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Affiliation(s)
- Dongdong Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Surendra Sarsaiya
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xu Qian
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Leilei Jin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Fuxing Shu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
| | | | - Jishuang Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
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Li X, Chen D, Carrión VJ, Revillini D, Yin S, Dong Y, Zhang T, Wang X, Delgado-Baquerizo M. Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections. Nat Commun 2023; 14:5090. [PMID: 37607924 PMCID: PMC10444831 DOI: 10.1038/s41467-023-40810-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.
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Affiliation(s)
- Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dele Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
| | - Daniel Revillini
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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Profile of Dr. Qirong Shen. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1725-1727. [PMID: 37452898 DOI: 10.1007/s11427-023-2355-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
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40
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Chen W, Modi D, Picot A. Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2736. [PMID: 37514350 PMCID: PMC10384710 DOI: 10.3390/plants12142736] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dixi Modi
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Zhu Q, Fei YJ, Wu YB, Luo DL, Chen M, Sun K, Zhang W, Dai CC. Endophytic Fungus Reshapes Spikelet Microbiome to Reduce Mycotoxin Produced by Fusarium proliferatum through Altering Rice Metabolites. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37466504 DOI: 10.1021/acs.jafc.3c02616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Rice spikelet rot disease (RSRD) caused by Fusarium proliferatum seriously reduces rice yield and produces mycotoxins that threaten human health. The root symbiotic endophytic fungus Phomopsis liquidambaris reduces RSRD incidence and fumonisins accumulation in grain by 21.5 and 9.3%, respectively, while the mechanism of disease resistance remains largely elusive. Here, we found that B3 significantly reduced the abundance of pathogen from 79.91 to 2.84% and considerably enriched resistant microbes Pseudomonas and Proteobacteria in the spikelet microbial community. Further study revealed that B3 altered the metabolites of spikelets, especially hordenine and l-aspartic acid, which played a key role in reshaping the microbiome and supporting the growth of the functional core microbe Pseudomonas, and inhibited the pathogen growth and mycotoxin production. This study provided a feasibility of regulating the function of aboveground microbial communities by manipulating plant subsurface tissues to control disease and mycotoxin pollutants in agricultural production.
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Affiliation(s)
- Qiang Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yan-Jun Fei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yi-Bo Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Man Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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Wang Y, Liu Z, Hao X, Wang Z, Wang Z, Liu S, Tao C, Wang D, Wang B, Shen Z, Shen Q, Li R. Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production. NPJ Biofilms Microbiomes 2023; 9:46. [PMID: 37407614 DOI: 10.1038/s41522-023-00416-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
The soil microbiota is critical to plant performance. Improving the ability of plant-associated soil probiotics is thus essential for establishing dependable and sustainable crop yields. Although fertilizer applications may provide an effective way of steering soil microbes, it is still unknown how the positive effects of soil-borne probiotics can be maximized and how their effects are mediated. This work aims to seek the ecological mechanisms involved in cabbage growth using bio-organic fertilizers. We conducted a long-term field experiment in which we amended soil with non-sterilized organic or sterilized organic fertilizer either containing Trichoderma guizhouense NJAU4742 or lacking this inoculum and tracked cabbage plant growth and the soil fungal community. Trichoderma-amended bio-organic fertilizers significantly increased cabbage plant biomass and this effect was attributed to changes in the resident fungal community composition, including an increase in the relative abundance and number of indigenous soil growth-promoting fungal taxa. We specifically highlight the fundamental role of the biodiversity and population density of these plant-beneficial fungal taxa in improving plant growth. Together, our results suggest that the beneficial effects of bio-organic fertilizer seem to be a combination of the biological inoculum within the organic amendment as well as the indirect promotion through effects on the diversity and composition of the soil resident plant-beneficial fungal microbiome.
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Affiliation(s)
- Yan Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
| | - Zhengyang Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
| | - Xinyi Hao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
| | - Ziqi Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
| | - Zhe Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
| | - Shanshan Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China.
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China.
| | - Dongsheng Wang
- Nanjing Institute of Vegetable Science, Nanjing, 210042, Jiangsu, P. R. China
| | - Bei Wang
- Nanjing Institute of Vegetable Science, Nanjing, 210042, Jiangsu, P. R. China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, P. R. China
- The Sanya Institute of Nanjing Agricultural University, Sanya, 572000, Hainan, P. R. China
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Yu X, Zhang Y, Shen M, Dong S, Zhang F, Gao Q, He P, Shen G, Yang J, Wang Z, Bo G. Soil Conditioner Affects Tobacco Rhizosphere Soil Microecology. MICROBIAL ECOLOGY 2023; 86:460-473. [PMID: 35596751 DOI: 10.1007/s00248-022-02030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Reasonable fertilization management can increase nutrient content and enzyme activity in rhizosphere soil, and even increase soil microbial richness. However, different fertilizers could raise distinct influences on the soil properties, including soil environmental factors (physicochemical properties and enzymatic activities) and microbial community. Here, the effects of two soil amendments (microbial fertilizer and woody peat) on environmental factors and microbial community structure in tobacco rhizosphere soil were evaluated, with the correlations between microbes and environmental factors explored. As the results, microbial fertilizer could effectively alleviate soil acidification, increase available potassium and organic matter contents in soil, and was also beneficial to increase nitrate reductase activity in rhizosphere soil. Fertilizers cause changes in the abundance of certain microbes in the soil. Besides, it was shown that the candidate phyla Gal15, Acidobacterota, Latescibacterota, Mortierellommycota, Basidiomycota, and Rozellomycota in tobacco rhizosphere soil had significant correlation with soil environmental factors. Through the functional analysis of these populations, it can be deduced that the changes in the abundance of certain microorganisms may be an important reason for the differences in environmental factors. All these indicated that the differences of environmental factors in different treatments are closely related to the abundance of some special soil microorganisms. Studying the life activities of these microbes would provide good guidance for exploring the interaction among crops, soil, and microorganisms and improving crop yields.
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Affiliation(s)
- Xiangquan Yu
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yuzhen Zhang
- Energy-Rich Compounds Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Minchong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Shanyu Dong
- Yichang Tobacco Company of Hubei Province, Yichang, China
| | - Fujun Zhang
- Linyi Tobacco Company of Shandong Province, Linyi, China
| | - Qiang Gao
- Linyi Tobacco Company of Shandong Province, Linyi, China
| | - Penglin He
- Linyi Tobacco Company of Shandong Province, Linyi, China
| | - Guoming Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jianming Yang
- Energy-Rich Compounds Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Zhaobao Wang
- Energy-Rich Compounds Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Guodong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China.
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Gu YY, Liang XY, Zhang HY, Fu R, Li M, Chen CJ. Effect of biochar and bioorganic fertilizer on the microbial diversity in the rhizosphere soil of Sesbania cannabina in saline-alkaline soil. Front Microbiol 2023; 14:1190716. [PMID: 37455751 PMCID: PMC10339320 DOI: 10.3389/fmicb.2023.1190716] [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: 03/21/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Biochar and bioorganic fertilizer (BOF) application in agriculture has garnered increasing interest recently. However, the effects of biochar and BOF on rhizosphere soil microecology, especially in a region with saline-alkaline soil, remain largely unexplored. Methods In this study, we performed Illumina-based 16S rRNA sequencing to investigate the effects of biochar with or without BOF addition, as well as at different addition rates and particles sizes, on the microecology of saline-alkaline rhizosphere soil. Results In the field experiment, biochar and BOF application altered the rhizosphere soil microecology. Actinobacteriota, Proteobacteria, and Chloroflexi accounted for >60% of the total bacterial population in each treatment. In the different treatments, Actinobacteria and Alphaproteobacteria were the predominant classes; Micromonosporales and Vicinamibacterales were the dominant orders; norank_f__Geminicoccaceae and Micromonosporaceae were the most abundant families; and Micromonospora and norank_f_Geminicoccaceae were the predominant genera. Application of biochar with or without BOF decreased soil electrical conductivity (EC) by 7% -11.58% only at the depth of 10 cm below the surface, again, soil EC can be significantly reduced by an average of 4% at 10 cm depth soil after planting Sesbania cannabina. Soil organic carbon, organic matter, available potassium, and available phosphorus contents had significant effects on the soil bacterial community structure. Conclusion Co-application of biochar and BOF resulted in the greatest improvement of rhizosphere soil microecology, either by promoting plant growth or improving the nutrition and physicochemical properties of soil, followed by BOF alone and biochar alone. Additionally, higher application rate of biochar was better than lower application rate, and fine biochar had a stronger effect than coarse biochar. These results provide guidance for the development of new saline-alkaline soil remediation strategies.
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Mehmood N, Saeed M, Zafarullah S, Hyder S, Rizvi ZF, Gondal AS, Jamil N, Iqbal R, Ali B, Ercisli S, Kupe M. Multifaceted Impacts of Plant-Beneficial Pseudomonas spp. in Managing Various Plant Diseases and Crop Yield Improvement. ACS OMEGA 2023; 8:22296-22315. [PMID: 37396244 PMCID: PMC10308577 DOI: 10.1021/acsomega.3c00870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023]
Abstract
The modern agricultural system has issues with the reduction of agricultural productivity due to a wide range of abiotic and biotic stresses. It is also expected that in the future the entire world population may rapidly increase and will surely demand more food. Farmers now utilize a massive quantity of synthetic fertilizers and pesticides for disease management and to increase food production. These synthetic fertilizers badly affect the environment, the texture of the soil, plant productivity, and human health. However, agricultural safety and sustainability depend on an ecofriendly and inexpensive biological application. In contrast to synthetic fertilizers, soil inoculation with plant-growth-promoting rhizobacteria (PGPR) is one of the excellent alternative options. In this regard, we focused on the best PGPR genera, Pseudomonas, which exists in the rhizosphere as well as inside the plant's body and plays a role in sustainable agriculture. Many Pseudomonas spp. control plant pathogens and play an effective role in disease management through direct and indirect mechanisms. Pseudomonas spp. fix the amount of atmospheric nitrogen, solubilize phosphorus and potassium, and also produce phytohormones, lytic enzymes, volatile organic compounds, antibiotics, and secondary metabolites during stress conditions. These compounds stimulate plant growth by inducing systemic resistance and by inhibiting the growth of pathogens. Furthermore, pseudomonads also protect plants during different stress conditions like heavy metal pollution, osmosis, temperature, oxidative stress, etc. Now, several Pseudomonas-based commercial biological control products have been promoted and marketed, but there are a few limitations that hinder the development of this technology for extensive usage in agricultural systems. The variability among the members of Pseudomonas spp. draws attention to the huge research interest in this genus. There is a need to explore the potential of native Pseudomonas spp. as biocontrol agents and to use them in biopesticide development to support sustainable agriculture.
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Affiliation(s)
- Najaf Mehmood
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Mahnoor Saeed
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Sana Zafarullah
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Sajjad Hyder
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Zarrin Fatima Rizvi
- Department
of Botany, Government College Women University
Sialkot, Sialkot 51310, Pakistan
| | - Amjad Shahzad Gondal
- Department
of Plant Pathology, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Nuzhat Jamil
- Department
of Botany, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Rashid Iqbal
- Department
of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur Pakistan, Bahawalpur 63100, Pakistan
| | - Baber Ali
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sezai Ercisli
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- HGF
Agro, Ata Teknokent, Erzurum TR-25240, Türkiye
| | - Muhammed Kupe
- Department
of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
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Kashyap AS, Manzar N, Meshram S, Sharma PK. Screening microbial inoculants and their interventions for cross-kingdom management of wilt disease of solanaceous crops- a step toward sustainable agriculture. Front Microbiol 2023; 14:1174532. [PMID: 37389335 PMCID: PMC10303155 DOI: 10.3389/fmicb.2023.1174532] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/18/2023] [Indexed: 07/01/2023] Open
Abstract
Microbial inoculants may be called magical bullets because they are small in size but have a huge impact on plant life and humans. The screening of these beneficial microbes will give us an evergreen technology to manage harmful diseases of cross-kingdom crops. The production of these crops is reducing as a result of multiple biotic factors and among them the bacterial wilt disease triggered by Ralstonia solanacearum is the most important in solanaceous crops. The examination of the diversity of bioinoculants has shown that more microbial species have biocontrol activity against soil-borne pathogens. Reduced crop output, lower yields, and greater cost of cultivation are among the major issues caused by diseases in agriculture around the world. It is universally true that soil-borne disease epidemics pose a greater threat to crops. These necessitate the use of eco-friendly microbial bioinoculants. This review article provides an overview of plant growth-promoting microorganisms bioinoculants, their various characteristics, biochemical and molecular screening insights, and modes of action and interaction. The discussion is concluded with a brief overview of potential future possibilities for the sustainable development of agriculture. This review will be useful for students and researchers to obtain existing knowledge of microbial inoculants, their activities, and their mechanisms, which will facilitate the development of environmentally friendly management strategies for cross-kingdom plant diseases.
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Affiliation(s)
- Abhijeet Shankar Kashyap
- Molecular Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Nazia Manzar
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara, Punjab, India
| | - Pawan Kumar Sharma
- Plant Pathology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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Liu S, Tao C, Zhang L, Wang Z, Xiong W, Xiang D, Sheng O, Wang J, Li R, Shen Z, Li C, Shen Q, Kowalchuk GA. Plant pathogen resistance is mediated by recruitment of specific rhizosphere fungi. THE ISME JOURNAL 2023; 17:931-942. [PMID: 37037925 PMCID: PMC10203115 DOI: 10.1038/s41396-023-01406-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
Beneficial interactions between plants and rhizosphere microorganisms are key determinants of plant health with the potential to enhance the sustainability of agricultural practices. However, pinpointing the mechanisms that determine plant disease protection is often difficult due to the complexity of microbial and plant-microbe interactions and their links with the plant's own defense systems. Here, we found that the resistance level of different banana varieties was correlated with the plant's ability to stimulate specific fungal taxa in the rhizosphere that are able to inhibit the Foc TR4 pathogen. These fungal taxa included members of the genera Trichoderma and Penicillium, and their growth was stimulated by plant exudates such as shikimic acid, D-(-)-ribofuranose, and propylene glycol. Furthermore, amending soils with these metabolites enhanced the resistance of a susceptible variety to Foc TR4, with no effect observed for the resistant variety. In total, our findings suggest that the ability to recruit pathogen-suppressive fungal taxa may be an important component in determining the level of pathogen resistance exhibited by plant varieties. This perspective opens up new avenues for improving plant health, in which both plant and associated microbial properties are considered.
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Affiliation(s)
- Shanshan Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Lingyin Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhe Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Dandan Xiang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China
| | - Ou Sheng
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Rong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China.
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan Province, China.
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong Province, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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Mao HC, Sun Y, Tao C, Deng X, Xu X, Shen Z, Zhang L, Zheng Z, Huang Y, Hao Y, Zhou G, Liu S, Li R, Guo K, Tian Z, Shen Q. Rhizosphere Microbiota Promotes the Growth of Soybeans in a Saline-Alkali Environment under Plastic Film Mulching. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091889. [PMID: 37176946 PMCID: PMC10180738 DOI: 10.3390/plants12091889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
The rhizosphere microbiota plays a critical and crucial role in plant health and growth, assisting plants in resisting adverse stresses, including soil salinity. Plastic film mulching is an important method to adjust soil properties and improve crop yield, especially in saline-alkali soil. However, it remains unclear whether and to what extent the association between these improvements and rhizosphere microbiota exists. Here, from a field survey and a greenhouse mesocosm experiment, we found that mulching plastic films on saline-alkali soil can promote the growth of soybeans in the field. Results of the greenhouse experiment showed that soybeans grew better in unsterilized saline-alkali soil than in sterilized saline-alkali soil under plastic film mulching. By detecting the variations in soil properties and analyzing the high-throughput sequencing data, we found that with the effect of film mulching, soil moisture content was effectively maintained, soil salinity was obviously reduced, and rhizosphere bacterial and fungal communities were significantly changed. Ulteriorly, correlation analysis methods were applied. The optimization of soil properties ameliorated the survival conditions of soil microbes and promoted the increase in relative abundance of potential beneficial microorganisms, contributing to the growth of soybeans. Furthermore, the classification of potential key rhizosphere microbial OTUs were identified. In summary, our study suggests the important influence of soil properties as drivers on the alteration of rhizosphere microbial communities and indicates the important role of rhizosphere microbiota in promoting plant performance in saline-alkali soil under plastic film mulching.
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Affiliation(s)
- Han-Cheng Mao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifei Sun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Xu Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenquan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Laijie Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zehui Zheng
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Yanhua Huang
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Yongren Hao
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Guoan Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shulin Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Guo
- Institute of Environment and Ecology, Shandong Normal University, No. 88, Wenhuadong Road, Lixia District, Ji'nan 250014, China
| | - Zhixi Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Bio-Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
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Tao C, Wang Z, Liu S, Lv N, Deng X, Xiong W, Shen Z, Zhang N, Geisen S, Li R, Shen Q, Kowalchuk GA. Additive fungal interactions drive biocontrol of Fusarium wilt disease. THE NEW PHYTOLOGIST 2023; 238:1198-1214. [PMID: 36740577 DOI: 10.1111/nph.18793] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Host-associated fungi can help protect plants from pathogens, and empirical evidence suggests that such microorganisms can be manipulated by introducing probiotic to increase disease suppression. However, we still generally lack the mechanistic knowledge of what determines the success of probiotic application, hampering the development of reliable disease suppression strategies. We conducted a three-season consecutive microcosm experiment in which we amended banana Fusarium wilt disease-conducive soil with Trichoderma-amended biofertilizer or lacking this inoculum. High-throughput sequencing was complemented with cultivation-based methods to follow changes in fungal microbiome and explore potential links with plant health. Trichoderma application increased banana biomass by decreasing disease incidence by up to 72%, and this effect was attributed to changes in fungal microbiome, including the reduction in Fusarium oxysporum density and enrichment of pathogen-suppressing fungi (Humicola). These changes were accompanied by an expansion in microbial carbon resource utilization potential, features that contribute to disease suppression. We further demonstrated the disease suppression actions of Trichoderma-Humicola consortia, and results suggest niche overlap with pathogen and induction of plant systemic resistance may be mechanisms driving the observed biocontrol effects. Together, we demonstrate that fungal inoculants can modify the composition and functioning of the resident soil fungal microbiome to suppress soilborne disease.
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Affiliation(s)
- Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China
| | - Zhe Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China
| | - Shanshan Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Nana Lv
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, 6700 AA, the Netherlands
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- The Sanya Institute of Nanjing Agricultural University, Sanya, Hainan, 572000, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, the Netherlands
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Li G, Wang K, Qin Q, Li Q, Mo F, Nangia V, Liu Y. Integrated Microbiome and Metabolomic Analysis Reveal Responses of Rhizosphere Bacterial Communities and Root exudate Composition to Drought and Genotype in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:19. [PMID: 37039929 PMCID: PMC10090257 DOI: 10.1186/s12284-023-00636-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND As climate change events become more frequent, drought is an increasing threat to agricultural production and food security. Crop rhizosphere microbiome and root exudates are critical regulators for drought adaptation, yet our understanding on the rhizosphere bacterial communities and root exudate composition as affected by drought stress is far from complete. In this study, we performed 16S rRNA gene amplicon sequencing and widely targeted metabolomic analysis of rhizosphere soil and root exudates from two contrasting rice genotypes (Nipponbare and Luodao 998) exposed to drought stress. RESULTS A reduction in plant phenotypes was observed under drought, and the inhibition was greater for roots than for shoots. Additionally, drought exerted a negligible effect on the alpha diversity of rhizosphere bacterial communities, but obviously altered their composition. In particular, drought led to a significant enrichment of Actinobacteria but a decrease in Firmicutes. We also found that abscisic acid in root exudates was clearly higher under drought, whereas lower jasmonic acid and L-cystine concentrations. As for plant genotypes, variations in plant traits of the drought-tolerant genotype Luodao 998 after drought were smaller than those of Nipponbare. Interestingly, drought triggered an increase in Bacillus, as well as an upregulation of most organic acids and a downregulation of all amino acids in Luodao 998. Notably, both Procrustes analysis and Mantel test demonstrated that rhizosphere microbiome and root exudate metabolomic profiles were highly correlated. A number of differentially abundant genera responded to drought and genotype, including Streptomyces, Bacillus and some members of Actinobacteria, were significantly associated with organic acid and amino acid contents in root exudates. Further soil incubation experiments showed that Streptomyces was regulated by abscisic acid and jasmonic acid under drought. CONCLUSIONS Our results reveal that both drought and genotype drive changes in the compositions of rice rhizosphere bacterial communities and root exudates under the greenhouse condition, and that organic acid exudation and suppression of amino acid exudation to select specific rhizosphere bacterial communities may be an important strategy for rice to cope with drought. These findings have important implications for improving the adaptability of rice to drought from the perspective of plant-microbe interactions.
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Affiliation(s)
- Gege Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kexin Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qun Qin
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qi Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fei Mo
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Vinay Nangia
- International Center for Agricultural Research in the Dry Areas, 999055, Rabat, Morocco
| | - Yang Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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