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Jiao Y, Sun X, Dong X, Yin J, Li Z, Zhang K, Altaf MM, Li D, Zhu Z. Enhancing mango yield and soil health with organic and slow-release fertilizers: A multifaceted evaluation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175297. [PMID: 39127209 DOI: 10.1016/j.scitotenv.2024.175297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/04/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
Excessive utilization of chemical fertilizers in mango orchards not only hampers the attainment of sustainable harvests but also poses significant ecological detriments. This investigation proposes a promising solution by advocating the judicious replacement of chemical fertilizers with organic fertilizer (OF) and slow-release fertilizer (SRF), with potential to bolster soil health and augment crop productivity. In light of the promise held by these alternatives, it is imperative to establish detailed fertilization protocols for enhanced sustainable practices in mango farming. This two-year field study employed a comprehensive suite of seven fertilization strategies, unveiling that a 25 % chemical fertilizers substitution with OF and SRF improved mango yields by 12.5 % and 11.3 %, respectively, over standard practices. Additionally, these approaches substantially augmented the nutritional quality of mangoes, evident from Vitamin C enhancements of 53.9 % to 56.9 %, and improvements in sugar-to-acid ratio (19.2 %-30.3 %) and solid-to-acid ratio (12.1 %-25.3 %). Notably, the application of OF and SRF led to increased leaf nitrogen and phosphorus concentrations, while simultaneously reducing soil phosphorus and potassium levels. Furthermore, these fertilizers fostered the growth of beneficial soil microorganisms, namely Actinobacteria and Proteobacteria, and strengthened the synergy within the soil bacterial community, hence optimizing bacterial competition and nutrient cycling. The study proposes that the adoption of OF or SRF can effectively regulate soil nutrient balance, promote resilient and functional soil bacterial ecosystems, and ultimately improve mango yield and fruit quality. It recommends a fertilization scheme incorporating 25 % organic or slow-release nitrogen to align with ecological sustainability goals, promoting a more vigorous and resilient soil and crop system.
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Affiliation(s)
- Yangqiu Jiao
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Jincheng Association for Science and Technology, Jincheng 048000, Shanxi Province, China
| | - Xiaoyan Sun
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Xuezhi Dong
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Jing Yin
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Shandong Vicome Greenland Chemical Co., Ltd, Jinan 250204, Shandong Province, China
| | - Zhidong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Kailu Zhang
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China; Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate School, Shenzhen 518000, Guangdong Province, China
| | - Muhammad Mohsin Altaf
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China
| | - Dong Li
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
| | - Zhiqiang Zhu
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan Province, China.
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Shao Z, Gu S, Zhang X, Xue J, Yan T, Guo S, Pommier T, Jousset A, Yang T, Xu Y, Shen Q, Wei Z. Siderophore interactions drive the ability of Pseudomonas spp . consortia to protect tomato against Ralstonia solanacearum. HORTICULTURE RESEARCH 2024; 11:uhae186. [PMID: 39247881 PMCID: PMC11377186 DOI: 10.1093/hr/uhae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024]
Abstract
The soil-borne bacterial pathogen Ralstonia solanacearum causes significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp. consortia in suppressing R. solanacearum , both in vitro and in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonas strains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.
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Affiliation(s)
- Zhengying Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaohua Gu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoni Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiao Xue
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Saisai Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Thomas Pommier
- Setec Energie Environnement, 97/101 bvd Vivier Merle, Lyon 69003, France
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianjie Yang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Educational Ministry Engineering Center of Resource-saving fertilizers,National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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3
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Ng CWW, Yan WH, Xia YT, Tsim KWK, To JCT. Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO 2 and are associated with indigenous microbiome. Front Microbiol 2024; 15:1426893. [PMID: 39252828 PMCID: PMC11381388 DOI: 10.3389/fmicb.2024.1426893] [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: 05/02/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024] Open
Abstract
Introduction Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood. Methods This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm). Results and Discussion It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.
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Affiliation(s)
- Charles Wang Wai Ng
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Wen Hui Yan
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yi Teng Xia
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Karl Wah Keung Tsim
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Justin Chun Ting To
- Department of Biology, The University of Western Ontario, London, ON, Canada
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Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol 2024:10.1038/s41579-024-01079-1. [PMID: 39147829 DOI: 10.1038/s41579-024-01079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.
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Affiliation(s)
| | | | - Tanja Kostić
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | - Günter Brader
- AIT Austrian Institute of Technology, Vienna, Austria
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Zhang Y, Gan G, Li Y, Li W, Jiang Y, Wang P, Hu J, Wang N, Quan X, Liu J, Raza W, Xu Y, Hohmann P, Jousset A, Wang Y, Shen Q, Jiang G, Wei Z. Exploring the temporal dynamics of a disease suppressive rhizo-microbiome in eggplants. iScience 2024; 27:110319. [PMID: 39055957 PMCID: PMC11269921 DOI: 10.1016/j.isci.2024.110319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The rhizosphere microbiome is important for plant health, yet their contributions to disease resistance and assembly dynamics remain unclear. This study employed rhizosphere microbiome transplantation (RMT) to delineate the impact of the rhizosphere microbiome and the immune response of eggplant (Solanum melongena) on resistance to bacterial wilt caused by Ralstonia solanacearum. We first identified disease-suppressive and disease-conducive rhizosphere microbiome in a susceptible tomato recipient. Using a non-destructive rhizobox and 16S rRNA amplicon sequencing, we monitored the dynamics of both microbiome types during the eggplant development. Most differences were observed at the early stage and then diminished over time. The suppressive microbiome maintained a higher proportion of initial community members throughout eggplant development and exhibited stronger deterministic processes in the early stage, underscoring the importance of plant selection in recruiting protective microbes for rhizosphere immunity. Our study sheds light on the development of microbiome-based strategies for plant disease management and resistance breeding.
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Affiliation(s)
- Yuling Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yarong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Jie Hu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands
| | - Ningqi Wang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Quan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jialin Liu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Waseem Raza
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Pierre Hohmann
- Department of Biology, Healthcare and the Environment, Universitat de Barcelona, 08028 Barcelona, Spain
- BonaPlanta, 08241 Manresa, Spain
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530000, China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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Laurich JR, Lash E, O'Brien AM, Pogoutse O, Frederickson ME. Community interactions among microbes give rise to host-microbiome mutualisms in an aquatic plant. mBio 2024; 15:e0097224. [PMID: 38904411 PMCID: PMC11324027 DOI: 10.1128/mbio.00972-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes. IMPORTANCE There is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.
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Affiliation(s)
- Jason R. Laurich
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Emma Lash
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Anna M. O'Brien
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
- Department of
Molecular, Cellular, and Biomedical Sciences, University of New
Hampshire, Durham,
New Hampshire, USA
| | - Oxana Pogoutse
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
| | - Megan E. Frederickson
- Department of Ecology
& Evolutionary Biology, University of
Toronto, Toronto,
Ontario, Canada
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7
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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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8
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Zhu H, Hu L, Wang Y, Mei P, Zhou F, Rozhkova T, Li C. Effects of Streptomyces sp. HU2014 inoculation on wheat growth and rhizosphere microbial diversity under hexavalent chromium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 276:116313. [PMID: 38626602 DOI: 10.1016/j.ecoenv.2024.116313] [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: 10/23/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Wheat (Triticum aestivum L.) is a major foodstuff for over 40% of the world's population. However, hexavalent chromium [Cr(VI)] in contaminated soil significantly affects wheat production and its ecological environment. Streptomyces sp. HU2014 was first used to investigate the effects of Cr (VI) stress on wheat growth. We analyzed the Cr(VI) concentration, physicochemical properties of wheat and soil, total Cr content, and microbial community structures during their interactions. HU2014 reduced the toxicity of Cr(VI) and promoted wheat growth by increasing total nitrogen, nitrate nitrogen, total phosphorus, and Olsen-phosphorus in Cr(VI)-contaminated soil. These four soil variables had strong positive effects on two bacterial taxa, Proteobacteria and Bacteroidota, in the HU2014 treatments. In addition, the level of the dominant Proteobacteria positively correlated with the total Cr content in the soil. Among the fungal communities, which had weaker correlations with soil variables compared with bacterial communities, Ascomycota was the most abundant. Our findings suggest that HU2014 can promote the phytoremediation of Cr(VI)-contaminated soil.
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Affiliation(s)
- Hongxia Zhu
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China; Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Xinxiang, Henan 453003, China
| | - Linfeng Hu
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Yunlong Wang
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Peipei Mei
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Feng Zhou
- Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, Xinxiang, Henan 453003, China
| | - Tetiana Rozhkova
- Department of general and soil microbiology, Institute of Microbiology and Virology named after D.K. Zabolotny National Academy of Sciences of Ukraine, Kyiv 03143, Ukraine
| | - Chengwei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450001, China.
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Jiao W, Wen J, Li N, Ou T, Qiu C, Ji Y, Lin K, Liu X, Xie J. The biocontrol potentials of rhizospheric bacterium Bacillus velezensis K0T24 against mulberry bacterial wilt disease. Arch Microbiol 2024; 206:213. [PMID: 38616201 DOI: 10.1007/s00203-024-03935-3] [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: 02/20/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
Mulberry bacterial wilt disease, caused by Ralstonia pseudosolanacearum, is a devastating soil-borne disease in the silk-mulberry-related industry. In this study, through high-throughput sequencing, we compared the rhizosphere bacterial composition of the mulberry-resistant cultivar (K10) and susceptible cultivar (G12), confirming Bacillus as a genus-level biomarker for K10. Next, twelve Bacillus spp. isolates, derived from the rhizosphere of K10, were screened for their antagonistic activity against R. pseudosolanacearum. The isolate showing strong antagonism was identified as B. velezensis K0T24 and selected for further analysis. The fermentation supernatant of B. velezensis K0T24 significantly inhibited the growth of R. pseudosolanacearum (82.47%) and the expression of its pathogenic genes. Using B. velezensis K0T24 in mulberry seedlings also increased defense enzyme activities and achieved a control efficacy of up to 55.17% against mulberry bacterial wilt disease. Collectively, our findings demonstrate the potential of B. velezensis K0T24 in suppressing mulberry bacterial wilt disease.
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Affiliation(s)
- Wenlian Jiao
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Ju Wen
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Na Li
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Ting Ou
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Changyu Qiu
- Guangxi Key Laboratory of Sericultural Genetic Improvement and Efficient Breeding, Guangxi Zhuang Autonomous Region Sericultural Technology Promotion Station, Nanning, Guangxi Zhuang Autonomous Region, 530007, China
| | - Yutong Ji
- Westa College, Southwest University, Chongqing, 400715, China
| | - Kai Lin
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Xiaojiao Liu
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
| | - Jie Xie
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Science, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
- Westa College, Southwest University, Chongqing, 400715, China.
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10
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Xing H, Chen W, Liu Y, Cahill JF. Local Community Assembly Mechanisms and the Size of Species Pool Jointly Explain the Beta Diversity of Soil Fungi. MICROBIAL ECOLOGY 2024; 87:58. [PMID: 38602532 PMCID: PMC11008070 DOI: 10.1007/s00248-024-02374-3] [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: 12/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Fungi play vital regulatory roles in terrestrial ecosystems. Local community assembly mechanisms, including deterministic and stochastic processes, as well as the size of regional species pools (gamma diversity), typically influence overall soil microbial community beta diversity patterns. However, there is limited evidence supporting their direct and indirect effects on beta diversity of different soil fungal functional groups in forest ecosystems. To address this gap, we collected 1606 soil samples from a 25-ha subtropical forest plot in southern China. Our goal was to determine the direct effects and indirect effects of regional species pools on the beta diversity of soil fungi, specifically arbuscular mycorrhizal (AM), ectomycorrhizal (EcM), plant-pathogenic, and saprotrophic fungi. We quantified the effects of soil properties, mycorrhizal tree abundances, and topographical factors on soil fungal diversity. The beta diversity of plant-pathogenic fungi was predominantly influenced by the size of the species pool. In contrast, the beta diversity of EcM fungi was primarily driven indirectly through community assembly processes. Neither of them had significant effects on the beta diversity of AM and saprotrophic fungi. Our results highlight that the direct and indirect effects of species pools on the beta diversity of soil functional groups of fungi can significantly differ even within a relatively small area. They also demonstrate the independent and combined effects of various factors in regulating the diversities of soil functional groups of fungi. Consequently, it is crucial to study the fungal community not only as a whole but also by considering different functional groups within the community.
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Affiliation(s)
- Hua Xing
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Minhuang District, 200241, Shanghai, China
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Wuwei Chen
- Qingyuan Bureau Natural Resources and Planning, Qingyuan, 323800, China
| | - Yu Liu
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Minhuang District, 200241, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200082, China.
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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11
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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12
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Wu CD, Fan YB, Chen X, Cao JW, Ye JY, Feng ML, Liu XX, Sun WJ, Liu RN, Wang AY. Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community. BMC PLANT BIOLOGY 2024; 24:263. [PMID: 38594616 PMCID: PMC11005247 DOI: 10.1186/s12870-024-04910-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat. RESULTS This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens. CONCLUSION This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.
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Affiliation(s)
- Chong-Die Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Yong-Bin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xue Chen
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jiang-Wei Cao
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Jing-Yi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Meng-Lei Feng
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Xing-Xing Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Wen-Jing Sun
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Rui-Na Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China
| | - Ai-Ying Wang
- College of Life Sciences, Shihezi University, Shihezi, China.
- Key Laboratory of Oasis Town and Mountain-Basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, China.
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13
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Tang Y, Zhou M, Yang C, Liu R, Du H, Ma M. Advances in isolated phages that affect Ralstonia solanacearum and their application in the biocontrol of bacterial wilt in plants. Lett Appl Microbiol 2024; 77:ovae037. [PMID: 38573829 DOI: 10.1093/lambio/ovae037] [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: 01/25/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Bacterial wilt is a widespread and devastating disease that impacts the production of numerous crucial crops worldwide. The main causative agent of the disease is Ralstonia solanacearum. Due to the pathogen's broad host range and prolonged survival in the soil, it is challenging to control the disease with conventional strategies. Therefore, it is of great importance to develop effective alternative disease control strategies. In recent years, phage therapy has emerged as an environmentally friendly and sustainable biocontrol alternative, demonstrating significant potential in controlling this severe disease. This paper summarized basic information about isolated phages that infect R. solanacearum, and presented some examples of their application in the biocontrol of bacterial wilt. The risks of phage application and future prospect in this area were also discussed. Overall, R. solanacearum phages have been isolated from various regions and environments worldwide. These phages belong mainly to the Inoviridae, Autographiviridae, Peduoviridae, and Cystoviridae families, with some being unclassified. Studies on the application of these phages have demonstrated their ability to reduce pathogenicity of R. solanacearum through direct lysis or indirect alteration of the pathogen's physiological properties. These findings suggested bacteriophage is a promising tool for biocontrol of bacterial wilt in plants.
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Affiliation(s)
- You Tang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Moxi Zhou
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Chuyun Yang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Rong Liu
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongyi Du
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Ming Ma
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
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14
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Clough SE, Elphinstone JG, Friman VP. Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria. J Evol Biol 2024; 37:225-237. [PMID: 38290003 DOI: 10.1093/jeb/voae002] [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: 06/26/2023] [Revised: 11/27/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strains and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.
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Affiliation(s)
- Sophie E Clough
- Department of Biology, University of York, York, United Kingdom
- Department of Biosciences, Durham University, Durham, United Kingdom
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - John G Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, York, United Kingdom
| | - Ville-Perti Friman
- Department of Biology, University of York, York, United Kingdom
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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15
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Van Gerrewey T, Navarrete O, Vandecruys M, Perneel M, Boon N, Geelen D. Bacterially enhanced plant-growing media for controlled environment agriculture. Microb Biotechnol 2024; 17:e14422. [PMID: 38380980 PMCID: PMC10880579 DOI: 10.1111/1751-7915.14422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.
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Affiliation(s)
- Thijs Van Gerrewey
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Urban Crop Solutions BVBAWaregemBelgium
- Agaris Belgium NVGentBelgium
| | | | | | - Maaike Perneel
- Cropfit, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
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16
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Pagenkopp Lohan KM, Gignoux-Wolfsohn SA, Ruiz GM. Biodiversity differentially impacts disease dynamics across marine and terrestrial habitats. Trends Parasitol 2024; 40:106-117. [PMID: 38212198 DOI: 10.1016/j.pt.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
The relationship between biodiversity and infectious disease, where increased biodiversity leads to decreased disease risk, originated from research in terrestrial disease systems and remains relatively underexplored in marine systems. Understanding the impacts of biodiversity on disease in marine versus terrestrial systems is key to continued marine ecosystem functioning, sustainable aquaculture, and restoration projects. We compare the biodiversity-disease relationship across terrestrial and marine systems, considering biodiversity at six levels: intraspecific host diversity, host microbiomes, interspecific host diversity, biotic vectors and reservoirs, parasite consumers, and parasites. We highlight gaps in knowledge regarding how these six levels of biodiversity impact diseases in marine systems and propose two model systems, the Perkinsus-oyster and Labyrinthula-seagrass systems, to address these gaps.
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Affiliation(s)
- Katrina M Pagenkopp Lohan
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD 21037, USA.
| | - Sarah A Gignoux-Wolfsohn
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD 21037, USA; Current address: Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Gregory M Ruiz
- Marine Invasions Research Laboratory, Smithsonian Environmental Research Center, Edgewater, MD 21037, USA
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17
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Meshram S, Adhikari TB. Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:364. [PMID: 38337897 PMCID: PMC10856849 DOI: 10.3390/plants13030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.
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Affiliation(s)
- Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara 144402, India;
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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18
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Wang B, Chen C, Xiao Y, Chen K, Wang J, Wang L, Li J, Kang Z, Zhou G. A core root bacteria contribute to plant growth and anisodine accumulation of Anisodus tanguticus. BMC PLANT BIOLOGY 2023; 23:655. [PMID: 38110871 PMCID: PMC10729362 DOI: 10.1186/s12870-023-04690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Although it is well recognized that core root microorganisms contribute to plant health and productivity, little is known about their role to the accumulation of secondary metabolites. The roots of Anisodus tanguticus, a traditional herbal medication utilized by Tibetan medicine, are rich in tropane alkaloids. We collected wild A. tanguticus populations throughout a 1500 km transect on the Qinghai-Tibetan Plateau. RESULTS Our results showed that despite sampling at a distance of 1500 km, the root of A. tanguticus selectively recruits core root bacteria. We obtained 102 root bacterial core OTUs, and although their number only accounted for 2.99% of the total, their relative abundance accounted for 73% of the total. Spearman correlation and random forest analyses revealed that the composition of core root microbiomes was related to anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. Among them, the main role is played by Rhizobacter, Variovorax, Polaromonas, and Mycobacterium genus that are significantly enriched in roots. Functional prediction by FAPROTAX showed that nitrogen-cycling microorganisms and pathogenic bacteria are strongly associated with anisodine contents, aboveground biomass and nitrogen contents of Anisodus tanguticus. CONCLUSIONS Our findings show that the root selectively recruits core root bacteria and revealed that the core microbiomes and microbial functions potentially contributed to the anisodine contents, aboveground biomass and nitrogen contents of the plant. This work may increase our understanding of the interactions between microorganisms and plants and improve our ability to manage root microbiota to promote sustainable production of herbal medicines.
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Affiliation(s)
- Bo Wang
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Chen
- College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Yuanming Xiao
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
| | - Kaiyang Chen
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Wang
- Qinghai University, Xining, 810016, China
| | - Lingling Wang
- Resource institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, 550000, China
| | - Jianan Li
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongxiu Kang
- Datong Beichuan Heyuan District National Nature Reserve, Xining, 810100, China
| | - Guoying Zhou
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, 810008, China.
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19
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Mehlferber EC, Debray R, Conover AE, Sherman JK, Kaulbach G, Reed R, McCue KF, Ferrel JE, Khanna R, Koskella B. Phyllosphere microbial associations improve plant reproductive success. FRONTIERS IN PLANT SCIENCE 2023; 14:1273330. [PMID: 38143578 PMCID: PMC10739325 DOI: 10.3389/fpls.2023.1273330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023]
Abstract
The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.
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Affiliation(s)
- Elijah C. Mehlferber
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Reena Debray
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Asa E. Conover
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Julia K. Sherman
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Griffin Kaulbach
- Department of Environmental Studies, Haverford College, PA, United States
| | - Robert Reed
- i-Cultiver, Inc., Manteca, CA, United States
| | - Kent F. McCue
- Crop Improvement and Genetics Research Unit, Agricultural Research Service, Western Regional Research Center, United States Department of Agriculture, Albany, CA, United States
| | - Jon E. Ferrel
- i-Cultiver, Inc., Manteca, CA, United States
- Azomite Mineral Products, Inc., Nephi, UT, United States
| | - Rajnish Khanna
- i-Cultiver, Inc., Manteca, CA, United States
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Britt Koskella
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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20
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities. PLANTS (BASEL, SWITZERLAND) 2023; 12:4074. [PMID: 38140401 PMCID: PMC10748132 DOI: 10.3390/plants12244074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023]
Abstract
This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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21
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Ma CY, Zhang W, Luo DL, Jiang HJ, Wu XH, Sun K, Dai CC. Fungal endophyte promotes plant growth and disease resistance of Arachis hypogaea L. by reshaping the core root microbiome under monocropping conditions. Microbiol Res 2023; 277:127491. [PMID: 37769598 DOI: 10.1016/j.micres.2023.127491] [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: 06/27/2023] [Revised: 09/03/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Fungal endophytes play critical roles in helping plants adapt to adverse environmental conditions. The root endophyte Phomopsis liquidambaris can promote the growth and disease control of peanut plants grown under monocropping systems; however, how such beneficial traits are produced is largely unknown. Since the plant endophytic microbiome is directly linked to plant growth and health, and the composition of which has been found to be potentially influenced by microbial inoculants, this study aims to clarify the roles of root endophytic bacterial communities in P. liquidambaris-mediated plant fitness enhancement under monocropping conditions. Here, we found that P. liquidambaris inoculation induced significant changes in the root bacterial community: enriching some beneficial bacteria such as Bradyrhizobium sp. and Streptomyces sp. in the roots, and improving the core microbial-based interaction network. Next, we assembled and simplified a synthetic community (SynII) based on P. liquidambaris-derived key taxa, including Bacillus sp. HB1, Bacillus sp. HB9, Burkholderia sp. MB7, Pseudomonas sp. MB2, Streptomyces sp. MB6, and Bradyrhizobium sp. MB15. Furthermore, the application of the simplified synthetic community suppressed root rot caused by Fusarium oxysporum, promoted plant growth, and increased peanut yields under continuous monocropping conditions. The resistance of synII to F. oxysporum is related to the increased activity of defense enzymes. In addition, synII application significantly increased shoot and root biomass, and yield by 35.56%, 81.19%, and 34.31%, respectively. Collectively, our results suggest that the reshaping of root core microbiota plays an important role in the probiotic-mediated adaptability of plants under adverse environments.
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Affiliation(s)
- Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiao-Han Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
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22
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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23
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Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
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24
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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25
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Zayed O, Hewedy OA, Abdelmoteleb A, Ali M, Youssef MS, Roumia AF, Seymour D, Yuan ZC. Nitrogen Journey in Plants: From Uptake to Metabolism, Stress Response, and Microbe Interaction. Biomolecules 2023; 13:1443. [PMID: 37892125 PMCID: PMC10605003 DOI: 10.3390/biom13101443] [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: 08/21/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Plants uptake and assimilate nitrogen from the soil in the form of nitrate, ammonium ions, and available amino acids from organic sources. Plant nitrate and ammonium transporters are responsible for nitrate and ammonium translocation from the soil into the roots. The unique structure of these transporters determines the specificity of each transporter, and structural analyses reveal the mechanisms by which these transporters function. Following absorption, the nitrogen metabolism pathway incorporates the nitrogen into organic compounds via glutamine synthetase and glutamate synthase that convert ammonium ions into glutamine and glutamate. Different isoforms of glutamine synthetase and glutamate synthase exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under stressful conditions, nitric oxide has been found to enhance plant survival under drought stress. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with nitric oxide identified as a potential mediator of responses to salt stress. Conversely, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity.
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Affiliation(s)
- Omar Zayed
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Omar A. Hewedy
- Genetics Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Ali Abdelmoteleb
- Botany Department, Faculty of Agriculture, Menoufia University, Shebin El-Kom 32511, Egypt;
| | - Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo 11753, Egypt;
| | - Mohamed S. Youssef
- Botany and Microbiology Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ahmed F. Roumia
- Department of Agricultural Biochemistry, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514, Egypt;
| | - Danelle Seymour
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 9250, USA;
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
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26
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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27
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Yang K, Fu R, Feng H, Jiang G, Finkel O, Sun T, Liu M, Huang B, Li S, Wang X, Yang T, Wang Y, Wang S, Xu Y, Shen Q, Friman VP, Jousset A, Wei Z. RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota. MOLECULAR PLANT 2023; 16:1379-1395. [PMID: 37563832 DOI: 10.1016/j.molp.2023.08.004] [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: 10/01/2022] [Revised: 05/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The RIPENING-INHIBITOR (RIN) transcriptional factor is a key regulator governing fruit ripening. While RIN also affects other physiological processes, its potential roles in triggering interactions with the rhizosphere microbiome and plant health are unknown. Here we show that RIN affects microbiome-mediated disease resistance via root exudation, leading to recruitment of microbiota that suppress the soil-borne, phytopathogenic Ralstonia solanacearum bacterium. Compared with the wild-type (WT) plant, RIN mutants had different root exudate profiles, which were associated with distinct changes in microbiome composition and diversity. Specifically, the relative abundances of antibiosis-associated genes and pathogen-suppressing Actinobacteria (Streptomyces) were clearly lower in the rhizosphere of rin mutants. The composition, diversity, and suppressiveness of rin plant microbiomes could be restored by the application of 3-hydroxyflavone and riboflavin, which were exuded in much lower concentrations by the rin mutant. Interestingly, RIN-mediated effects on root exudates, Actinobacteria, and disease suppression were evident from the seedling stage, indicating that RIN plays a dual role in the early assembly of disease-suppressive microbiota and late fruit development. Collectively, our work suggests that, while plant disease resistance is a complex trait driven by interactions between the plant, rhizosphere microbiome, and the pathogen, it can be indirectly manipulated using "prebiotic" compounds that promote the recruitment of disease-suppressive microbiota.
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Affiliation(s)
- Keming Yang
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China; College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ruixin Fu
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China; School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China
| | - Haichao Feng
- College of Agriculture, Henan University, Zhengzhou 450046, China
| | - Gaofei Jiang
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Omri Finkel
- Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tianyu Sun
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Mingchun Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Shan Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China.
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Shimei Wang
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China; Department of Biology, University of York, York YO10 5DD, UK; Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China, 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, Jiangsu 210095, China.
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28
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Liu W, Cui X, Wang X, Shen C, Ji L, Zhang M, Wong MH, Zhang J, Shan S. Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere. mSystems 2023; 8:e0019823. [PMID: 37382454 PMCID: PMC10469604 DOI: 10.1128/msystems.00198-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023] Open
Abstract
Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.
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Affiliation(s)
- Wenbo Liu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xin Cui
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xinhai Wang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing, China
| | - Cheng Shen
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Lingfei Ji
- Department of Biology, University of York, Wentworth Way, York, United Kingdom
| | - Min Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Ming Hung Wong
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
- Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
| | - Jin Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
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Liu L, Cheng L, Liu K, Yu T, Liu Q, Gong Z, Cai Z, Liu J, Zhao X, Nian H, Ma Q, Lian T. Transgenic soybean of GsMYB10 shapes rhizosphere microbes to promote resistance to aluminum (Al) toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131621. [PMID: 37187122 DOI: 10.1016/j.jhazmat.2023.131621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Plant resistance genes could affect rhizosphere microbiota, which in turn enhanced plant resistance to stresses. Our previous study found that overexpression of the GsMYB10 gene led to enhanced tolerance of soybean plants to aluminum (Al) toxicity. However, whether GsMYB10 gene could regulate rhizosphere microbiota to mitigate Al toxicity remains unclear. Here, we analyzed the rhizosphere microbiomes of HC6 soybean (WT) and transgenic soybean (trans-GsMYB10) at three Al concentrations, and constructed three different synthetic microbial communities (SynComs), including bacterial, fungal and cross-kingdom (bacteria and fungi) SynComs to verify their role in improving Al tolerance of soybean. Trans-GsMYB10 shaped the rhizosphere microbial communities and harbored some beneficial microbes, such as Bacillus, Aspergillus and Talaromyces under Al toxicity. Fungal and cross-kingdom SynComs showed a more effective role than the bacterial one in resistance to Al stress, and these SynComs helped soybean resist Al toxicity via affecting some functional genes that involved cell wall biosynthesis and organic acid transport etc. Overall, this study reveals the mechanism of soybean functional genes regulating the synergistic resistance of rhizosphere microbiota and plants to Al toxicity, and also highlights the possibility of focusing on the rhizobial microbial community as a potential molecular breeding target to produce crops.
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Affiliation(s)
- Lingrui Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Kun Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Taobing Yu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhihui Gong
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Junjie Liu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Xueqiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China; The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
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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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Benchlih S, Esmaeel Q, Aberkani K, Tahiri A, Belabess Z, Lahlali R, Barka EA. Modes of Action of Biocontrol Agents and Elicitors for sustainable Protection against Bacterial Canker of Tomato. Microorganisms 2023; 11:microorganisms11030726. [PMID: 36985299 PMCID: PMC10054590 DOI: 10.3390/microorganisms11030726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Tomato is one of the world’s most commonly grown and consumed vegetables. However, it can be attacked by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm), which causes bacterial canker on tomato plants, resulting in significant financial losses in field production and greenhouses worldwide. The current management strategies rely principally on the application of various chemical pesticides and antibiotics, which represent a real danger to the environment and human safety. Plant growth-promoting rhizobacteria (PGPR) have emerged as an attractive alternative to agrochemical crop protection methods. PGPR act through several mechanisms to support plant growth and performance, while also preventing pathogen infection. This review highlights the importance of bacterial canker disease and the pathogenicity of Cmm. We emphasize the application of PGPR as an ecological and cost-effective approach to the biocontrol of Cmm, specifying the complex modes of biocontrol agents (BCAs), and presenting their direct/indirect mechanisms of action that enable them to effectively protect tomato crops. Pseudomonas and Bacillus are considered to be the most interesting PGPR species for the biological control of Cmm worldwide. Improving plants’ innate defense mechanisms is one of the main biocontrol mechanisms of PGPR to manage bacterial canker and to limit its occurrence and gravity. Herein, we further discuss elicitors as a new management strategy to control Cmm, which are found to be highly effective in stimulating the plant immune system, decreasing disease severity, and minimizing pesticide use.
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Affiliation(s)
- Salma Benchlih
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km 10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco
- Unité de Recherche Résistance Induite et Bio-Protection des Plantes-EA 4707-USC INRAE1488, Université de Reims Champagne-Ardenne, 51100 Reims, France
- Faculté Poly-Disciplinaire de Nador, University Mohammed Premier, Oujda 60000, Morocco
| | - Qassim Esmaeel
- Unité de Recherche Résistance Induite et Bio-Protection des Plantes-EA 4707-USC INRAE1488, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Kamal Aberkani
- Faculté Poly-Disciplinaire de Nador, University Mohammed Premier, Oujda 60000, Morocco
| | - Abdessalem Tahiri
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km 10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco
| | - Zineb Belabess
- Plant Protection Laboratory, Regional Center of Agricultural Research of Meknes, National Institute of Agricultural Research, Km 13, Route Haj Kaddour, BP.578, Meknes 50001, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknès, Km 10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco
- Correspondence: (R.L.); (E.A.B.)
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-Protection des Plantes-EA 4707-USC INRAE1488, Université de Reims Champagne-Ardenne, 51100 Reims, France
- Correspondence: (R.L.); (E.A.B.)
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Poppeliers SW, Sánchez-Gil JJ, de Jonge R. Microbes to support plant health: understanding bioinoculant success in complex conditions. Curr Opin Microbiol 2023; 73:102286. [PMID: 36878082 DOI: 10.1016/j.mib.2023.102286] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for plant performance and health. When applied in agriculture to improve crop yield and performance, these microbes are commonly referred to as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically in the field, hampering their applicability. Invasion of the rhizosphere microbiome is a critical determinant for bioinoculant success. Invasion is a complex phenomenon that is shaped by interactions with the local, resident microbiome and the host plant. Here, we explore all of these dimensions by cross-cutting ecological theory and molecular biology of microbial invasion in the rhizosphere. We refer to the famous Chinese philosopher and strategist Sun Tzu, who believed that solutions for problems require deep understanding of the problems themselves, to review the major biotic factors determining bioinoculant effectiveness.
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Affiliation(s)
- Sanne Wm Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
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Yang B, Zheng M, Dong W, Xu P, Zheng Y, Yang W, Luo Y, Guo J, Niu D, Yu Y, Jiang C. Plant Disease Resistance-Related Pathways Recruit Beneficial Bacteria by Remodeling Root Exudates upon Bacillus cereus AR156 Treatment. Microbiol Spectr 2023; 11:e0361122. [PMID: 36786562 PMCID: PMC10100852 DOI: 10.1128/spectrum.03611-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
The environmentally friendly biological control strategy that relies on beneficial bacterial inoculants to improve plant disease resistance is a promising strategy. Previously, it has been demonstrated that biocontrol bacteria treatments can change the plant rhizosphere microbiota but whether plant signaling pathways, especially those related to disease resistance, mediate the changes in rhizosphere microbiota has not been explored. Here, we investigated the complex interplay among biocontrol strains, plant disease resistance-related pathways, root exudates, rhizosphere microorganisms, and pathogens to further clarify the biocontrol mechanism of biocontrol bacteria by using plant signaling pathway mutants. Bacillus cereus AR156, which was previously isolated from forest soil by our laboratory, can significantly control tomato bacterial wilt disease in greenhouse and field experiments. Moreover, compared with the control treatment, the B. cereus AR156 treatment had a significant effect on the soil microbiome and recruited 35 genera of bacteria to enrich the rhizosphere of tomato. Among them, the relative rhizosphere abundance of nine genera, including Ammoniphilus, Bacillus, Bosea, Candidimonas, Flexivirga, Brevundimonas, Bordetella, Dyella, and Candidatus_Berkiella, was regulated by plant disease resistance-related signaling pathways and B. cereus AR156. Linear correlation analysis showed that the relative abundances of six genera in the rhizosphere were significantly negatively correlated with pathogen colonization in roots. These rhizosphere bacteria were affected by plant root exudates that are regulated by signaling pathways. IMPORTANCE Our data suggest that B. cereus AR156 can promote the enrichment of beneficial microorganisms in the plant rhizosphere by regulating salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET) signaling pathways in plants, thereby playing a role in controlling bacterial wilt disease. Meanwhile, Spearman correlation analysis showed that the relative abundances of these beneficial bacteria were correlated with the secretion of root exudates. Our study reveals a new mechanism for SA and JA/ET signals to participate in the adjustment of plant resistance whereby the signaling pathways adjust the rhizosphere microecology by changing the root exudates and thus change plant resistance. On the other hand, biocontrol strains can utilize this mechanism to recruit beneficial bacteria by activating disease resistance-related signaling pathways to confine the infection and spread of pathogens. Finally, our data also provide a new idea for the in-depth study of biocontrol mechanisms.
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Affiliation(s)
- Bingye Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Mingzi Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Wenpan Dong
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Peiling Xu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Wei Yang
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake/Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake/Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Jianhua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Yiyang Yu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
| | - Chunhao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
- Engineering Center of Bioresource Pesticide in Jiangsu Province, Nanjing, China
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Lv N, Tao C, Ou Y, Wang J, Deng X, Liu H, Shen Z, Li R, Shen Q. Root-Associated Antagonistic Pseudomonas spp. Contribute to Soil Suppressiveness against Banana Fusarium Wilt Disease of Banana. Microbiol Spectr 2023; 11:e0352522. [PMID: 36786644 PMCID: PMC10100972 DOI: 10.1128/spectrum.03525-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Members of the microbiotas colonizing the plant endophytic compartments and the surrounding bulk and rhizosphere soil play an important role in determining plant health. However, the relative contributions of the soil and endophytic microbiomes and their mechanistic roles in achieving disease suppression remain elusive. To disentangle the relative importance of the different microbiomes in the various plant compartments in inhibiting pathogen infection, we conducted a field experiment to track changes in the composition of microbial communities in bulk and rhizosphere soil and of root endophytes and leaf endosphere collected from bananas planted on Fusarium-infested orchards in disease-suppressive and disease-conducive soils. We found that the rhizosphere and roots were the two dominant plant parts whose bacterial communities contributed to pathogen suppression. We further observed that Pseudomonas was potentially a key organism acting as a pathogen antagonist, as illustrated by microbial community composition and network analysis. Subsequently, culturable pathogen-antagonistic Pseudomonas strains were isolated, and their potential suppressive functions or possible antibiosis in terms of auxin or siderophore synthesis and phosphate solubilization were screened to analyze the mode of action of candidate disease-suppressive Pseudomonas strains. In a follow-up in vivo and greenhouse experiment, we revealed that microbial consortia of culturable Pseudomonas strains P8 and S25 (or S36), isolated from banana plantlet rhizosphere and roots, respectively, significantly suppressed the survival of pathogens in the soil, manipulated the soil microbiome, and stimulated indigenous beneficial microbes. Overall, our study demonstrated that root-associated microbiomes, especially the antagonistic Pseudomonas sp. components, contribute markedly to soil suppression of banana Fusarium wilt. IMPORTANCE Soil suppression of Fusarium wilt disease has been proven to be linked with the local microbial community. However, the contribution of endophytic microbes to disease suppression in wilt-suppressive soils remains unclear. Moreover, the key microbes involving in Fusarium wilt-suppressive soils and in the endophytic populations have not been fully characterized. In this study, we demonstrate that root-associated microbes play vitally important roles in disease suppression. Root-associated Pseudomonas consortia were recognized as a key component in inhibiting pathogen abundance associated with the host banana plants. This finding is crucial to developing alternate strategies for soilborne disease management by harnessing the plant microbiome.
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Affiliation(s)
- Nana Lv
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Yannan Ou
- 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
| | - Jiabao 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of 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, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, Jiangsu, People’s Republic of China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan, People’s Republic of China
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Ren Z, Chen AJ, Zong Q, Du Z, Guo Q, Liu T, Chen W, Gao L. Microbiome Signature of Endophytes in Wheat Seed Response to Wheat Dwarf Bunt Caused by Tilletia controversa Kühn. Microbiol Spectr 2023; 11:e0039022. [PMID: 36625645 PMCID: PMC9927297 DOI: 10.1128/spectrum.00390-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/20/2022] [Indexed: 01/11/2023] Open
Abstract
Wheat dwarf bunt leads to the replacement of seeds with fungal galls containing millions of teliospores of the pathogen Tilletia controversa Kühn. As one of the most devastating internationally quarantined wheat diseases, wheat dwarf bunt spreads to cause distant outbreaks by seeds containing teliospores. In this study, based on a combination of amplicon sequencing and isolation approaches, we analyzed the seed microbiome signatures of endophytes between resistant and susceptible cultivars after infection with T. controversa. Among 310 bacterial species obtained only by amplicon sequencing and 51 species obtained only by isolation, we found 14 overlapping species by both methods; we detected 128 fungal species only by amplicon sequencing, 56 only by isolation, and 5 species by both methods. The results indicated that resistant uninfected cultivars hosted endophytic communities that were much more stable and beneficial to plant health than those in susceptible infected cultivars. The susceptible group showed higher diversity than the resistant group, the infected group showed more diversity than the uninfected group, and the microbial communities in seeds were related to infection or resistance to the pathogen. Some antagonistic microbes significantly suppressed the germination rate of the pathogen's teliospores, providing clues for future studies aimed at developing strategies against wheat dwarf bunt. Collectively, this research advances the understanding of the microbial assembly of wheat seeds upon exposure to fungal pathogen (T. controversa) infection. IMPORTANCE This is the first study on the microbiome signature of endophytes in wheat seed response to wheat dwarf bunt caused by Tilletia controversa Kühn. Some antagonistic microbes suppressed the germination of teliospores of the pathogen significantly, which will provide clues for future studies against wheat dwarf bunt. Collectively, this research first advances the understanding of the microbial assembly of wheat seed upon exposure to the fungal pathogen (T. controversa) infection.
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Affiliation(s)
- Zhaoyu Ren
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Amanda Juan Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, People’s Republic of China
| | - Qianqian Zong
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- Xinjiang Agricultural University, Urumqi, Xinjiang, People’s Republic of China
| | - Zhenzhen Du
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Qingyuan Guo
- Xinjiang Agricultural University, Urumqi, Xinjiang, People’s Republic of China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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Yang K, Wang X, Hou R, Lu C, Fan Z, Li J, Wang S, Xu Y, Shen Q, Friman VP, Wei Z. Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease. MICROBIOME 2023; 11:16. [PMID: 36721270 PMCID: PMC9890766 DOI: 10.1186/s40168-023-01463-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/09/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen. RESULTS Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen. CONCLUSIONS Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.
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Affiliation(s)
- Keming Yang
- Joint International Research Laboratory of Soil Health, 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, China
| | - Xiaofang Wang
- Joint International Research Laboratory of Soil Health, 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, China
| | - Rujiao Hou
- Joint International Research Laboratory of Soil Health, 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, China
| | - Chunxia Lu
- Joint International Research Laboratory of Soil Health, 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, China
| | - Zhe Fan
- Joint International Research Laboratory of Soil Health, 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, China
| | - Jingxuan Li
- Joint International Research Laboratory of Soil Health, 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, China
| | - Shuo Wang
- Joint International Research Laboratory of Soil Health, 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, China
| | - Yangchun Xu
- Joint International Research Laboratory of Soil Health, 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, China
| | - Qirong Shen
- Joint International Research Laboratory of Soil Health, 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, China
| | - Ville-Petri Friman
- Joint International Research Laboratory of Soil Health, 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, China.
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
- Department of Microbiology, University of Helsinki, 00014, Helsinki, Finland.
| | - Zhong Wei
- Joint International Research Laboratory of Soil Health, 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, China.
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Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome. Microorganisms 2023; 11:microorganisms11010224. [PMID: 36677516 PMCID: PMC9867489 DOI: 10.3390/microorganisms11010224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.
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Zhao L, He Y, Zheng Y, Xu Y, Shi S, Fan M, Gu S, Li G, Tianli W, Wang J, Li J, Deng X, Liao X, Du J, Nian F. Differences in soil physicochemical properties and rhizosphere microbial communities of flue-cured tobacco at different transplantation stages and locations. Front Microbiol 2023; 14:1141720. [PMID: 37152740 PMCID: PMC10157256 DOI: 10.3389/fmicb.2023.1141720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/03/2023] [Indexed: 05/09/2023] Open
Abstract
Rhizosphere microbiota play an important role in regulating soil physical and chemical properties and improving crop production performance. This study analyzed the relationship between the diversity of rhizosphere microbiota and the yield and quality of flue-cured tobacco at different transplant times (D30 group, D60 group and D90 group) and in different regions [Linxiang Boshang (BS) and Linxiang ZhangDuo (ZD)] by high-throughput sequencing technology. The results showed that there were significant differences in the physicochemical properties and rhizosphere microbiota of flue-cured tobacco rhizosphere soil at different transplanting times, and that the relative abundance of Bacillus in the rhizosphere microbiota of the D60 group was significantly increased. RDA and Pearson correlation analysis showed that Bacillus, Streptomyces and Sphingomonas were significantly correlated with soil physical and chemical properties. PIGRUSt2 function prediction results showed that compared with the D30 group, the D60 group had significantly increased metabolic pathways such as the superpathway of pyrimidine deoxyribonucleoside salvage, allantoin degradation to glyoxylate III and pyrimidine deoxyribonucleotides de novo biosynthesis III metabolic pathways. The D90 group had significantly increased metabolic pathways such as ubiquitol-8 biosynthesis (prokaryotic), ubiquitol-7 biosynthesis (prokaryotic) and ubiquitol-10 biosynthesis (prokaryotic) compared with the D60 group. In addition, the yield and quality of flue-cured tobacco in the BS region were significantly higher than those in the ZD region, and the relative abundance of Firmicutes and Bacillus in the rhizosphere microbiota of flue-cured tobacco in the BS region at the D60 transplant stage was significantly higher than that in the ZD region. In addition, the results of the hierarchical sample metabolic pathway abundance map showed that the PWY-6572 metabolic pathway was mainly realized by Paenibacillus, and that the relative abundance of flue-cured tobacco rhizosphere microbiota (Paenibacillus) participating in PWY-6572 in the D60 transplant period in the BS region was significantly higher than that in the ZD region. In conclusion, different transplanting periods of flue-cured tobacco have important effects on soil physical and chemical properties and rhizosphere microbial communities. There were significant differences in the rhizosphere microbiota and function of flue-cured tobacco in different regions, which may affect the performance and quality of this type of tobacco.
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Affiliation(s)
- Leifeng Zhao
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuansheng He
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Yuanxian Zheng
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Yinlian Xu
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Shoujie Shi
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Meixun Fan
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Shaolong Gu
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Guohong Li
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Wajie Tianli
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Jiming Wang
- Lincang Branch Company of Yunnan Tobacco Company, Lincang, Yunnan, China
| | - Junying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xiaolin Liao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jun Du
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Jun Du,
| | - Fuzhao Nian
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
- Fuzhao Nian,
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Verma KK, Song XP, Li DM, Singh M, Wu JM, Singh RK, Sharma A, Zhang BQ, Li YR. Silicon and soil microorganisms improve rhizospheric soil health with bacterial community, plant growth, performance and yield. PLANT SIGNALING & BEHAVIOR 2022; 17:2104004. [PMID: 35943127 PMCID: PMC9364706 DOI: 10.1080/15592324.2022.2104004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The interaction of silicon and soil microorganisms stimulates crop enhancement to ensure sustainable agriculture. Silicon may potentially increase nutrient availability in rhizosphere with improved plants' growth, development as it does not produce phytotoxicity. The rhizospheric microbiome accommodates a variety of microbial species that live in a small area of soil directly associated with the hidden half plants' system. Plant growth-promoting rhizobacteria (PGPR) play a major role in plant development in response to adverse climatic conditions. PGPRs may enhance the growth, quality, productivity in variety of crops, and mitigate abiotic stresses by reprogramming stress-induced physiological variations in plants via different mechanisms, such as synthesis of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, exopolysaccharides, volatile organic compounds, atmospheric nitrogen fixation, and phosphate solubilization. Our article eye upon interactions of silicon and plant microbes which seems to be an opportunity for sustainable agriculture for series of crops and cropping systems in years to come, essential to safeguard the food security for masses.
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Affiliation(s)
- Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Dong-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Munna Singh
- Department of Botany, University of Lucknow, Lucknow, India
| | - Jian-Ming Wu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Bao-Qing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
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Zhou X, Wang J, Liu F, Liang J, Zhao P, Tsui CKM, Cai L. Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease. Nat Commun 2022; 13:7890. [PMID: 36550095 PMCID: PMC9780251 DOI: 10.1038/s41467-022-35452-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
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Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Jinting Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, Canada
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, 100101, Beijing, P. R. China.
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Nakayasu M, Takamatsu K, Yazaki K, Sugiyama A. Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms. Biosci Biotechnol Biochem 2022; 87:13-20. [PMID: 36373409 DOI: 10.1093/bbb/zbac181] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Plants interact with microorganisms in the phyllosphere and rhizosphere. Here the roots exude plant specialized metabolites (PSMs) that have diverse biological and ecological functions. Recent reports have shown that these PSMs influence the rhizosphere microbiome, which is essential for the plant's growth and health. This review summarizes several specialized metabolites secreted into the rhizosphere of the tomato plant (Solanum lycopersicum), which is an important model species for plant research and a commercial crop. In this review, we focused on the effects of such plant metabolites on plant-microbe interactions. We also reviewed recent studies on improving the growth of tomatoes by analyzing and reconstructing the rhizosphere microbiome and discussed the challenges to be addressed in establishing sustainable agriculture.
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Affiliation(s)
- Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Kyoko Takamatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan
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Nogalska A, Przemieniecki SW, Krzebietke SJ, Załuski D, Kosewska A, Skwierawska M, Sienkiewicz S. The Effect of Mealworm Frass on the Chemical and Microbiological Properties of Horticultural Peat in an Incubation Experiment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 20:21. [PMID: 36612343 PMCID: PMC9819234 DOI: 10.3390/ijerph20010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Insect farming is growing in popularity, and in addition to insect meal, it generates waste products such as exuviae and frass, which can be recycled in agriculture. The aim of this incubation experiment was to evaluate the effect of Tenebrio molitor L. frass on selected chemical and biological properties of deacidified peat, which is widely used in horticulture. The optimal rate of frass fertilizer in peat for growing vegetables and ornamental plants was determined, with special emphasis on mineral nitrogen levels. Peat was fertilized with five nitrogen rates, 0, 50, 100, 200, and 400 mg dm-3, and supplied with frass or urea. The study demonstrated that frass can be used as organic fertilizer. An increase in the nitrogen rate significantly increased mineral nitrogen content and electrical conductivity and decreased Ca content in peat. Both frass and urea increased the ammonification rate at the beginning of incubation and the nitrification rate from the second week of the experiment. Higher frass rates (5 and 10 g dm-3) increased the content of plant-available nutrients (nitrogen, phosphorus, magnesium, potassium, and sodium) in peat as well as the abundance of microorganisms supporting organic matter mineralization. Unlike frass, urea increased the counts of nitrogen-fixing bacteria in peat.
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Affiliation(s)
- Anna Nogalska
- Department of Agricultural and Environmental Chemistry, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Oczapowskiego 8, 10-719 Olsztyn, Poland
| | - Sebastian Wojciech Przemieniecki
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-719 Olsztyn, Poland
| | - Sławomir Józef Krzebietke
- Department of Agricultural and Environmental Chemistry, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Oczapowskiego 8, 10-719 Olsztyn, Poland
| | - Dariusz Załuski
- Department of Genetics, Plant Breeding and Bioresource Engineering, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-719 Olsztyn, Poland
| | - Agnieszka Kosewska
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-719 Olsztyn, Poland
| | - Małgorzata Skwierawska
- Department of Agricultural and Environmental Chemistry, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Oczapowskiego 8, 10-719 Olsztyn, Poland
| | - Stanisław Sienkiewicz
- Department of Agricultural and Environmental Chemistry, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Oczapowskiego 8, 10-719 Olsztyn, Poland
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Du C, Yang D, Ye Y, Pan L, Zhang J, Jiang S, Fu G. Construction of a compound microbial agent for biocontrol against Fusarium wilt of banana. Front Microbiol 2022; 13:1066807. [PMID: 36605520 PMCID: PMC9807594 DOI: 10.3389/fmicb.2022.1066807] [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: 10/11/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Banana wilt caused by Fusarium oxysporum f. sp. cubense has devastated a large number of banana plantations worldwide. Biological control is a possible method to conquer this disease. However, the control effect was often low and unstable while a single biocontrol strain had been applied in the field. Therefore, this study aimed to construct an effective compound microbial agent to control Fusarium wilt of banana (FWB) in the field. In addition to it, the compounding strategy of combining single strains for improving the control effect was investigated. Based on the compatibility test, five representative biocontrol strains were selected for the combination of all possible permutations. The pot experiment indicated that every biocontrol strain and their 26 combinations could control FWB to varying degrees. The control effect of combinations on FWB was higher than that of a single strain. In terms of the number of combinatorial biocontrol strains, the control effect of the four-strain combinations was the highest. According to the taxonomic differences of the five biocontrol strains, 26 biocontrol strain combinations could be divided into four groups. Among the strains in the combination, the larger the taxonomic differences the more easily it was to obtain a higher control effect. To obtain stable and efficient combinations, eight combinations were selected out and evaluated for their effectiveness in controlling FWB in different type soil. Compared with the other seven combinations, the four-strain combination T28 (Pt05 + Bc11 + Ba62 + gz-2) got the highest and stablest control effect in the four types of soil in greenhouse. And then the control effect of combination T28 was evaluated in field conditions, compared with commercially agents Bacillus subtilis, Trichoderma harzianum, and carbendazim. After four consecutive applications in the field, the control effect of T28 against FWB was the highest, reaching 57.14%. The results showed that combination T28 had a good application prospect, and the finding provided a reference for the construction of compound microbial agents.
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Affiliation(s)
- Chanjuan Du
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Di Yang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunfeng Ye
- Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lianfu Pan
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jin Zhang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shangbo Jiang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Gang Fu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Coker J, Zhalnina K, Marotz C, Thiruppathy D, Tjuanta M, D’Elia G, Hailu R, Mahosky T, Rowan M, Northen TR, Zengler K. A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology. mSystems 2022; 7:e0095122. [PMID: 36472419 PMCID: PMC9765266 DOI: 10.1128/msystems.00951-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.
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Affiliation(s)
- Joanna Coker
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Deepan Thiruppathy
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Megan Tjuanta
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Gavin D’Elia
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Rodas Hailu
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Talon Mahosky
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Meagan Rowan
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
- The DOE Joint Genome Institute, Berkeley Lab, Berkeley, California, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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45
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Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress. Sci Rep 2022; 12:21124. [PMID: 36476722 PMCID: PMC9729608 DOI: 10.1038/s41598-022-25731-z] [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: 04/27/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.
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46
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Hansen ML, Wibowo M, Jarmusch SA, Larsen TO, Jelsbak L. Sequential interspecies interactions affect production of antimicrobial secondary metabolites in Pseudomonas protegens DTU9.1. THE ISME JOURNAL 2022; 16:2680-2690. [PMID: 36123523 PMCID: PMC9666462 DOI: 10.1038/s41396-022-01322-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 12/15/2022]
Abstract
Soil and rhizosphere microbiomes play important roles in suppression of plant pathogens through production of antagonistic secondary metabolites, yet mechanisms that determine the strength of pathogen control are not well understood. Many Pseudomonas species are associated with soil and rhizosphere microbiomes, and their ability to suppress pathogens is well documented. Here, we investigate how interactions within the Pseudomonas genus affect their production of antimicrobial metabolites. From a biosensor-based screen, we identify P. capeferrum species as capable of modulating secondary metabolite production in P. protegens. We show that P. capeferrum alters production of pyoluteorin and 2,4-diacetylphloroglucinol (DAPG) in P. protegens via two distinct and sequential mechanisms that depends on spatial proximity of the two species. Specifically, P. capeferrum secretes a diffusible signal that induce pyoluteorin production up to 100-fold in neighboring P. protegens colonies. In contrast, the interaction results in reduced DAPG production, but only within mixed-species colonies. Additionally, we found that increased pyoluteorin production and cell lysis of P. capeferrum is required for inhibition of DAPG production, suggesting that pyoluteorin-facilitated antibiosis of P. protegens on P. capeferrum leads to release of cell-associated metabolites and subsequent inhibition of DAPG production in P. protegens. As the interaction modulates in vitro bioactivity of the species, genus-specific interactions may assist in improving efficacy of biocontrol strains and consortia.
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Affiliation(s)
- Morten Lindqvist Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs Lyngby, Denmark
| | - Mario Wibowo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs Lyngby, Denmark
| | - Scott Alexander Jarmusch
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800, Kgs Lyngby, Denmark.
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47
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Zhu B, Jia X, Hai X, Zhang Y, Li Q, Ye J, Zhang Q, Li Q. Screening and Identification of p-Hydroxybenzoic Acid-Degrading Strain ZL22 from Wuyi Tea Continuous Cropping Soil. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722100769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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48
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Li M, Pommier T, Yin Y, Cao W, Zhang X, Hu J, Hautier Y, Yang T, Xu Y, Shen Q, Kowalchuk GA, Jousset A, Wei Z. Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions. Environ Microbiol 2022; 24:5680-5689. [PMID: 36053873 DOI: 10.1111/1462-2920.16184] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.
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Affiliation(s)
- Mei Li
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.,Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Yue Yin
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Wenhui Cao
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Xiaohui Zhang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jie Hu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands.,UMR 6553 Ecobio, CNRS-University of Rennes, Rennes Cedex, France
| | - Yann Hautier
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Tianjie Yang
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yangchun Xu
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qirong Shen
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Zhong Wei
- Joint International Research Laboratory of Soil Health, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Bio-interaction and Plant Health, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
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Tian M, Wei S, Bian R, Luo J, Khan HA, Tai H, Kondo H, Hadidi A, Andika IB, Sun L. Natural Cross-Kingdom Spread of Apple Scar Skin Viroid from Apple Trees to Fungi. Cells 2022; 11:cells11223686. [PMID: 36429116 PMCID: PMC9688150 DOI: 10.3390/cells11223686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Viroids are the smallest known infectious agents that are thought to only infect plants. Here, we reveal that several species of plant pathogenic fungi that were isolated from apple trees infected with apple scar skin viroid (ASSVd) carried ASSVd naturally. This finding indicates the spread of viroids to fungi under natural conditions and further suggests the possible existence of mycoviroids in nature. A total of 117 fungal isolates were isolated from ASSVd-infected apple trees, with the majority (85.5%) being an ascomycete Alternaria alternata and the remaining isolates being other plant-pathogenic or -endophytic fungi. Out of the examined samples, viroids were detected in 81 isolates (69.2%) including A. alternata as well as other fungal species. The phenotypic comparison of ASSVd-free specimens developed by single-spore isolation and ASSVd-infected fungal isogenic lines showed that ASSVd affected the growth and pathogenicity of certain fungal species. ASSVd confers hypovirulence on ascomycete Epicoccum nigrum. The mycobiome analysis of apple tree-associated fungi showed that ASSVd infection did not generally affect the diversity and structure of fungal communities but specifically increased the abundance of Alternaria species. Taken together, these data reveal the occurrence of the natural spread of viroids to plants; additionally, as an integral component of the ecosystem, viroids may affect the abundance of certain fungal species in plants. Moreover, this study provides further evidence that viroid infection could induce symptoms in certain filamentous fungi.
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Affiliation(s)
- Mengyuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Shuang Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Ruiling Bian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Jingxian Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Haris Ahmed Khan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Tai
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Ahmed Hadidi
- U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
- Correspondence:
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50
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Zhou N, Mei CM, Zhu XY, Zhao JJ, Ma MG, Li WD. Research progress of rhizosphere microorganisms in Fritillaria L. medicinal plants. Front Bioeng Biotechnol 2022; 10:1054757. [PMID: 36420438 PMCID: PMC9676442 DOI: 10.3389/fbioe.2022.1054757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/25/2022] [Indexed: 12/01/2023] Open
Abstract
The soil's rhizosphere is a highly active place where the exchange of substances and information occurs among plants, soils, and microorganisms. The microorganisms involved are crucial to the activities of plant growth and development, metabolism, and reproduction. Fritillaria L. medicinal plants are unique Chinese medicinal ingredients, but the continuous cropping obstacles formed in the artificial planting process is severely harmful to the growth and development of these medicinal plants. In this review, we summarized the current species and distribution of Fritillaria L. in China, and analyzed the changes in microbial diversity (mainly among bacteria and fungi) in the rhizosphere of these plants under long-term continuous cropping. The fungi showed an increasing trend in the soil rhizosphere, resulting in the transition of the soil from the high-fertility "bacterial type" to the low-fertility "fungal type" as planting years increased. Furthermore, the interaction between Fritillaria L. medicinal plants and the rhizosphere microorganisms was reviewed, and promising applications for the rhizosphere microbiome in the cultivation of Fritillaria L. medicinal plants were suggested. It is expected that this review will facilitate the in-depth understanding of rhizosphere microorganisms in the growth, accumulation of active ingredients, and disease control of Fritillaria L.
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Affiliation(s)
- Nong Zhou
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Chun-Mei Mei
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xing-Yu Zhu
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing-Jing Zhao
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Ming-Guo Ma
- Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-region Drug in the Three Gorges Reservoir Region, College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
- Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing, China
| | - Wei-Dong Li
- College of Pharmacy, Engineering Center of State Ministry of Education for Standardization of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, China
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