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Macharoen P, Mhuantong W, Wannawong T, Leesutthiphonchai W, Tanasupawat S, Suwannarach N, Kuncharoen N. Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand. Folia Microbiol (Praha) 2024; 69:941-952. [PMID: 38315309 DOI: 10.1007/s12223-024-01140-9] [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: 07/18/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024]
Abstract
Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.
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Affiliation(s)
- Pipat Macharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Wuttichai Mhuantong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Thippawan Wannawong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10300, Thailand
| | - Nakarin Suwannarach
- Center Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Khatri S, Bhattacharjee A, Shivay YS, Sharma S. Transplantation of soil from organic field confers disease suppressive ability to conducive soil. World J Microbiol Biotechnol 2024; 40:112. [PMID: 38416182 DOI: 10.1007/s11274-024-03895-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/11/2024] [Indexed: 02/29/2024]
Abstract
Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as "disease-suppressive". The effectiveness of the transformed soil was established with the model plant wheat (Triticum aestivum) grown under natural conditions, with regard to its potential in inhibiting fungal phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The conducive soil inoculated with the disease-suppressive soil performed better than the control conducive soil in terms of reduced disease severity in plants, improved soil nutrient content, increased activity of hydrolytic enzymes, and increased abundance of structural and functional microbial markers. The study demonstrates the efficacy of the soil microbiome under long-term organic agriculture in transforming disease-conducive soil into disease-suppressive soils. Such practises are simple and easy to implement, and could greatly improve the sustainability and crop yield in developing countries.
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Affiliation(s)
- Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Yashbir S Shivay
- Division of Agronomy, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Kang H, Lin Z, Yuan X, Shi Y, Xie X, Li L, Fan T, Li B, Chai A. The occurrence of clubroot in cruciferous crops correlates with the chemical and microbial characteristics of soils. Front Microbiol 2024; 14:1293360. [PMID: 38260873 PMCID: PMC10800485 DOI: 10.3389/fmicb.2023.1293360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Clubroot disease, caused by Plasmodiophora brassicae, is a serious soil-borne disease in Brassica crops worldwide. It seriously occurs in conducive soils of southern China, while never happens in some areas of northern China with suppressive soils. To understanding the differences, we measured the soil suppressiveness, chemical properties, and microbial communities in suppressive and conducive soils by bioassay and sequencing of 16S and 18S rRNA amplicons. The biological basis of clubroot suppressiveness was supported by the ability to remove it by pasteurization. The pH value and calcium content in the suppressive soils were higher than those in the conducive soils. Suppressive soils were associated with higher fungal diversity and bacterial abundance. The fungal phyla Chytridiomycota, Olpidiomycota, and Mucoromycota and the bacterial phyla Acidobacteriota and Gemmatimonadota were enriched in suppressive soils. More abundant beneficial microbes, including Chaetomium and Lysobacter, were found in the suppressive soils than in the conducive soils. Molecular ecological network analysis revealed that the fungal network of suppressive soils was more complex than that of conducive soils. Our results indicate that plant health is closely related to soil physicochemical and biological properties. This study is of great significance for developing strategies for clubtroot disease prevention and control.
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Affiliation(s)
- Huajun Kang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zihan Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tengfei Fan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D. Microbial diversity in soils suppressive to Fusarium diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1228749. [PMID: 38111879 PMCID: PMC10726057 DOI: 10.3389/fpls.2023.1228749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.
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Affiliation(s)
- Irena Todorović
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Aizi T, Lijuan L, Lihua L, Wei L, Jiamei Q. Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest. BMC Genom Data 2023; 24:51. [PMID: 37710149 PMCID: PMC10500862 DOI: 10.1186/s12863-023-01154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng. METHODS Illumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure. RESULTS The species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2 years, 5 years, and 18 years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng. CONCLUSIONS The results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.
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Affiliation(s)
- Tong Aizi
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Lijuan
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Lihua
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Liu Wei
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China
| | - Qin Jiamei
- Key Laboratory of Evaluation and Application of Changbai Mountain Biological Germplasm Resources of Jilin Province, College of Life Science, Tonghua Normal University, Tonghua, 134002, China.
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Yang P, Qu C, Yuan M, Xi B, Jia X, Zhang B, Zhang L. Genetic Basis and Expression Pattern Indicate the Biocontrol Potential and Soil Adaption of Lysobacter capsici CK09. Microorganisms 2023; 11:1768. [PMID: 37512940 PMCID: PMC10384520 DOI: 10.3390/microorganisms11071768] [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: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Lysobacter species have attracted increasing attention in recent years due to their capacities to produce diverse secondary metabolites against phytopathogens. In this research, we analyzed the genomic and transcriptomic patterns of Lysobacter capsici CK09. Our data showed that L. capsici CK09 harbored various contact-independent biocontrol traits, such as fungal cell wall lytic enzymes and HSAF/WAP-8294A2 biosynthesis, as well as several contact-dependent machineries, including type 2/4/6 secretion systems. Additionally, a variety of hydrolytic enzymes, particularly extracellular enzymes, were found in the L. capsici CK09 genome and predicted to improve its adaption in soil. Furthermore, several systems, including type 4 pili, type 3 secretion system and polysaccharide biosynthesis, can provide a selective advantage to L. capsici CK09, enabling the species to live on the surface in soil. The expression of these genes was then confirmed via transcriptomic analysis, indicating the activities of these genes. Collectively, our research provides a comprehensive understanding of the biocontrol potential and soil adaption of L. capsici CK09 and implies the potential of this strain for application in the future.
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Affiliation(s)
- Pu Yang
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Chaofan Qu
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Miaomiao Yuan
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Bo Xi
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Xiu Jia
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, Germany
| | - Ben Zhang
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Lizhen Zhang
- School of Life Science, Shanxi University, Taiyuan 030006, China
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Wen T, Ding Z, Thomashow LS, Hale L, Yang S, Xie P, Liu X, Wang H, Shen Q, Yuan J. Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil. THE NEW PHYTOLOGIST 2023; 238:2634-2650. [PMID: 36932631 DOI: 10.1111/nph.18886] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information needs to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH• ) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system, and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a 'cry for help' case, wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.
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Affiliation(s)
- Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhexu Ding
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164, USA
| | - Lauren Hale
- US Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Avenue, Parlier, CA, 93648, USA
| | - Shengdie Yang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Penghao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Liu
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Heqi Wang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
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Sagova-Mareckova M, Omelka M, Kopecky J. The Golden Goal of Soil Management: Disease-Suppressive Soils. PHYTOPATHOLOGY 2023; 113:741-752. [PMID: 36510361 DOI: 10.1094/phyto-09-22-0324-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.
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Affiliation(s)
- Marketa Sagova-Mareckova
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamycka 129, 165 00, Prague-Suchdol, Czechia
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovska 83, Prague 8, 186 75, Czechia
| | - Jan Kopecky
- Group Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6-Ruzyne, 161 06, Czechia
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Kong HG, Sang MK, An JH, Kim S, Jin YJ, Song J. Changes in the Composition and Microbial Community of the Pepper Rhizosphere in Field with Bacterial Wilt Disease. THE PLANT PATHOLOGY JOURNAL 2022; 38:692-699. [PMID: 36503199 PMCID: PMC9742803 DOI: 10.5423/ppj.nt.09.2022.0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Bacterial wilt caused by Ralstonia solanacearum is considered one of the most harmful diseases of pepper plants. Recently, research on plant disease control through the rhizosphere microbiome has been actively conducted. In this study, the relationship with disease occurrence between the neighboring plant confirmed by analyzing the physicochemical properties of the rhizosphere soil and changes in the microbial community. The results confirmed that the microbial community changes significantly depending on the organic matters, P2O5, and clay in the soil. Despite significant differences in microbial communities according to soil composition, Actinobacteriota at the phylum level was higher in healthy plant rhizosphere (mean of relative abundance, D: 8.05 ± 1.13; H: 10.06 ± 1.59). These results suggest that Actinobacteriota may be associated with bacterial wilt disease. In this study, we present basic information for constructing of healthy soil in the future by presenting the major microbial groups that can suppress bacterial wilt.
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Affiliation(s)
- Hyun Gi Kong
- Department of Plant Medicine, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644,
Korea
| | - Mee Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Ju Hee An
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Songhwa Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Yong Ju Jin
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365,
Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365,
Korea
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Shi H, Xu P, Wu S, Yu W, Cheng Y, Chen Z, Yang X, Yu X, Li B, Ding A, Wang W, Sun Y. Analysis of rhizosphere bacterial communities of tobacco resistant and non-resistant to bacterial wilt in different regions. Sci Rep 2022; 12:18309. [PMID: 36316337 PMCID: PMC9622857 DOI: 10.1038/s41598-022-20293-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Tobacco bacterial wilt has seriously affected tobacco production. Ethyl methanesulfonate (EMS) induced tobacco bacterial wilt resistant mutants are important for the control of tobacco bacterial wilt. High-throughput sequencing technology was used to study the rhizosphere bacterial community assemblages of bacterial wilt resistant mutant tobacco rhizosphere soil (namely KS), bacterial wilt susceptible tobacco rhizosphere soil (namely GS) and bulk soil (namely BS) in Xuancheng, Huanxi, Yibin and Luzhou. Alpha analysis showed that the bacterial community diversity and richness of KS and GS in the four regions were not significantly different. However, analysis of intergroup variation in the top 15 bacterial communities in terms of abundance showed that the bacterial communities of KS and GS were significantly different from BS, respectively. In addition, pH, alkali-hydrolysable nitrogen (AN) and soil organic carbon (SOC) were positively correlated with the bacterial community of KS and negatively correlated with GS in the other three regions except Huanxi. Network analysis showed that the three soils in the four regions did not show a consistent pattern of network complexity. PICRUSt functional prediction analysis showed that the COG functions were similar in all samples. All colonies were involved in RNA processing and modification, chromatin structure and dynamics, etc. In conclusion, our experiments showed that rhizosphere bacterial communities of tobacco in different regions have different compositional patterns, which are strongly related to soil factors.
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Affiliation(s)
- Haoqi Shi
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Peiwen Xu
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shengxin Wu
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Wen Yu
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Yazhi Cheng
- Fujian Institute of Tobacco Agricultural Sciences, Fuzhou, 350003 China
| | - Zhihua Chen
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Xingyou Yang
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Xiangwen Yu
- Sichuan Tobacco Science Institute, Sichuan Branch of China National Tobacco Corporation, Chengdu, 615000 China
| | - Bingjie Li
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Anming Ding
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
| | - Weifeng Wang
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
| | - Yuhe Sun
- grid.464493.80000 0004 1773 8570Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101 China
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11
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Liu X, Liu L, Gong J, Zhang L, Jiang Q, Huang K, Ding W. Soil conditions on bacterial wilt disease affect bacterial and fungal assemblage in the rhizosphere. AMB Express 2022; 12:110. [PMID: 36036292 PMCID: PMC9424452 DOI: 10.1186/s13568-022-01455-1] [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: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
Natural soil has the ability to suppress the soil-borne pathogen to a certain extent, and the assemblage of soil microbiome plays a crucial role in maintaining such ability. Long-term monoculture accelerates the forms of soil microbiome and leads to either disease conducive or suppressive soils. Here, we explored the impact of soil conditions on bacterial wilt disease (healthy or diseased) under long-term tobacco monoculture on the assemblage of bacterial and fungal communities in bulk and rhizosphere soils during the growth periods. With Illumina sequencing, we compared the bacterial and fungal composition of soil samples from tobacco bacterial wilt diseased fields and healthy fields in three growth periods. We found that Proteobacteria and Ascomycota were the most abundant phylum for bacteria and fungi, respectively. Factors of soil conditions and tobacco growth periods can significantly influence the microbial composition in bulk soil samples, while the factor of soil conditions mainly determined the microbial composition in rhizosphere soil samples. Next, rhizosphere samples were further analyzed with LEfSe to determine the discriminative taxa affected by the factor of soil conditions. For bacteria, the genus Ralstonia was found in the diseased soils, whereas the genus Flavobacterium was the only shared taxon in healthy soils; for fungi, the genus Chaetomium was the most significant taxon in healthy soils. Besides, network analysis confirmed that the topologies of networks of healthy soils were higher than that of diseased soils. Together, our results suggest that microbial assemblage in the rhizosphere will be largely affected by soil conditions especially after long-term monoculture.
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Affiliation(s)
- Xiaojiao Liu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding in Ministry of Agriculture, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, 400715, China.,Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Liehua Liu
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Jie Gong
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Lixin Zhang
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Qipeng Jiang
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Kuo Huang
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China.,Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Henan, 450001, China
| | - Wei Ding
- Microecological Process and Regulation Key Laboratory, College of Plant Protection, Southwest University, Chongqing, 400715, China.
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12
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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13
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Su D, Chen S, Zhou W, Yang J, Luo Z, Zhang Z, Tian Y, Dong Q, Shen X, Wei S, Tong J, Cui X. Comparative Analysis of the Microbial Community Structures Between Healthy and Anthracnose-Infected Strawberry Rhizosphere Soils Using Illumina Sequencing Technology in Yunnan Province, Southwest of China. Front Microbiol 2022; 13:881450. [PMID: 35651487 PMCID: PMC9149601 DOI: 10.3389/fmicb.2022.881450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Anthracnose caused by Colletotrichum spp. was widespread in recent years and resulted in great damage to strawberry production. Soil microbial communities were key contributors to host nutrition, development, and immunity; however, the difference between the microbial communities of healthy and anthracnose-infected strawberry rhizosphere soils remains unclear. In this study, the Illumina sequencing technique was used to comparatively study the prokaryotic and fungal community compositions and structures between healthy and anthracnose-infected strawberry rhizosphere soils in Yuxi, Yunnan Province. Both microbial community diversities and richness of anthracnose-infected strawberry rhizosphere soils were higher than those of healthy strawberry rhizosphere soils. A total of 2,518 prokaryotic and 556 fungal operational taxonomic units (OTUs) were obtained at the 97% similarity threshold. Proteobacteria, Thaumarchaeota, and Acidobacteria were the dominant prokaryotic phyla; Ascomycota, unclassified_k__Fungi, and Mortierellomycota were the dominant fungal phyla. The relative abundances of beneficial bacterial phyla Actinobacteria and Firmicutes, genera Streptomyces, Azospirillum, and Bacillus were significantly reduced in anthracnose-infected strawberry rhizosphere soils; the relative abundance of beneficial fungal species Trichoderma asperellum shows a similar tendency with bacterial abundance. Besides Colletotrichum, 15 other potential fungal pathogen genera and seven fungal pathogen species were identified; among the potential pathogen genera and species, eight pathogen genera and Fusarium oxysporum showed significant differences between healthy and anthracnose-infected strawberry rhizosphere soils. The results suggested that strawberry planted in this area may be infected by other fungal pathogens except for Colletotrichum spp. Our present research will provide theoretical basis and data reference for the isolation and identification of strawberry pathogens and potential probiotics in future works.
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Affiliation(s)
- Daifa Su
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Shanyan Chen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Wenxing Zhou
- Kunming Academy of Agricultural Science, Kunming, China
| | - Junyu Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Zhiwei Luo
- Kunming Academy of Agricultural Science, Kunming, China
| | | | - Yunxia Tian
- Kunming Academy of Agricultural Science, Kunming, China
| | - Qionge Dong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Xuemei Shen
- Kunming Academy of Agricultural Science, Kunming, China
| | - Shijie Wei
- Kunming Academy of Agricultural Science, Kunming, China
| | - Jiangyun Tong
- Kunming Academy of Agricultural Science, Kunming, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
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14
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Xiang F, Sheng J, Li G, Ma J, Wang X, Jiang C, Zhang Z. Black soldier fly larvae vermicompost alters soil biochemistry and bacterial community composition. Appl Microbiol Biotechnol 2022; 106:4315-4328. [PMID: 35595931 DOI: 10.1007/s00253-022-11947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 11/02/2022]
Abstract
Black soldier fly larvae (Hermetia illucens L. BSFL) bioconversion is a promising biotechnology for food waste recycling, yet little is known about how BSFL vermicompost affects soil health in terms of element availability and related microbial response. In this work, a field soil experiment for luffa (Luffa cylindrica (L.) Roem.) growth was conducted to examine the impacts of BSFL vermicompost (BV, 9750 kg ha-1, equal to total N input rate of chemically treated soil (CK)) on soil biochemistry and bacterial communities. Relative to CK, application of BV significantly increased total soil carbon by 149% and enhanced catalase and urease activity by 59.2% and 16.2%, respectively. BV increased the degree of aromaticity and humification in dissolved organic matter (DOM) in soil by 28.6% and 27.3%, respectively, compared to CK treatment. Among bacterial communities in soil, Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria were the phyla that showed the most substantial alteration in response to BV. Redundancy analysis further revealed that the bacterial community structure was affected by DOM and total phosphorus. Functional analyses indicated that BV enhanced xylanolysis (55.4%) and nitrogen fixation (46.3%), but inhibited nitrification (59.8%). BSFL vermicompost input might effectively prevent the harm of soil borne pathogens (e.g., wilt). Moreover, these function groups strongly correlated with Clostridiales, Actinomycetales, and Nitrospirales. Our study reveals that BSFL vermicompost promoted soil nutrient availability, microbial community succession, and biochemical function optimization, which is conducive to the popularization and application of BSFL vermicompost in the field of soil health. KEY POINTS: • Vermicompost enhanced catalase and urease levels while increased DOM aromaticity. • Vermicompost enriched Bacteroidetes and Firmicutes and improved soil health.
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Affiliation(s)
- FangMing Xiang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China
| | - JianLin Sheng
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - Gang Li
- Yangtze Delta Region Healthy Agriculture Institute, TongXiang Economic HiTech Zone, Building 12#, Development Ave 133, TongXiang, 314515, People's Republic of China
| | - JingJin Ma
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China.,HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China
| | - XianZhe Wang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - ChengLiang Jiang
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - ZhiJian Zhang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China. .,China Academy of West Region Development, ZheJiang University, YuHangTang Ave 866, HangZhou, 310058, People's Republic of China.
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15
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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16
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Wu X, Wu C, Lu D, Wu Y, Ye Z, Xia L, Sun Y, Bao E, Ye L, Tang Y, Cao K. Variation of Soil Microbial Community and Sterilization to Fusarium oxysporum f. sp. niveum Play Roles in Slightly Acidic Electrolyzed Water-Alleviated Watermelon Continuous Cropping Obstacle. Front Microbiol 2022; 13:837121. [PMID: 35572699 PMCID: PMC9097028 DOI: 10.3389/fmicb.2022.837121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
It is critical to exploit technologies for alleviating watermelon continuous cropping obstacle which frequently occurs and results in the limiting production and economic losses of watermelon. This study aimed to explore the effects of slightly acidic electrolyzed water (SAEW) on watermelon continuous cropping obstacles. The results showed that SAEW significantly improved the growth of watermelon seedlings cultivated in continuous cropping soil and caused a mass of changes to the diversity of the soil microbial community. Compared with Con, SAEW decreased the diversity index of bacteria by 2%, 0.48%, and 3.16%, while it increased the diversity index of fungus by 5.68%, 10.78%, and 7.54% in Shannon, Chao1, and ACE index, respectively. Besides, the enrichment level of Fusarium oxysporum f. sp. niveum (FON) was remarkably downregulated by 50.2% at 14 days of SAEW treatment, which could decrease the incidence of Fusarium wilt disease. The wet and dry weights of FON mycelia in the fluid medium were depressed more than 93%, and the number of FON colonies in continuous cropping soil was reduced by 83.56% with SAEW treatment. Additionally, a strong correlation between watermelon, FON, and SAEW was presented by correlation analysis. Furthermore, the content of endogenous reactive oxygen species (ROS) was over quadruply increased by SAEW, which may contribute to the sterilizing effect of SAEW on FON. Taken together, our findings demonstrated that exogenous SAEW could alter the soil microbial diversity and decrease the accumulation of FON, which improved the growth of watermelon seedlings and finally alleviated continuous cropping obstacles of watermelon.
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Affiliation(s)
- Xue Wu
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Cuinan Wu
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Daipeng Lu
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yiwen Wu
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhangying Ye
- School of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Liru Xia
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Yudong Sun
- Jiangsu Xuhuai Region Huaiyin Institute of Agricultural Science, Huai’an, China
| | - Encai Bao
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Lin Ye
- Agriculture College, Ningxia University, Yingchuan, China
| | - Yuxin Tang
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Kai Cao
- The Agriculture Ministry Key Laboratory of Agricultural Engineering in the Middle and Lower Reaches of Yangtze River, Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
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17
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Leitão F, Pinto G, Amaral J, Monteiro P, Henriques I. New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker. TREE PHYSIOLOGY 2022; 42:600-615. [PMID: 34508603 DOI: 10.1093/treephys/tpab119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 05/24/2023]
Abstract
The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant growth promoting (PGP) traits and/or anti-fungal activity. Plants of this species also displayed higher levels of phenolic compounds. F. circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants' resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.
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Affiliation(s)
- Frederico Leitão
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Glória Pinto
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Joana Amaral
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Pedro Monteiro
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Faculty of Science and Technology, Department of Life Sciences and CESAM, University of Coimbra, Coimbra, Portugal
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18
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Jiang G, Zhang Y, Gan G, Li W, Wan W, Jiang Y, Yang T, Zhang Y, Xu Y, Wang Y, Shen Q, Wei Z, Dini-Andreote F. Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation. ISME COMMUNICATIONS 2022; 2:10. [PMID: 37938685 PMCID: PMC9723603 DOI: 10.1038/s43705-022-00094-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 04/20/2023]
Abstract
The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.
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Affiliation(s)
- Gaofei Jiang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yuling Zhang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wen Wan
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Tianjie Yang
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yong Zhang
- College of Resources and Environment, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Yangchun Xu
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China.
| | - Qirong Shen
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Zhong Wei
- Laboratory of Bio-interactions and Crop Health, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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19
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Uwaremwe C, Yue L, Wang Y, Tian Y, Zhao X, Liu Y, Zhou Q, Zhang Y, Wang R. An Endophytic Strain of Bacillus amyloliquefaciens Suppresses Fusarium oxysporum Infection of Chinese Wolfberry by Altering Its Rhizosphere Bacterial Community. Front Microbiol 2022; 12:782523. [PMID: 35069484 PMCID: PMC8767019 DOI: 10.3389/fmicb.2021.782523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Root rot disease is a serious infection leading to production loss of Chinese wolfberry (Lycium barbarum). This study tested the potential for two bacterial biological control agents, Bacillus amyloliquefaciens HSB1 and FZB42, against five fungal pathogens that frequently cause root rot in Chinese wolfberry. Both HSB1 and FZB42 were found to inhibit fungal mycelial growth, in vitro and in planta, as well as to promote the growth of wolfberry seedlings. In fact, a biocontrol experiment showed efficiency of 100% with at least one treatment involving each biocontrol strain against Fusarium oxysporum. Metagenomic sequencing was used to assess bacterial community shifts in the wolfberry rhizosphere upon introduction of each biocontrol strain. Results showed that HSB1 and FZB42 differentially altered the abundances of different taxa present and positively influenced various functions of inherent wolfberry rhizosphere bacteria. This study highlights the application of biocontrol method in the suppression of fungal pathogens that cause root rot disease in wolfberry, which is useful for agricultural extension agents and commercial growers.
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Affiliation(s)
- Constantine Uwaremwe
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences (CAS), Mengla, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Yue
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun Wang
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China
| | - Yuan Tian
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xia Zhao
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qin Zhou
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yubao Zhang
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ruoyu Wang
- Gaolan Station of Agricultural and Ecological Experiment, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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20
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Pacheco-Moreno A, Stefanato FL, Ford JJ, Trippel C, Uszkoreit S, Ferrafiat L, Grenga L, Dickens R, Kelly N, Kingdon AD, Ambrosetti L, Nepogodiev SA, Findlay KC, Cheema J, Trick M, Chandra G, Tomalin G, Malone JG, Truman AW. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition. eLife 2021; 10:71900. [PMID: 34792466 PMCID: PMC8719888 DOI: 10.7554/elife.71900] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs. Potato scab and blight are two major diseases which can cause heavy crop losses. They are caused, respectively, by the bacterium Streptomyces scabies and an oomycete (a fungus-like organism) known as Phytophthora infestans. Fighting these disease-causing microorganisms can involve crop management techniques – for example, ensuring that a field is well irrigated helps to keep S. scabies at bay. Harnessing biological control agents can also offer ways to control disease while respecting the environment. Biocontrol bacteria, such as Pseudomonas, can produce compounds that keep S. scabies and P. infestans in check. However, the identity of these molecules and how irrigation can influence Pseudomonas population remains unknown. To examine these questions, Pacheco-Moreno et al. sampled and isolated hundreds of Pseudomonas strains from a commercial potato field, closely examining the genomes of 69 of these. Comparing the genetic information of strains based on whether they could control the growth of S. scabies revealed that compounds known as cyclic lipopeptides are key to controlling the growth of S. scabies and P. infestans. Whether the field was irrigated also had a large impact on the strains forming the Pseudomonas population. Working out how Pseudomonas bacteria block disease could speed up the search for biological control agents. The approach developed by Pacheco-Moreno et al. could help to predict which strains might be most effective based on their genetic features. Similar experiments could also work for other combinations of plants and diseases.
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Affiliation(s)
- Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jonathan J Ford
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Christine Trippel
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Simon Uszkoreit
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Laura Ferrafiat
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Lucia Grenga
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Ruth Dickens
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nathan Kelly
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alexander Dh Kingdon
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Liana Ambrosetti
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, United Kingdom
| | - Kim C Findlay
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, United Kingdom
| | - Jitender Cheema
- Department of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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21
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Huang Y, Wang HC, Cai LT, Li W, Pan D, Xiang L, Su X, Li Z, Adil MF, Shamsi IH. Phyllospheric Microbial Composition and Diversity of the Tobacco Leaves Infected by Didymella segeticola. Front Microbiol 2021; 12:699699. [PMID: 34721315 PMCID: PMC8551862 DOI: 10.3389/fmicb.2021.699699] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
A Myriad of biotic and abiotic factors inevitably affects the growth and production of tobacco (Nicotiana tabacum L.), which is a model crop and sought-after worldwide for its foliage. Among the various impacts the level of disease severity poses on plants, the influence on the dynamics of phyllospheric microbial diversity is of utmost importance. In China, recurring reports of a phyto-pathogen, Didymella segeticola, a causal agent of tobacco leaf spot, accentuate the need for its in-depth investigation. Here, a high-throughput sequencing technique, IonS5TMXL was employed to analyze tobacco leaves infected by D. segeticola at different disease severity levels, ranging from T1G (least disease index) to T4G (highest disease index), in an attempt to explore the composition and diversity of phyllospheric microbiota. In all healthy and diseased tobacco leaves, the most dominant fungal phylum was Ascomycota with a high prevalence of genus Didymella, followed by Boeremia, Meyerozyma and Alternaria, whereas in the case of bacterial phyla, Proteobacteria was prominent with Pseudomonas being a predominant genus, followed by Pantoea. The relative abundance of fungi, i.e., Didymella and Boeremia (Ascomycota) and bacteria, i.e., Pseudomonas and Pantoea (Proteobacteria) were higher in diseased groups compared to healthy groups. Healthy tissues exhibited relatively rich and diverse fungal communities in contrast with diseased groups. The infection of D. segeticola had a complex and significant effect on fungal as well as bacterial alpha diversity. FUNGuild analysis indicated that the relative abundance of pathotrophs and saprotrophs in diseased tissues proportionally increased with disease severity. PICRUSt analysis of diseased tissues indicated that the relative abundance of bacterial cell motility and membrane transport-related gene sequences elevated with an increase in disease severity from T1G to T3G and then tended to decrease at T4G. Conclusively, the current study shows the typical characteristics of the tobacco leaf microbiome and provides insights into the distinct microbiome shifts on tobacco leaves infected by D. segeticola.
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Affiliation(s)
- Yu Huang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China.,College of Agriculture, Guizhou University, Guiyang, China
| | - Han-Cheng Wang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liu-Ti Cai
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Wenhong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Daiwei Pan
- Faculty of Science, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Ligang Xiang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiankun Su
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Zhong Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Muhammad Faheem Adil
- Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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22
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Durán P, Tortella G, Sadowsky MJ, Viscardi S, Barra PJ, Mora MDLL. Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change. BIOLOGY 2021; 10:865. [PMID: 34571742 PMCID: PMC8472835 DOI: 10.3390/biology10090865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.
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Affiliation(s)
- Paola Durán
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Gonzalo Tortella
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile;
| | - Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, Minneapolis, MN 55108, USA;
| | - Sharon Viscardi
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, P.O. Box 15-D, Temuco 4813302, Chile;
| | - Patricio Javier Barra
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Maria de la Luz Mora
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
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23
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Wang Z, Li Y, Zhao Y, Zhuang L, Yu Y, Wang M, Liu J, Wang Q. A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms. Microb Biotechnol 2021; 14:1961-1975. [PMID: 34231972 PMCID: PMC8449676 DOI: 10.1111/1751-7915.13876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/01/2022] Open
Abstract
The effect of a microbial consortium-based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha-1 ) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon-degrading and nitrogen metabolism properties were observed in the MCB product-treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product-treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.
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Affiliation(s)
- Zhenshuo Wang
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Yan Li
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Yu Zhao
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Lubo Zhuang
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Yue Yu
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Mengyao Wang
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant BiotechnologyCollege of Landscape Architecture and Life Science/Institute of Special PlantsChongqing University of Arts and SciencesYongchuan, Chongqing402160China
| | - Qi Wang
- Department of Plant PathologyMOA Key Lab of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijing100193China
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24
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Du JX, Li Y, Ur-Rehman S, Mukhtar I, Yin Z, Dong H, Wang H, Zhang X, Gao Z, Zhao X, Xin X, Ding X. Synergistically promoting plant health by harnessing synthetic microbial communities and prebiotics. iScience 2021; 24:102918. [PMID: 34430808 PMCID: PMC8365361 DOI: 10.1016/j.isci.2021.102918] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Soil-borne diseases cause serious economic losses in agriculture. Managing diseases with microbial preparations is an excellent approach to soil-borne disease prevention. However, microbial preparations often exhibit unstable effects, limiting their large-scale application. This review introduces and summarizes disease-suppressive soils, the relationship between carbon sources and the microbial community, and the application of human microbial preparation concepts to plant microbial preparations. We also propose an innovative synthetic microbial community assembly strategy with synergistic prebiotics to promote healthy plant growth and resistance to disease. In this review, a new approach is proposed to improve traditional microbial preparations; provide a better understanding of the relationships among carbon sources, beneficial microorganisms, and plants; and lay a theoretical foundation for developing new microbial preparations.
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Affiliation(s)
- Jianfeng X. Du
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Saif- Ur-Rehman
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Irum Mukhtar
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Hansong Dong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
| | - Hongfeng Wang
- Shandong Pengbo Biotechnology Co., LTD, Taian 271018, China
| | - Xiaoying Zhang
- Shandong Pengbo Biotechnology Co., LTD, Taian 271018, China
| | - Zheng Gao
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, P.R. China
| | - Xiangyu Zhao
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, P.R. China
| | - Xiufang Xin
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Science and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial Sciences, Shanghai, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, Shandong 271018, P. R. China
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25
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Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production. Microorganisms 2021; 9:microorganisms9081660. [PMID: 34442738 PMCID: PMC8400219 DOI: 10.3390/microorganisms9081660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022] Open
Abstract
Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production.
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26
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Shen X, Wang B, Yang N, Zhang L, Shen D, Wu H, Dong Y, Niu B, Chou SH, Puopolo G, Fan J, Qian G. Lysobacter enzymogenes antagonizes soilborne bacteria using the type IV secretion system. Environ Microbiol 2021; 23:4673-4688. [PMID: 34227200 DOI: 10.1111/1462-2920.15662] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 07/03/2021] [Indexed: 12/23/2022]
Abstract
Soil microbiome comprises numerous microbial species that continuously interact with each other. Among the modes of diverse interactions, cell-cell killing may play a key role in shaping the microbiome composition. Bacteria deploy various secretion systems to fend off other microorganisms and Type IV Secretion System (T4SS) in pathogenic bacteria was shown to function as a contact-dependent, inter-bacterial killing system only recently. The present study investigated the role played by T4SS in the killing behaviour of the soilborne biocontrol bacterium Lysobacter enzymogenes OH11. Results showed that L. enzymogenes OH11 genome encompasses genes encoding all the components of T4SS and effectors potentially involved in inter-bacterial killing system. Generation of knock-out mutants revealed that L. enzymogenes OH11 uses T4SS as the main contact-dependent weapon against other soilborne bacteria. The T4SS-mediated killing behaviour of L. enzymogenes OH11 decreased the antibacterial and antifungal activity of two Pseudomonas spp. but at the same time, protected carrot from infection by Pectobacterium carotovorum. Overall, this study showed for the first time the involvement of T4SS in the killing behaviour of L. enzymogenes and its impact on the multiple interactions occurring in the soil microbiome.
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Affiliation(s)
- Xi Shen
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxin Wang
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Nianda Yang
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Lulu Zhang
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Danyu Shen
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Huijun Wu
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Dong
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Ben Niu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Gerardo Puopolo
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, 38098, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, San Michele all'Adige, 38098, Italy
| | - Jiaqin Fan
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
| | - Guoliang Qian
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, China
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27
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An Examination of Fungal and Bacterial Assemblages in Bulk and Rhizosphere Soils under Solanum tuberosum in Southeastern Wyoming, USA. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Solanum tuberosum, commonly known as potato, is the most important non-cereal crop in the world. However, its cultivation is prone to disease and other issues. In recent years, a newfound interest in the soil microbiome and the potential benefits it may convey has led researchers to study plant–microbe interactions in great detail and has led to the identification of putative beneficial microbial taxa. In this survey, we examined fungal and bacterial diversity using high-throughput sequencing in soils under a potato crop in southeastern Wyoming, USA. Our results show decreased microbial diversity in the rhizosphere, with increases in the abundances of arbuscular mycorrhizal fungi as well as pathogenic microbes. We show coarse taxonomic differences in microbial assemblages when comparing the bulk and rhizosphere soils for bacteria but not for fungi, suggesting that the two kingdoms respond differently to the selective pressures of the rhizosphere. Using cooccurrence network analysis, we identify microbes that may serve as keystone taxa and provide benefits to their host plants through competitive exclusion of detrimental pathogenic taxa and increased nutrient availability. Our results provide additional information on the structure and complexity of the potato rhizosphere microbiome and highlight candidate taxa for microbial isolation and inoculation.
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28
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Zhang X, Xue C, Fang D, He X, Wei M, Zhuo C, Jin J, Shen B, Li R, Ling N, Shen Q. Manipulating the soil microbiomes during a community recovery process with plant beneficial species for the suppression of Fusarium wilt of watermelon. AMB Express 2021; 11:87. [PMID: 34117935 PMCID: PMC8197695 DOI: 10.1186/s13568-021-01225-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/28/2021] [Indexed: 11/30/2022] Open
Abstract
Fusarium wilt is a devastating disease which impacts watermelon production. Soil fumigation using dazomet followed by biological organic fertilizer was applied to suppress the Fusarium wilt disease. We propose that fumigation suppresses the soil indigenous community, especially the soil-borne pathogens, while the utilization of bio-organic fertilizer facilitates the recovery of the soil microbiome to a beneficial, suppressive state through the introduction of plant growth-promoting microorganisms. Greenhouse experiment showed that applied biological organic fertilizer after dazomet fumigation effective restrain the disease incidence with a 93.6% disease control. Fumigation strongly decreased soil microbial diversity and altered relative taxa abundances, suggesting the possibility of niche release by the resident soil microbial community. Fumigation followed by bio-fertilizer transformed the soil microbial community composition and resulted in higher relative abundances of beneficial microbial groups such as Bacillus (8.5%) and Trichoderma (13.5%), coupled with lower Fusarium abundance compared to other treatments. Network analysis illustrated that soil fumigation decreased interactions within the soil microbial community with less nodes and links while bio-fertilizer addition promoted node interactions. In addition, bio-fertilizer addition after fumigation resulted in the beneficial species becoming the key network connectors. Collectively, fumigation appears to release the resident soil niche resulting in lower diversity while the beneficial microbes introduced by bio-fertilizer addition colonize these niches, leading to a more complex community with fewer pathogens that suppresses Fusarium wilt disease incidence.
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29
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Shi W, Su G, Li M, Wang B, Lin R, Yang Y, Wei T, Zhou B, Gao Z. Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab. Front Microbiol 2021; 12:616013. [PMID: 33633704 PMCID: PMC7900429 DOI: 10.3389/fmicb.2021.616013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/13/2021] [Indexed: 11/24/2022] Open
Abstract
The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Gaoya Su
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Yutian Yang
- Agriculture Research Institute of Zaozhuang, Zaozhuang, China
| | - Tao Wei
- Agriculture Research Institute of Zaozhuang, Zaozhuang, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, China.,National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, China
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China.,College of Life Sciences, Shandong Agricultural University, Tai'an, China
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Tong AZ, Liu W, Liu Q, Xia GQ, Zhu JY. Diversity and composition of the Panax ginseng rhizosphere microbiome in various cultivation modesand ages. BMC Microbiol 2021; 21:18. [PMID: 33419388 PMCID: PMC7792351 DOI: 10.1186/s12866-020-02081-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
Background Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored. Methods Amplicon sequencing of bacterial 16S rRNA genes and fungal ITS regions were analyzed for microbial community composition and diversity. Results The obtained sequencing data were reasonable for estimating soil microbial diversity. We observed significant variations in richness, diversity, and relative abundances of microbial taxa between farmland, deforestation field, and different cultivation years. The bacterial communities of LCK (forest soil where P. ginseng was not grown) had a much higher richness and diversity than those in NCK (farmland soil where P. ginseng was not grown). The increase in cultivation years of P. ginseng in farmland and deforestation field significantly changed the diversity of soil microbial communities. In addition, the accumulation of P. ginseng soil-borne pathogens (Monographella cucumerina, Ilyonectria mors-panacis, I. robusta, Fusarium solani, and Nectria ramulariae) varied with the cropping age of P. ginseng. Conclusion Soil microbial diversity and function were significantly poorer in farmland than in the deforestation field and were affected by P. ginseng planting years. The abundance of common soil-borne pathogens of P. ginseng increased with the cultivation age and led to an imbalance in the microbial community. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02081-2.
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Affiliation(s)
- Ai-Zi Tong
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
| | - Wei Liu
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China.
| | - Qiang Liu
- Chinese Institute of Jilin Ginseng, Tonghua, 134002, China
| | - Guang-Qing Xia
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
| | - Jun-Yi Zhu
- School of Life Science, Tonghua Normal University, No.950 Yu Cai Road, Dongchang District, Tonghua, 134002, China
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Jayaraman S, Naorem A, Lal R, Dalal RC, Sinha N, Patra A, Chaudhari S. Disease-Suppressive Soils-Beyond Food Production: a Critical Review. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2021; 21:1437-1465. [PMID: 33746349 PMCID: PMC7953945 DOI: 10.1007/s42729-021-00451-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/21/2021] [Indexed: 05/09/2023]
Abstract
In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.
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Affiliation(s)
- Somasundaram Jayaraman
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Naorem
- ICAR– Central Arid Zone Research Institute, Regional Research Station-Kukma, Bhuj, Gujarat 370105 India
| | - Rattan Lal
- Carbon Management Sequestration Center, The Ohio State University, 2021 Coffey Rd, Columbus, OH USA
| | - Ram C. Dalal
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - N.K. Sinha
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Patra
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - S.K. Chaudhari
- Indian Council of Agricultural Research, KAB-II, New Delhi, India
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Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review. SUSTAINABILITY 2020. [DOI: 10.3390/su13010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.
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Ma X, Du M, Liu P, Tang Y, Li H, Yuan Q, Ruan Y, Meng L, Zhang J, Lin M, Liu Z. Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China. Arch Microbiol 2020; 203:913-925. [PMID: 33078269 DOI: 10.1007/s00203-020-02086-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/18/2020] [Accepted: 10/06/2020] [Indexed: 11/29/2022]
Abstract
Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.
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Affiliation(s)
- Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Minglun Du
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Peng Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Yanqiong Tang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Hong Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Qianhua Yuan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Yunze Ruan
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Lei Meng
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jiachao Zhang
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhu Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.
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Saad MM, Eida AA, Hirt H. Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3878-3901. [PMID: 32157287 PMCID: PMC7450670 DOI: 10.1093/jxb/eraa111] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/09/2020] [Indexed: 05/05/2023]
Abstract
Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.
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Affiliation(s)
- Maged M Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Abdul Aziz Eida
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette Cedex, France
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Lankau EW, Xue D, Christensen R, Gevens AJ, Lankau RA. Management and Soil Conditions Influence Common Scab Severity on Potato Tubers Via Indirect Effects on Soil Microbial Communities. PHYTOPATHOLOGY 2020; 110:1049-1055. [PMID: 31939718 DOI: 10.1094/phyto-06-19-0223-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Common scab, caused by Streptomyces scabies and related species, is a potato tuber blemish disease that causes reductions in marketable yield worldwide. Evidence of suppression of common scab by indigenous soil microbial populations has been found in several studies. However, we lack a comprehensive understanding of how common scab severity relates functionally to potato varieties, farming systems, soil physical and chemical properties, and soil microbial communities. These factors may affect disease directly or indirectly by affecting one of the other variables. We performed a survey of 30 sampling locations across 12 fields in Wisconsin and used structural equation modeling to disentangle the direct effects of potato market classes, farm management (conventional versus organic), and soil physiochemical properties on common scab severity from their indirect effects mediated through soil bacterial and fungal communities. We found that, although potato market classes affected disease severity directly, the effects of farm management and soil physiochemistry were best explained as indirect, mediated by their impacts on soil bacterial communities. This suggests that evaluating the consequences of specific management practices for soil microbial communities may be useful for understanding disease pressure across fields.
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Affiliation(s)
- Emily W Lankau
- Department of Animal Sciences, University of Wisconsin, Madison, WI
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | - Dianne Xue
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | | | - Amanda J Gevens
- Department of Plant Pathology, University of Wisconsin, Madison, WI
| | - Richard A Lankau
- Department of Plant Pathology, University of Wisconsin, Madison, WI
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Zhang J, Wei L, Yang J, Ahmed W, Wang Y, Fu L, Ji G. Probiotic Consortia: Reshaping the Rhizospheric Microbiome and Its Role in Suppressing Root-Rot Disease of Panax notoginseng. Front Microbiol 2020; 11:701. [PMID: 32425904 PMCID: PMC7203884 DOI: 10.3389/fmicb.2020.00701] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Root-rot disease caused by Fusarium oxysporum is a growing problem in agriculture for commercial cultivation of Panax notoginseng. Diverse microbes colonize plant roots, and numerous earlier studies have characterized the rhizospheric microbiome of P. notoginseng; nevertheless, the function of probiotic consortia on the rhizospheric microbiome against the root-rot disease remain elusive. We have compared and described the rhizospheric microbiome of lightly and severely diseased P. notoginseng as well as the interactions of the probiotic consortia and rhizospheric microbiome, and their function to alleviate the plant diseases were explored by inoculating probiotic consortia in bulk soil. From the perspective of microbial diversity, the rhizospheric dominant bacterial and fungal genera were utterly different between lightly and severely diseased plants. Through inoculating assembled probiotic consortia to diseased plant roots, we found that the application of probiotic consortia reshaped the rhizosphere microbiome, increasing the relative abundance of bacteria and fungi, while the relative abundance of potential pathogens was decreased significantly. We developed a microcosm system that provides a preliminary ecological framework for constructing an active probiotic community to reshape soil microbiota and restrain the disease. Microbial community structure differs between lightly and seriously diseased plants. The application of probiotic consortia changes the imbalance of micro-ecology to a state of relative health, reducing plant mortality. Plant disease suppression may be achieved by seeking and applying antagonistic microbes based on their direct inhibitory capability or by restructuring the soil microbiome structure and function.
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Affiliation(s)
- Jinhao Zhang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Lanfang Wei
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Jun Yang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Waqar Ahmed
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yating Wang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Lina Fu
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China.,Agriculture and Rural Affairs Committee of Fengdu County, Chongqing, China
| | - Guanghai Ji
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
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Zhang Y, Hu A, Zhou J, Zhang W, Li P. Comparison of bacterial communities in soil samples with and without tomato bacterial wilt caused by Ralstonia solanacearum species complex. BMC Microbiol 2020; 20:89. [PMID: 32290811 PMCID: PMC7155298 DOI: 10.1186/s12866-020-01774-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ralstonia solanacearum is one of the most notorious soil-borne phytopathogens. It causes a severe wilt disease with deadly effects on many economically important crops. The microbita of disease-suppressive soils are thought that they can contribute to the disease resistance of crop plants, thus, evaluation of the microbial community and their interaction characteristics between suppressive soil (SS) and conducive soil (CS) will help to understand resistance mechanism. To do this, the bacterial community structure, correlation analysis with soil chemical properties, interaction network of SS (nearly no disease in three years), and CS (suffered heavy bacterial wilt disease) were analyzed. RESULTS A higher bacterial community diversity index was found in SS, the relative abundance of Nocardioides, Gaiella and norank_f_Anaerolineaceae were significantly more than that of the CS. Moreover, the relative abundance of main genera Bacillus, norank_o_Gaiellales, Roseiflexus, and norank_o_Gemmatimonadaceae were significantly more than that of the CS. Redundancy analysis at the genus level indicated that the available phosphate played a key role in the bacterial community distribution, and its role was negatively correlated with soil pH, organic matter content, alkali-hydrolyzable nitrogen, and available potassium contents. Interaction network analysis further demonstrated that greater diversity at the genus level existed in the SS network and formed a stable network. Additionally, the species of Mycobacterium, Cyanobacteria, and Rhodobiaceae are the key components that sustain the network stability. Seven clusters of orthologous groups exhibited significant differences between SS and CS. Moreover, 55 bacterial strains with distinct antagonistic activities to R. solancearum were isolated and identified from the healthy tomato plant rhizosphere soil of the CS. CONCLUSIONS Our findings indicate that the bacterial diversity and interaction network differed between the CS and SS samples, providing a good foundation in the study of bacterial wilt.
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Affiliation(s)
- Ying Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Anna Hu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
| | - Peng Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Gu Z, Wang M, Wang Y, Zhu L, Mur LAJ, Hu J, Guo S. Nitrate Stabilizes the Rhizospheric Fungal Community to Suppress Fusarium Wilt Disease in Cucumber. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:590-599. [PMID: 32073377 DOI: 10.1094/mpmi-07-19-0198-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nitrogen forms can regulate soil-borne Fusarium wilt suppression, but the related mechanisms are largely unknown, especially possible action via the rhizospheric microbial community. Soil analysis, MiSeq high-throughput sequencing analysis, community diversity, and network analysis were used to characterize the impact of different nitrogen forms (nitrate and ammonium) on rhizospheric fungal communities and the contribution of nitrate to the suppression to Fusarium oxysporum f. sp. cucumerinum compared with ammonium. Nitrate-grown cucumber showed a lower disease index and F. oxysporum f. sp. cucumerinum abundance in the rhizosphere. In comparisons with ammonium nutrients, nitrate-fed plants maintained a higher soil rhizosphere pH, microbial biomass carbon content, microbial biomass nitrogen content, as well as fungal community richness and diversity following F. oxysporum f. sp. cucumerinum incubation. All these factors were negatively related with disease index. Network analysis showed fewer nodes and edges in the ammonium treatments compared with nitrate treatments. The relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Saprotroph fungi explained 82% of the variability of rhizosphere F. oxysporum f. sp. cucumerinum abundance. In conclusion, after pathogen inoculation under nitrate nutrition, the less-affected microbial composition, community diversity, and community internal relations, which resulted from the more diverse and robust microbial population, potentially contributed to greater Fusarium wilt suppression.
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Affiliation(s)
- Zechen Gu
- 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, China
| | - Min 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, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ying 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, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Linxing Zhu
- 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, China
| | - Luis Alejandro Jose Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, U.K
| | - Jun Hu
- 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, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Brescia F, Marchetti-Deschmann M, Musetti R, Perazzolli M, Pertot I, Puopolo G. The rhizosphere signature on the cell motility, biofilm formation and secondary metabolite production of a plant-associated Lysobacter strain. Microbiol Res 2020; 234:126424. [PMID: 32036275 DOI: 10.1016/j.micres.2020.126424] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/10/2020] [Accepted: 01/26/2020] [Indexed: 12/15/2022]
Abstract
Lysobacter spp. are common bacterial inhabitants of the rhizosphere of diverse plant species. However, the impact of the rhizosphere conditions on their physiology is still relatively understudied. To provide clues on the behaviour of Lysobacter spp. in this ecological niche, we investigated the physiology of L. capsici AZ78 (AZ78), a biocontrol strain isolated from tobacco rhizosphere, on a common synthetic growth medium (LBA) and on a growth medium containing components of the plant rhizosphere (RMA). The presence of a halo surrounding the AZ78 colony on RMA was a first visible effect related to differences in growth medium composition and it corresponded to the formation of a large outer ring. The lower quantity of nutrients available in RMA as compared with LBA was associated to a higher expression of a gene encoding cAMP-receptor-like protein (Clp), responsible for cell motility and biofilm formation regulation. AZ78 cells on RMA were motile, equipped with cell surface appendages and organised in small groups embedded in a dense layer of fibrils. Metabolic profiling by mass spectrometry imaging revealed increased diversity of analytes produced by AZ78 on RMA as compared with LBA. In particular, putative cyclic lipodepsipeptides, polycyclic tetramate macrolactams, cyclic macrolactams and other putative secondary metabolites with antibiotic activity were identified. Overall, the results obtained in this study shed a light on AZ78 potential to thrive in the rhizosphere by its ability to move, form biofilm and release secondary metabolites.
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Affiliation(s)
- Francesca Brescia
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; PhD school in Agricultural Science and Biotechnology, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Vienna, 1060, Austria
| | - Rita Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, 33100, Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy.
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Zhang J, Wei L, Yang J, Ahmed W, Wang Y, Fu L, Ji G. Probiotic Consortia: Reshaping the Rhizospheric Microbiome and Its Role in Suppressing Root-Rot Disease of Panax notoginseng. Front Microbiol 2020. [PMID: 32425904 DOI: 10.3389/fpls.2017.0701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Root-rot disease caused by Fusarium oxysporum is a growing problem in agriculture for commercial cultivation of Panax notoginseng. Diverse microbes colonize plant roots, and numerous earlier studies have characterized the rhizospheric microbiome of P. notoginseng; nevertheless, the function of probiotic consortia on the rhizospheric microbiome against the root-rot disease remain elusive. We have compared and described the rhizospheric microbiome of lightly and severely diseased P. notoginseng as well as the interactions of the probiotic consortia and rhizospheric microbiome, and their function to alleviate the plant diseases were explored by inoculating probiotic consortia in bulk soil. From the perspective of microbial diversity, the rhizospheric dominant bacterial and fungal genera were utterly different between lightly and severely diseased plants. Through inoculating assembled probiotic consortia to diseased plant roots, we found that the application of probiotic consortia reshaped the rhizosphere microbiome, increasing the relative abundance of bacteria and fungi, while the relative abundance of potential pathogens was decreased significantly. We developed a microcosm system that provides a preliminary ecological framework for constructing an active probiotic community to reshape soil microbiota and restrain the disease. Microbial community structure differs between lightly and seriously diseased plants. The application of probiotic consortia changes the imbalance of micro-ecology to a state of relative health, reducing plant mortality. Plant disease suppression may be achieved by seeking and applying antagonistic microbes based on their direct inhibitory capability or by restructuring the soil microbiome structure and function.
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Affiliation(s)
- Jinhao Zhang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Lanfang Wei
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Jun Yang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Waqar Ahmed
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yating Wang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Lina Fu
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
- Agriculture and Rural Affairs Committee of Fengdu County, Chongqing, China
| | - Guanghai Ji
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management Under the Ministry of Education, Yunnan Agricultural University, Kunming, China
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Tang T, Sun X, Liu Q, Dong Y, Xiang Y. Different effects of soil bacterial communities affected by biocontrol agent YH-07 on tomato Fusarium wilt inhibition. RSC Adv 2020; 10:34977-34985. [PMID: 35515690 PMCID: PMC9056849 DOI: 10.1039/d0ra05452f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
The model plant tomato was used to verify the effect and mechanism of a novel discovered strain YH-07 which is a potential agent for biological control of soil borne disease named tomato Fusarium wilt.
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Affiliation(s)
- Tongtong Tang
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
| | - Xing Sun
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
| | - Qin Liu
- Institute of Soil Science Chinese Academy of Sciences
- Nanjing 210008
- China
- University of Chinese Academy of Sciences
- Beijing 100049
| | - Yuanhua Dong
- Institute of Soil Science Chinese Academy of Sciences
- Nanjing 210008
- China
- University of Chinese Academy of Sciences
- Beijing 100049
| | - Yuyong Xiang
- School of Biological Science and Food Engineering
- Chuzhou University
- Chuzhou 239000
- China
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Xi H, Shen J, Qu Z, Yang D, Liu S, Nie X, Zhu L. Effects of Long-term Cotton Continuous Cropping on Soil Microbiome. Sci Rep 2019; 9:18297. [PMID: 31797982 PMCID: PMC6892916 DOI: 10.1038/s41598-019-54771-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 11/24/2022] Open
Abstract
Verticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.
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Affiliation(s)
- Hui Xi
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Jili Shen
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Dingyi Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Shiming Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China
| | - Xinhui Nie
- College of Agronomy, Shihezi University, Shihezi, 832000, P.R. China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, P.R. China.
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Ou Y, Penton CR, Geisen S, Shen Z, Sun Y, Lv N, Wang B, Ruan Y, Xiong W, Li R, Shen Q. Deciphering Underlying Drivers of Disease Suppressiveness Against Pathogenic Fusarium oxysporum. Front Microbiol 2019; 10:2535. [PMID: 31781059 PMCID: PMC6861331 DOI: 10.3389/fmicb.2019.02535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/21/2019] [Indexed: 11/13/2022] Open
Abstract
Soil-borne diseases, especially those caused by fungal pathogens, lead to profound annual yield losses. One key example for such a disease is Fusarium wilt disease in banana. In some soils, plants do not show disease symptoms, even if the disease-causing pathogens are present. However, the underlying agents that make soils suppressive against Fusarium wilt remain elusive. In this study, we aimed to determine the underlying microbial agents governing soil disease-suppressiveness. We traced the shift of microbiomes during the invasion of disease-causing Fusarium oxysporum f. sp. cubense in disease-suppressive and disease-conducive soils. We found distinct microbiome structures in the suppressive and conducive soils after pathogen invasion. The alpha diversity indices increased (or did not significantly change) and decreased, respectively, in the suppressive and conducive soils, indicating that the shift pattern of the microbiome with pathogen invasion was notably different between the suppressive and conductive soils. Microbiome networks were more complex with higher numbers of links and revealed more negative links, especially between bacterial taxa and the disease-causing Fusarium, in suppressive soils than in conducive soils. We identified the bacterial genera Chryseolinea, Terrimonas, and Ohtaekwangia as key groups that likely confer suppressiveness against disease-causing Fusarium. Overall, our study provides the first insights into agents potentially underlying the disease suppressiveness of soils against Fusarium wilt pathogen invasion. The results of this study may help to guide efforts for targeted cultivation and application of these potential biocontrol agents, which might lead to the development of effective biocontrol agents against Fusarium wilt disease.
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Affiliation(s)
- Yannan Ou
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - C Ryan Penton
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ, United States
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yifei Sun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Nana Lv
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Beibei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Wu Xiong
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Rong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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Kopecky J, Samkova Z, Sarikhani E, Kyselková M, Omelka M, Kristufek V, Divis J, Grundmann GG, Moënne-Loccoz Y, Sagova-Mareckova M. Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab. Sci Rep 2019; 9:14883. [PMID: 31619759 PMCID: PMC6796001 DOI: 10.1038/s41598-019-51570-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/28/2019] [Indexed: 12/20/2022] Open
Abstract
Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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Affiliation(s)
- Jan Kopecky
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Zuzana Samkova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Ensyeh Sarikhani
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Martina Kyselková
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovská 83, 186 75, Prague 8, Czech Republic
| | - Vaclav Kristufek
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jiri Divis
- Faculty of Agriculture, University of South Bohemia, Studentská 13, 370 05, České Budějovice, Czech Republic
| | - Geneviève G Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, Prague 6, Czech Republic.
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Luo L, Zhang Z, Wang P, Han Y, Jin D, Su P, Tan X, Zhang D, Muhammad-Rizwan H, Lu X, Liu Y. Variations in phyllosphere microbial community along with the development of angular leaf-spot of cucumber. AMB Express 2019; 9:76. [PMID: 31134393 PMCID: PMC6536563 DOI: 10.1186/s13568-019-0800-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/16/2019] [Indexed: 01/07/2023] Open
Abstract
The phyllosphere is colonized by a wide variety of microorganisms including epiphytes, plant-pathogenic fungus, bacteria, as well as human or animal pathogens. However, little is known about how microbial community composition changes with the development of angular leaf-spot of cucumber. Here, 18 mixed samples were collected based on the lesion coverage rate (LCR) of angular leaf-spot of cucumber from three disease severity groups (DM1: symptomatic-mild, DM2: symptomatic-moderate, DM3: symptomatic-severe). In our study, the microbial community structure and diversity were examined by Illumina MiSeq sequencing. A significant differences was observed in α diversity and community structure among three disease severity groups. The phyllosphere microbiota was observed to be dominated by bacterial populations from Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal species from Ascomycota and Basidiomycota. In addition, some plant-specific microbe such as Sphingomonas, Methylobacterium, Pseudomonas, and Alternaria showed significant changes in their relative abundance of population. The LCR was correlated negatively with Sphingomonas, Methylobacterium, Quadrisphaera, and Lactobacillus, whereas correlated positively with Pseudomonas and Kineococcus (p < 0.05). The LCR was negatively correlated with Alternaria and Arthrinium of the fungal communities (p < 0.05). Molecular ecological networks of the microbial communities were constructed to show the interactions among the OTUs. Our current results indicated that the competitive relationships among species were broken with the development of angular leaf-spot of cucumber. The microbial community composition changed over the development of angular leaf-spot of cucumber. The result of molecular ecological networks indicated that the overall bacterial community tends toward mutualism from the competition. The development of angular leaf-spot of cucumber affected the ecosystem functioning by disrupting the stability of the microbial community network. This work will help us to understand the host plant-specific microbial community structures and shows how these communities change throughout the development of angular leaf-spot of cucumber.
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Dong L, Li Y, Xu J, Yang J, Wei G, Shen L, Ding W, Chen S. Biofertilizers regulate the soil microbial community and enhance Panax ginseng yields. Chin Med 2019; 14:20. [PMID: 31143242 PMCID: PMC6533694 DOI: 10.1186/s13020-019-0241-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 12/02/2022] Open
Abstract
Background Panax ginseng is widely used as functional food and traditional Chinese medicine. To satisfy the market supply and medication safety, biofertilizers are used as agents to stimulate the growth and production of P. ginseng. Methods In this study, we used high-throughput sequencing and quantitative polymerase chain reaction to analyze microbial community in soils treated with biofertilizers during the development stages of P. ginseng. Ginsenoside content was detected using high-performance liquid chromatography analysis to evaluate the effects of biofertilizer application. Results In this study, the incidence rate of P. ginseng root rot significantly declined by 40.3–47.3% after application of disease-biocontrol biofertilizers. Bacterial diversity showed increasing trends in soils treated with 3.0–4.5 ml kg−1 of disease-biocontrol biofertilizers compared with those in untreated soils. Principal coordinate analysis ordination revealed that bacterial communities were changed by biofertilizers depending on their application concentration. Relative abundance of potentially beneficial bacterial agents, such as Bacillus, Burkholderia, Rhizobium, Streptomyces, and Mycobacterium, significantly increased compared with that in control. Fusarium of low abundance observed in soils treated with biofertilizers compared with that in untreated soils. P. ginseng yield was enhanced by 17.0–19.1%, and ginsenoside (Rg1 and Rb1) contents were improved after biofertilizer application. Conclusions Our results reveal that biofertilizers reduced the incidence rate of root rot, increased bacterial diversity, promoted the relative abundance of potentially beneficial bacterial taxa, decreased the abundance of potentially harmful bacterial agents, and then enhanced the yield and quality of P. ginseng. Electronic supplementary material The online version of this article (10.1186/s13020-019-0241-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linlin Dong
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yong Li
- 2Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 China
| | - Jiang Xu
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Juan Yang
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Guangfei Wei
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Liang Shen
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Wanlong Ding
- 2Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 China
| | - Shilin Chen
- 1Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
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Jeanne T, Parent SÉ, Hogue R. Using a soil bacterial species balance index to estimate potato crop productivity. PLoS One 2019; 14:e0214089. [PMID: 30901358 PMCID: PMC6430509 DOI: 10.1371/journal.pone.0214089] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
The development of ‘molecular-omic’ tools and computing analysis platforms have greatly enhanced our ability to assess the impacts of agricultural practices and crop management protocols on soil microbial diversity. However, biotic factors are rarely factored into agricultural management models. Today it is possible to identify specific microbiomes and define biotic components that contribute to soil quality. We assessed the bacterial diversity of soils in 51 potato production plots. We describe a strategy for identifying a potato-crop-productivity bacterial species balance index based on amplicon sequence variants. We observed a significant impact of soil texture balances on potato yields; however, the Shannon and Chao1 richness indices and Pielou’s evenness index poorly correlated with these yields. Nonetheless, we were able to estimate the portion of the total bacterial microbiome related to potato yield using an integrated species balances index derived from the elements of the bacterial microbiome that positively or negatively correlate with residual potato yields. This innovative strategy based on a microbiome selection procedure greatly enhances our ability to interpret the impact of agricultural practices and cropping system management choices on microbial diversity and potato yield. This strategy provides an additional tool that will aid growers and the broader agricultural sector in their decision-making processes concerning the soil quality and crop productivity.
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Affiliation(s)
- Thomas Jeanne
- Institut de recherche et de développement en agroenvironnement (IRDA), Quebec City, Quebec, Canada
- * E-mail:
| | | | - Richard Hogue
- Institut de recherche et de développement en agroenvironnement (IRDA), Quebec City, Quebec, Canada
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Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu M. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci Rep 2019; 9:1715. [PMID: 30737419 PMCID: PMC6368641 DOI: 10.1038/s41598-018-37559-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 11/22/2022] Open
Abstract
Crop rotation and intercropping with Allium plants suppresses Fusarium wilt in various crops. However, the mechanisms underlying this phenomenon have not been fully elucidated. This study was designed to assess the role of microorganisms inhabiting Allium rhizospheres and antifungal compounds produced by Allium roots in Fusarium wilt suppression by Allium cultivation. Suppression of cucumber Fusarium wilt and the pathogen multiplication by Allium (Welsh onion and/or onion)-cultivated soils were eliminated by heat treatment at 60 °C, whereas those by Welsh onion-root extract were lost at 40 °C. The addition of antibacterial antibiotics eliminated the suppressive effect of Welsh onion-cultivated soil on pathogen multiplication, suggesting the contribution of antagonistic gram-negative bacteria to the soil suppressiveness. The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. Flavobacterium species recovered from the rhizosphere soils of these Allium plants suppressed Fusarium wilt on cucumber seedlings. Furthermore, confocal laser scanning microscopy revealed that Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Taken together, we infer that the accumulation of antagonistic Flavobacterium species plays a key role in Fusarium wilt suppression by Allium cultivation.
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Affiliation(s)
- Tomoki Nishioka
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Malek Marian
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Issei Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Yuhko Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Masafumi Shimizu
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan.
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Li H, Wang J, Liu Q, Zhou Z, Chen F, Xiang D. Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing. J Basic Microbiol 2018; 59:181-191. [PMID: 30288775 DOI: 10.1002/jobm.201800304] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/13/2018] [Accepted: 09/11/2018] [Indexed: 11/11/2022]
Abstract
Soil bacteria play key roles in determining soil health and plant growth. In this study, four sweet potato fields that had been consecutively monocultured for 1, 2, 3, and 4 years were used to investigate the effect of monoculture on soil physicochemical properties and soil bacterial communities. The results revealed that continuous cropping led to a significant decline in soil pH, soil organic carbon, and soil bacterial abundance. Miseq pyrosequencing analysis of 16S rRNA genes revealed that Proteobacteria and Bacteroidetes were the main phyla in the sweet potato monoculture soils, comprising up to 66.24% of the total sequences. The relative abundances of beneficial bacteria, including Actinobacteria, Gemmatimonadetes, Firmicutes, Xanthomonadaceae, Rhodospirillaceae, and Syntrophobacteraceae, as well as their subgroups at the genus and operational taxonomic unit (OTU) levels, decreased considerably as the number of continuous cropping years increased. In contrast, the number of potentially pathogenic bacteria, such as Acidobacteria, Sphingomonadaceae, and Pedobacter accumulated with increasing years. The results also showed the alterations to the bacterial community in the sweet potato monoculture soils were mainly driven by soil pH and soil organic matter. Overall, the decline in soil quality after successive sweet potato monoculture can be attributed to the imbalance in soil properties and soil microbes, including the decrease in soil pH and soil organic carbon, and the enrichment of pathogenic bacteria at the expense of plant-beneficial bacteria.
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Affiliation(s)
- Huan Li
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Jinqiang Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Qing Liu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Zhengfeng Zhou
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
| | - Falin Chen
- Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Dan Xiang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, China
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Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, Huang Q, Bai Y, Vivanco JM, Kowalchuk GA, Berendsen RL, Shen Q. Root exudates drive the soil-borne legacy of aboveground pathogen infection. MICROBIOME 2018; 6:156. [PMID: 30208962 PMCID: PMC6136170 DOI: 10.1186/s40168-018-0537-x] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/23/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants. RESULTS Plants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response. CONCLUSION Collectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.
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Affiliation(s)
- Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Zhao
- School of Geography Science, Nanjing Normal University, Nanjing, 210021, China
| | - Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengli Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pim Goossens
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Qiwei Huang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101, China
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture and Center for Rhizosphere Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization; National Engineering Research Center for Organic-based Fertilizers; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
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