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Tienda S, Vida C, Villar-Moreno R, de Vicente A, Cazorla FM. Development of a Pseudomonas-based biocontrol consortium with effective root colonization and extended beneficial side effects for plants under high-temperature stress. Microbiol Res 2024; 285:127761. [PMID: 38761488 DOI: 10.1016/j.micres.2024.127761] [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: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
The root microbiota plays a crucial role in plant performance. The use of microbial consortia is considered a very useful tool for studying microbial interactions in the rhizosphere of different agricultural crop plants. Thus, a consortium of 3 compatible beneficial rhizospheric Pseudomonas strains previously isolated from the avocado rhizosphere, was constructed. The consortium is composed of two compatible biocontrol P. chlororaphis strains (PCL1601 and PCL1606), and the biocontrol rhizobacterium Pseudomonas alcaligenes AVO110, which are all efficient root colonizers of avocado and tomato plants. These three strains were compatible with each other and reached stable levels both in liquid media and on plant roots. Bacterial strains were fluorescent tagged, and colonization-related traits were analyzed in vitro, revealing formation of mixed biofilm networks without exclusion of any of the strains. Additionally, bacterial colonization patterns compatible with the different strains were observed, with high survival traits on avocado and tomato roots. The bacteria composing the consortium shared the same root habitat and exhibited biocontrol activity against soil-borne fungal pathogens at similar levels to those displayed by the individual strains. As expected, because these strains were isolated from avocado roots, this Pseudomonas-based consortium had more stable bacterial counts on avocado roots than on tomato roots; however, inoculation of tomato roots with this consortium was shown to protect tomato plants under high-temperature stress. The results revealed that this consortium has side beneficial effect for tomato plants under high-temperature stress, thus improving the potential performance of the individual strains. We concluded that this rhizobacterial consortium do not improve the plant protection against soil-borne phytopathogenic fungi displayed by the single strains; however, its inoculation can show an specific improvement of plant performance on a horticultural non-host plant (such as tomato) when the plant was challenged by high temperature stress, thus extending the beneficial role of this bacterial consortium.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, Málaga 29071, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, Málaga 29010, Spain
| | - Carmen Vida
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, Málaga 29071, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, Málaga 29010, Spain
| | - Rafael Villar-Moreno
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, Málaga 29071, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, Málaga 29010, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, Málaga 29071, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, Málaga 29010, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, Málaga 29071, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, Málaga 29010, Spain.
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Yan J, Hu X, Qian L, Fu X, Wang L. Tidal organic input restricts CO 2 sequestration capacity of estuarine wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:63580-63591. [PMID: 37055687 DOI: 10.1007/s11356-023-26642-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 04/15/2023]
Abstract
The inland and estuary wetlands that characterized by different natural environment perform distinctly in soil carbon (C) sink. It was deemed that estuary wetland has a higher organic C accumulation rate than inland wetland, due to its higher primary production and tidal organics input, thus having higher organic C sink capacity. While from CO2 budge in view, whether does the large organic input from tide restrict CO2 sequestration capacity of estuary wetland has not been discussed comparing with inland wetland. In this study, inland and estuary wetlands were selected to study the potential of CO2 sequestration capacity. It was found that inland wetland had most of soil organic carbon (SOC) derived from plant C, which brought remarkable organic C content and nourished higher microbial biomass, dehydrogenase, and β_glucosidase than estuary wetland. The estuary wetland instead accumulated less SOC, a considerable proportion of which came from tidal waters, therefore supporting lower microbial biomass and enzyme activities than that in inland wetland. However, estuary wetland was evaluated having higher capability in SOC mineralization than inland wetland in consideration of soil respiration (SR) and SR quotient. It was concluded that tidal organic C accelerated the SOC mineralization in estuarine wetland, thus weakening the CO2 sequestration. These results implied the importance of pollution control for reservation CO2 sink function in estuarine wetland.
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Affiliation(s)
- Jianfang Yan
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
| | - Xin Hu
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
- Key Laboratory of Watershed Earth Surface Processes and Ecological Security, Zhejiang Normal University, Jinhua, Zhejiang, 321004, China
| | - Liwei Qian
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Xiaohua Fu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Lei Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
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Wu Z, Tang Z, Yu T, Zhang J, Zheng Y, Yang J, Wu Y, Sun Q. Nitrogen fertilization rates mediate rhizosphere soil carbon emissions of continuous peanut monoculture by altering cellulose-specific microbess. FRONTIERS IN PLANT SCIENCE 2023; 14:1109860. [PMID: 36938001 PMCID: PMC10021708 DOI: 10.3389/fpls.2023.1109860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Crops influence both soil microbial communities and soil organic carbon (SOC) cycling through rhizosphere processes, yet their responses to nitrogen (N) fertilization have not been well investigated under continuous monoculture. METHODS In this study, rhizosphere soil microbial communities from a 5-year continuous mono-cropped peanut land were examined using Illumina HighSeq sequencing, with an N fertilization gradient that included 0 (N0), 60 (N60), 120 (N120) and 180 (N180) kg hm-2. Soil respiration rate (R s) and its temperature sensitivity (Q 10) were determined, with soil carbon-acquiring enzyme activities assayed. RESULTS AND DISCUSSION The obtained results showed that with N fertilization, soil mineral N (Nmin) was highly increased and the soil C/N ratio was decreased; yields were unchanged, but root biomass was stimulated only at N120. The activities of β-1,4-glucosidase and polyphenol oxidase were reduced across application rates, but that of β-1,4-cellobiohydrolase was increased only at N120. Bacterial alpha diversity was unchanged, but fungal richness and diversity were increased at N60 and N120. For bacterial groups, the relative abundance of Acidobacteria was reduced, while those of Alphaproteobacteria and Gammaproteobacteria were increased at N60 and N120. For fungal members, the pathogenic Sordariomycetes was inhibited, but the saprotrophic Agaricomycetes was promoted, regardless of N fertilization rates. RDA identified different factors driving the variations in bacterial (root biomass) and fungal (Nmin) community composition. N fertilization increased R s slightly at N60 and significantly at N120, mainly through the promotion of cellulose-related microbes, and decreased R s slightly at N180, likely due to carbon limitation. N fertilization reduced microbial biomass carbon (MBC) at N60, N120 and N180, decreased SOC at N120 and N180, and suppressed dissolved organic carbon (DOC) at N180. In addition, the unchanged Q 10 may be a joint result of several mechanisms that counteracted each other. These results are of critical importance for assessing the sustainability of continuously monocultured ecosystems, especially when confronting global climate change.
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Affiliation(s)
- Zhengfeng Wu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Zhaohui Tang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Tianyi Yu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Jiancheng Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Yongmei Zheng
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Jishun Yang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Yue Wu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
| | - Qiqi Sun
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, China
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Ikeda S, Okazaki K, Takahashi H, Tsurumaru H, Minamisawa K. Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan. Microbes Environ 2023; 38. [PMID: 36754423 PMCID: PMC10037095 DOI: 10.1264/jsme2.me22071] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.
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Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Hiroyuki Takahashi
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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Villar-Moreno R, Tienda S, Gutiérrez-Barranquero JA, Carrión VJ, de Vicente A, Cazorla FM, Arrebola E. Interplay between rhizospheric Pseudomonas chlororaphis strains lays the basis for beneficial bacterial consortia. FRONTIERS IN PLANT SCIENCE 2022; 13:1063182. [PMID: 36589057 PMCID: PMC9797978 DOI: 10.3389/fpls.2022.1063182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas chlororaphis (Pc) representatives are found as part of the rhizosphere-associated microbiome, and different rhizospheric Pc strains frequently perform beneficial activities for the plant. In this study we described the interactions between the rhizospheric Pc strains PCL1601, PCL1606 and PCL1607 with a focus on their effects on root performance. Differences among the three rhizospheric Pc strains selected were first observed in phylogenetic studies and confirmed by genome analysis, which showed variation in the presence of genes related to antifungal compounds or siderophore production, among others. Observation of the interactions among these strains under lab conditions revealed that PCL1606 has a better adaptation to environments rich in nutrients, and forms biofilms. Interaction experiments on plant roots confirmed the role of the different phenotypes in their lifestyle. The PCL1606 strain was the best adapted to the habitat of avocado roots, and PCL1607 was the least, and disappeared from the plant root scenario after a few days of interaction. These results confirm that 2 out 3 rhizospheric Pc strains were fully compatible (PCL1601 and PCL1606), efficiently colonizing avocado roots and showing biocontrol activity against the fungal pathogen Rosellinia necatrix. The third strain (PCL1607) has colonizing abilities when it is alone on the root but displayed difficulties under the competition scenario, and did not cause deleterious effects on the other Pc competitors when they were present. These results suggest that strains PCL1601 and PCL1606 are very well adapted to the avocado root environment and could constitute a basis for constructing a more complex beneficial microbial synthetic community associated with avocado plant roots.
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Affiliation(s)
- Rafael Villar-Moreno
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jose A. Gutiérrez-Barranquero
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Víctor J. Carrión
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Antonio de Vicente
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Eva Arrebola
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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Mayerhofer J, Thuerig B, Oberhaensli T, Enderle E, Lutz S, Ahrens CH, Fuchs JG, Widmer F. Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane. FEMS Microbiol Ecol 2021; 97:6373440. [PMID: 34549287 PMCID: PMC8478479 DOI: 10.1093/femsec/fiab134] [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: 05/08/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Compost applications vary in their plant growth promotion and plant disease suppression, likely due to differences in physico-chemical and biological parameters. Our hypothesis was that bacteria are important for plant growth promotion and disease suppression of composts and, therefore, composts having these traits would contain similar sets of indicative bacterial taxa. Seventeen composts prepared from five different commercial providers and different starting materials were classified accordingly with bioassays using cress plants and the pathogen Pythium ultimum. Using a metabarcoding approach, bacterial communities were assessed in bulk composts and cress rhizoplanes. Six and nine composts showed significant disease suppression or growth promotion, respectively, but these traits did not correlate. Growth promotion correlated positively with nitrate content of composts, whereas disease suppression correlated negatively with factors representing compost age. Growth promotion and disease suppression explained significant portions of variation in bacterial community structures, i.e. 11.5% and 14.7%, respectively. Among the sequence variants (SVs) associated with growth promotion, Microvirga, Acinetobacter, Streptomyces, Bradyrhizobium and Bacillus were highly promising, while in suppressive composts, Ureibacillus,Thermogutta and Sphingopyxis were most promising. Associated SVs represent the basis for developing prediction tools for growth promotion and disease suppression, a highly desired goal for targeted compost production and application.
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Affiliation(s)
| | - Barbara Thuerig
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Thomas Oberhaensli
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Eileen Enderle
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Stefanie Lutz
- Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, 8820, Wädenswil, Switzerland
| | - Christian H Ahrens
- Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, 8820, Wädenswil, Switzerland.,Bioinformatics and Proteogenomics, SIB Swiss Institute of Bioinformatics, 8820, Wädenswil, Switzerland
| | - Jacques G Fuchs
- Crop Protection and Phytopathology, FiBL Research Institute of Organic Agriculture, 5070, Frick, Switzerland
| | - Franco Widmer
- Molecular Ecology, Agroscope, 8046, Zurich, Switzerland
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Tienda S, Vida C, Lagendijk E, de Weert S, Linares I, González-Fernández J, Guirado E, de Vicente A, Cazorla FM. Soil Application of a Formulated Biocontrol Rhizobacterium, Pseudomonas chlororaphis PCL1606, Induces Soil Suppressiveness by Impacting Specific Microbial Communities. Front Microbiol 2020; 11:1874. [PMID: 32849458 PMCID: PMC7426498 DOI: 10.3389/fmicb.2020.01874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/16/2020] [Indexed: 12/14/2022] Open
Abstract
Biocontrol bacteria can be used for plant protection against some plant diseases. Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model bacterium isolated from the avocado rhizosphere with strong antifungal antagonism mediated by the production of 2-hexyl, 5-propil resorcinol (HPR). Additionally, PcPCL1606 has biological control against different soil-borne fungal pathogens, including the causal agent of the white root rot of many woody crops and avocado in the Mediterranean area, Rosellinia necatrix. The objective of this study was to assess whether the semicommercial application of PcPCL1606 to soil can potentially affect avocado soil and rhizosphere microbial communities and their activities in natural conditions and under R. necatrix infection. To test the putative effects of PcPCL1606 on soil eukaryotic and prokaryotic communities, a formulated PcPCL1606 was prepared and applied to the soil of avocado plants growing in mesocosm experiments, and the communities were analyzed by using 16S/ITS metagenomics. PcPCL1606 survived until the end of the experiments. The effect of PcPCL1606 application on prokaryotic communities in soil and rhizosphere samples from natural soil was not detectable, and very minor changes were observed in eukaryotic communities. In the infested soils, the presence of R. necatrix strongly impacted the soil and rhizosphere microbial communities. However, after PcPCL1606 was applied to soil infested with R. necatrix, the prokaryotic community reacted by increasing the relative abundance of few families with protective features against fungal soilborne pathogens and organic matter decomposition (Chitinophagaceae, Cytophagaceae), but no new prokaryotic families were detected. The treatment of PcPCL1606 impacted the fungal profile, which strongly reduced the presence of R. necatrix in avocado soil and rhizosphere, minimizing its effect on the rest of the microbial communities. The bacterial treatment of formulated PcPCL1606 on avocado soils infested with R. necatrix resulted in biological control of the pathogen. This suppressiveness phenotype was analyzed, and PcPCL1606 has a key role in suppressiveness induction; in addition, this phenotype was strongly dependent on the production of HPR.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Carmen Vida
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Ellen Lagendijk
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Sandra de Weert
- Koppert Biological Systems, Berkel en Rodenrijs, Netherlands
| | - Irene Linares
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jorge González-Fernández
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Emilio Guirado
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Estación Experimental “La Mayora”, Algarrobo, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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Lutz S, Thuerig B, Oberhaensli T, Mayerhofer J, Fuchs JG, Widmer F, Freimoser FM, Ahrens CH. Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics. Front Microbiol 2020; 11:1810. [PMID: 32849417 PMCID: PMC7406687 DOI: 10.3389/fmicb.2020.01810] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.
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Affiliation(s)
- Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Barbara Thuerig
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Thomas Oberhaensli
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | | | - Jacques G Fuchs
- Research Institute of Organic Agriculture (FiBL), Department of Crop Sciences, Frick, Switzerland
| | - Franco Widmer
- Agroscope, Research Group Molecular Ecology, Zurich, Switzerland
| | - Florian M Freimoser
- Agroscope, Research Group Phytopathology and Zoology in Fruit and Vegetable Production, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
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Tzec-Interián JA, Desgarennes D, Carrión G, Monribot-Villanueva JL, Guerrero-Analco JA, Ferrera-Rodríguez O, Santos-Rodríguez DL, Liahut-Guin N, Caballero-Reyes GE, Ortiz-Castro R. Characterization of plant growth-promoting bacteria associated with avocado trees (Persea americana Miller) and their potential use in the biocontrol of Scirtothrips perseae (avocado thrips). PLoS One 2020; 15:e0231215. [PMID: 32267901 PMCID: PMC7141680 DOI: 10.1371/journal.pone.0231215] [Citation(s) in RCA: 12] [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: 11/18/2019] [Accepted: 03/18/2020] [Indexed: 11/25/2022] Open
Abstract
Plants interact with a great variety of microorganisms that inhabit the rhizosphere or the epiphytic and endophytic phyllosphere and that play critical roles in plant growth as well as the biocontrol of phytopathogens and insect pests. Avocado fruit damage caused by the thrips species Scirtothrips perseae leads to economic losses of 12–51% in many countries. In this study, a screening of bacteria associated with the rhizosphere or endophytic phyllosphere of avocado roots was performed to identify bacterial isolates with plant growth-promoting activity in vitro assays with Arabidopsis seedlings and to assess the biocontrol activity of the isolates against Scirtothrips perseae. The isolates with beneficial, pathogenic and/or neutral effects on Arabidopsis seedlings were identified. The plant growth-promoting bacteria were clustered in two different groups (G1 and G3B) based on their effects on root architecture and auxin responses, particularly bacteria of the Pseudomonas genus (MRf4-2, MRf4-4 and TRf2-7) and one Serratia sp. (TS3-6). Twenty strains were selected based on their plant growth promotion characteristics to evaluate their potential as thrips biocontrol agents. Analyzing the biocontrol activity of S. perseae, it was identified that Chryseobacterium sp. shows an entomopathogenic effect on avocado thrips survival. Through the metabolic profiling of compounds produced by bacteria with plant growth promotion activity, bioactive cyclodipeptides (CDPs) that could be responsible for the plant growth-promoting activity in Arabidopsis were identified in Pseudomonas, Serratia and Stenotrophomonas. This study unravels the diversity of bacteria from the avocado rhizosphere and highlights the potential of a unique isolate to achieve the biocontrol of S. perseae.
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Affiliation(s)
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
- * E-mail: (ROC); (GC)
| | | | | | | | | | - Nut Liahut-Guin
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, México
| | | | - Randy Ortiz-Castro
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, México
- Catedratico-CONACyT en el Instituto de Ecología A. C., Xalapa, Veracruz, México
- * E-mail: (ROC); (GC)
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10
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Ntalli N, Adamski Z, Doula M, Monokrousos N. Nematicidal Amendments and Soil Remediation. PLANTS (BASEL, SWITZERLAND) 2020; 9:E429. [PMID: 32244565 PMCID: PMC7238745 DOI: 10.3390/plants9040429] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/03/2020] [Accepted: 03/21/2020] [Indexed: 12/20/2022]
Abstract
The intensification of agriculture has created concerns about soil degradation and toxicity of agricultural chemicals to non-target organisms. As a result, there is great urgency for discovering new ecofriendly tools for pest management and plant nutrition. Botanical matrices and their extracts and purified secondary metabolites have received much research interest, but time-consuming registration issues have slowed their adoption. In contrast, cultural practices such as use of plant matrices as soil amendments could be immediately used as plant protectants or organic fertilizers. Herein, we focus on some types of soil amendments of botanical origin and their utilization for nematicidal activity and enhancement of plant nutrition. The mode of action is discussed in terms of parasite control as well as plant growth stimulation.
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Affiliation(s)
- Nikoletta Ntalli
- Department of Pesticides Control and Phytopharmacy, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece
| | - Zbigniew Adamski
- Electron and Confocal Microscope Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland;
- Department of Animal Physiology and Development, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maria Doula
- Laboratory of Non-Parasitic Diseases, Benaki Phytopathological Institute, 8 S. Delta Str., 14561 Athens, Greece;
| | - Nikolaos Monokrousos
- Laboratory of Molecular Ecology, International Hellenic University, 57001 Thessaloniki, Greece;
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11
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Fernandez-Bayo JD, Shea EA, Parr AE, Achmon Y, Stapleton JJ, VanderGheynst JS, Hodson AK, Simmons CW. Almond processing residues as a source of organic acid biopesticides during biosolarization. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 101:74-82. [PMID: 31604160 PMCID: PMC8759351 DOI: 10.1016/j.wasman.2019.09.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 08/13/2019] [Accepted: 09/20/2019] [Indexed: 05/30/2023]
Abstract
Biosolarization utilizes organic amendments to produce biopesticide compounds in soil that can work in tandem with other stresses to inactivate agricultural pests. The prospect of using by-products from industrial almond processing as amendments for biosolarization was assessed. Soil mesocosms were used to simulate biosolarization using various almond by-products, application rates, and incubation times. Several potentially biopesticidal organic acids were identified and quantified in the soil, and the toxicity of soil extracts was evaluated for the root lesion nematode (Pratylenchus vulnus). It was determined that both almond hulls and a mixture of hulls and shells harbored several acids, the concentration of which was enhanced 1-7 fold via fermentation by native soil microbes. Organic acid concentration in the soil showed a significant linear relationship with the quantity of waste biomass amended. Extracts from soils containing at least 2.5% incorporated biomass by dry weight showed a 84-100% mortality of nematodes, which corresponded to acid concentrations 0.75 mg/g (2.0 g/L) or greater. This study showed that almond processing by-products - hulls and a hull and shell mixture - were suitable amendments for control of P. vulnus and potentially other soil agricultural pests in the context of biosolarization.
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Affiliation(s)
- Jesus D Fernandez-Bayo
- Department of Biological and Agricultural Engineering, University of California, Davis, USA
| | - Emily A Shea
- Department of Food Science and Technology, University of California, Davis, USA
| | - Amy E Parr
- Department of Food Science and Technology, University of California, Davis, USA
| | - Yigal Achmon
- Department of Biotechnology and Food Engineering, Guangdong Technion Israel Institute of Technology, Shantou 515063 Guangdong Province, China
| | - James J Stapleton
- Statewide Integrated Pest Management Program, University of California, Kearney Agricultural Research and Extension Center, USA
| | - Jean S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, Davis, USA; Department of Bioengineering, University of Massachusetts, Dartmouth, MA, USA
| | - Amanda K Hodson
- Department of Entomology and Nematology, University of California, Davis, USA
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12
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Liu D, Sun H, Ma H. Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria. Front Microbiol 2019; 10:1350. [PMID: 31275274 PMCID: PMC6591430 DOI: 10.3389/fmicb.2019.01350] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022] Open
Abstract
Plant roots host diverse microbes that are closely associated with root fitness. Currently, the relationship between microbes and rusty roots of Panax ginseng remains unclear. Here, we described the root-associated microbiome in rusty and healthy ginseng by metagenomic sequencing of 16S rRNA and ITS regions. Being enriched in Diseased-roots (Dr) of ginseng and their rhizosphere soil, the fungus of Ilyonectria, was identified as the most probable cause of the disease after ITS analysis. Meanwhile, an increase of Mortierella was observed in Healthy-roots (Hr). Surprisingly, an enriched Fusarium was found in both Hr and their rhizosphere soil. Besides, in comparison with Hr, decreased relative abundance of Actinomycetales and increased relative abundance of Pseudomonadales was observed in Dr after 16S rRNA analysis. What's more, we isolated several microorganisms as antagonists that showed strong inhibiting effects on Ilyonectria in plate assays. In field trials, inoculation of Bacillus sp. S-11 displayed apparent suppression effect against Ilyonectria and shifted microbial communities in rhizosphere soil. Our research identified key microbiota involved in rusty roots of P. ginseng and offered potential biocontrol solutions to rusty disease.
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Affiliation(s)
- Defei Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huanjun Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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13
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Arrebola E, Tienda S, Vida C, de Vicente A, Cazorla FM. Fitness Features Involved in the Biocontrol Interaction of Pseudomonas chlororaphis With Host Plants: The Case Study of PcPCL1606. Front Microbiol 2019; 10:719. [PMID: 31024497 PMCID: PMC6469467 DOI: 10.3389/fmicb.2019.00719] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/21/2019] [Indexed: 12/31/2022] Open
Abstract
The goal of this mini review is to summarize the relevant contribution of some beneficial traits to the behavior of the species Pseudomonas chlororaphis, and using that information, to give a practical point of view using the model biocontrol strain P. chlororaphis PCL1606 (PcPCL1606). Among the group of plant-beneficial rhizobacteria, P. chlororaphis has emerged as a plant- and soil-related bacterium that is mainly known because of its biological control of phytopathogenic fungi. Many traits have been reported to be crucial during the multitrophic interaction involving the plant, the fungal pathogen and the soil environment. To explore the different biocontrol-related traits, the biocontrol rhizobacterium PcPCL1606 has been used as a model in recent studies. This bacterium is antagonistic to many phytopathogenic fungi and displays effective biocontrol against fungal phytopathogens. Antagonistic and biocontrol activities are directly related to the production of the compound 2-hexyl, 5-propyl resorcinol (HPR), despite the production of other antifungal compounds. Furthermore, PcPCL1606 has displayed additional traits regarding its fitness in soil and plant root environments such as soil survival, efficient plant root colonization, cell-to-cell interaction or promotion of plant growth.
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Affiliation(s)
- Eva Arrebola
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" IHSM, UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" IHSM, UMA-CSIC, Málaga, Spain
| | - Carmen Vida
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" IHSM, UMA-CSIC, Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" IHSM, UMA-CSIC, Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.,Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" IHSM, UMA-CSIC, Málaga, Spain
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14
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Siegel-Hertz K, Edel-Hermann V, Chapelle E, Terrat S, Raaijmakers JM, Steinberg C. Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region. Front Microbiol 2018; 9:568. [PMID: 29670584 PMCID: PMC5893819 DOI: 10.3389/fmicb.2018.00568] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/13/2018] [Indexed: 12/30/2022] Open
Abstract
Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil. Furthermore, we succeeded in partly transferring Fusarium wilt-suppressiveness to the conducive soil by mixing 10% (w/w) of the suppressive soil into the conducive soil. Fungal diversity differed significantly between the suppressive and conducive soils. Among dominant fungal operational taxonomic units (OTUs) affiliated to known genera, 17 OTUs were detected exclusively in the suppressive soil. These OTUs were assigned to the Acremonium, Chaetomium, Cladosporium, Clonostachys, Fusarium, Ceratobasidium, Mortierella, Penicillium, Scytalidium, and Verticillium genera. Additionally, the relative abundance of specific members of the bacterial community was significantly higher in the suppressive and mixed soils than in the conducive soil. OTUs found more abundant in Fusarium wilt-suppressive soils were affiliated to the bacterial genera Adhaeribacter, Massilia, Microvirga, Rhizobium, Rhizobacter, Arthrobacter, Amycolatopsis, Rubrobacter, Paenibacillus, Stenotrophomonas, and Geobacter. Several of the fungal and bacterial genera detected exclusively or more abundantly in the Fusarium wilt-suppressive soil included genera known for their activity against F. oxysporum. Overall, this study supports the potential role of known fungal and bacterial genera in Fusarium wilt suppressive soils from Châteaurenard and pinpoints new bacterial and fungal genera for their putative role in Fusarium wilt suppressiveness.
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Affiliation(s)
- Katarzyna Siegel-Hertz
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Véronique Edel-Hermann
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Emilie Chapelle
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne Franche-Comté, Dijon, France
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15
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Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture. Int J Mol Sci 2018. [PMID: 29538311 PMCID: PMC5877711 DOI: 10.3390/ijms19030850] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.
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16
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Inderbitzin P, Ward J, Barbella A, Solares N, Izyumin D, Burman P, Chellemi DO, Subbarao KV. Soil Microbiomes Associated with Verticillium Wilt-Suppressive Broccoli and Chitin Amendments are Enriched with Potential Biocontrol Agents. PHYTOPATHOLOGY 2018; 108:31-43. [PMID: 28876209 DOI: 10.1094/phyto-07-17-0242-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two naturally infested Verticillium wilt-conducive soils from the Salinas Valley of coastal California were amended with disease-suppressive broccoli residue or crab meal amendments, and changes to the soil prokaryote community were monitored using Illumina sequencing of a 16S ribosomal RNA gene library generated from 160 bulk soil samples. The experiment was run in a greenhouse, twice, with eggplant as the Verticillium wilt-susceptible host. Disease suppression, plant height, soil microsclerotia density, and soil chitinase activity were assessed at the conclusion of each experiment. In soil with high microsclerotia density, all amendments significantly reduced Verticillium wilt severity and microsclerotia density, and increased soil chitinase activity. Plant height was increased only in the broccoli-containing treatments. In total, 8,790 error-corrected sequence variants representing 1,917,893 different sequences were included in the analyses. The treatments had a significant impact on the soil microbiome community structure but measures of α diversity did not vary between treatments. Community structure correlated with disease score, plant height, microsclerotia density, and soil chitinase activity, suggesting that the prokaryote community may affect the disease-related response variables or vice versa. Similarly, the abundance of 107 sequence variants correlated with disease-related response variables, which included variants from genera with known antagonists of filamentous fungal plant pathogens, such as Pseudomonas and Streptomyces. Overall, genera with antifungal antagonists were more abundant in amended soils than unamended soils, and constituted up to 8.9% of all sequences in broccoli+crabmeal-amended soil. This study demonstrates that substrate-mediated shifts in soil prokaryote communities are associated with the transition of Verticillium wilt-conducive soils to Verticillium wilt-suppressive soils, and suggests that soils likely harbor numerous additional antagonists of fungal plant pathogens that contribute to the biological suppression of plant disease.
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Affiliation(s)
- Patrik Inderbitzin
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Judson Ward
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Alexandra Barbella
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Natalie Solares
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Dmitriy Izyumin
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Prabir Burman
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Dan O Chellemi
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Krishna V Subbarao
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
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17
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Vida C, Cazorla FM, de Vicente A. Characterization of biocontrol bacterial strains isolated from a suppressiveness-induced soil after amendment with composted almond shells. Res Microbiol 2017; 168:583-593. [PMID: 28373145 DOI: 10.1016/j.resmic.2017.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022]
Abstract
The improvement in soil quality of avocado crops through organic amendments with composted almond shells has a positive effect on crop yield and plant health, and enhances soil suppressiveness against the phytopathogenic fungus Rosellinia necatrix. In previous studies, induced soil suppressiveness against this pathogen was related to stimulation of Gammaproteobacteria, especially some members of Pseudomonas spp. with biocontrol-related activities. In this work, we isolated bacteria from this suppressiveness-induced amended soil using a selective medium for Pseudomonas-like microorganisms. We characterized the obtained bacterial collection to aid in identification, including metabolic profiles, antagonistic responses, hybridization to biosynthetic genes of antifungal compounds, production of lytic exoenzymatic activities and plant growth-promotion-related traits, and sequenced and compared amplified 16S rDNA genes from representative bacteria. The final selection of representative strains mainly belonged to the genus Pseudomonas, but also included the genera Serratia and Stenotrophomonas. Their biocontrol-related activities were assayed using the experimental avocado model, and results showed that all selected strains protected the avocado roots against R. necatrix. This work confirmed the biocontrol activity of these Gammaproteobacteria-related members against R. necatrix following specific stimulation in a suppressiveness-induced soil after a composted almond shell application.
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Affiliation(s)
- Carmen Vida
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, 29071 Málaga, Spain.
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, 29071 Málaga, Spain.
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora"-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, 29071 Málaga, Spain.
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18
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Martin FN. Development of alternative strategies for management of soilborne pathogens currently controlled with methyl bromide. ANNUAL REVIEW OF PHYTOPATHOLOGY 2003; 107:256-263. [PMID: 14527332 DOI: 10.1094/phyto-09-16-0330-rvw] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The current standard treatment for management of soilborne pests in some high-value crop production systems is preplant fumigation with mixtures of methyl bromide and chloropicrin. With the impending phase-out of methyl bromide, the agricultural industries that rely on soil fumigation face the need for development of alternative pest management strategies. To maintain farm productivity, immediate term research has focused on evaluation of alternative fumigants, modification of current crop production practices to accommodate their use, and improvement of application technologies to reduce the environmental effects of fumigant applications. Longer-term research goals have focused on developing a more integrated approach for pest management that incorporates the use of cultural practices to reduce pathogen pressure, host resistance to disease, and biological approaches for stimulating plant growth and control of root diseases.
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Affiliation(s)
- Frank N Martin
- USDA-ARS, 1636 East Alisal Street, Salinas, California 93905, USA.
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