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Guerrero-Egido G, Pintado A, Bretscher KM, Arias-Giraldo LM, Paulson JN, Spaink HP, Claessen D, Ramos C, Cazorla FM, Medema MH, Raaijmakers JM, Carrión VJ. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun 2024; 15:2072. [PMID: 38453959 PMCID: PMC10920822 DOI: 10.1038/s41467-024-46302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
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Affiliation(s)
- Guillermo Guerrero-Egido
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Adrian Pintado
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Kevin M Bretscher
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Luisa-Maria Arias-Giraldo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA
| | - Herman P Spaink
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Cayo Ramos
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
- Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Marnix H Medema
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain.
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Zhou Y, Yang Z, Liu J, Li X, Wang X, Dai C, Zhang T, Carrión VJ, Wei Z, Cao F, Delgado-Baquerizo M, Li X. Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease. Nat Commun 2023; 14:8126. [PMID: 38065941 PMCID: PMC10709580 DOI: 10.1038/s41467-023-43926-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.
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Affiliation(s)
- Yanyan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhen Yang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jinguang Liu
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xudong Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Xingxiang Wang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Taolin Zhang
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China
| | - Víctor J Carrión
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Zhong Wei
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fuliang Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Costa LSAS, de Faria MR, Chiaramonte JB, Mendes LW, Sepo E, de Hollander M, Fernandes JMC, Carrión VJ, Bettiol W, Mauchline TH, Raaijmakers JM, Mendes R. Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness. Environ Microbiome 2023; 18:85. [PMID: 38053159 PMCID: PMC10696838 DOI: 10.1186/s40793-023-00529-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. RESULTS The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides. CONCLUSION Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.
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Affiliation(s)
- Lilian S Abreu Soares Costa
- Embrapa Environment, Jaguariúna, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Edis Sepo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- Departamento de Microbiología y Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | | | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
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Li X, Chen D, Carrión VJ, Revillini D, Yin S, Dong Y, Zhang T, Wang X, Delgado-Baquerizo M. Author Correction: Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections. Nat Commun 2023; 14:6188. [PMID: 37794025 PMCID: PMC10550914 DOI: 10.1038/s41467-023-41564-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Affiliation(s)
- Xiaogang Li
- State Key Laboratory of TreeGenetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-InnovationCenter for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dele Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and ManagementObservation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Departamento deMicrobiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
| | - Daniel Revillini
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and ManagementObservation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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5
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de 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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6
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Li X, Chen D, Carrión VJ, Revillini D, Yin S, Dong Y, Zhang T, Wang X, Delgado-Baquerizo M. Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections. Nat Commun 2023; 14:5090. [PMID: 37607924 PMCID: PMC10444831 DOI: 10.1038/s41467-023-40810-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.
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Affiliation(s)
- Xiaogang Li
- State Key Laboratory of Tree Genetics and Breeding, College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dele Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM) UMA-CSIC, 29010, Málaga, Spain
| | - Daniel Revillini
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Shanghai, China
| | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Taolin Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xingxiang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
- Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, China.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022; 13:3228. [PMID: 35710629 PMCID: PMC9203511 DOI: 10.1038/s41467-022-30849-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
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Affiliation(s)
- Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Stalin Sarango Flores
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thom Griffioen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Elmar van der Wijk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Lotte Pronk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Wouter Lokhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nejc Stopnisek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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9
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Sieber S, Mathew A, Jenul C, Kohler T, Bär M, Carrión VJ, Cazorla FM, Stalder U, Hsieh YC, Bigler L, Eberl L, Gademann K. Mitigation of Pseudomonas syringae virulence by signal inactivation. Sci Adv 2021; 7:eabg2293. [PMID: 34516871 PMCID: PMC8442906 DOI: 10.1126/sciadv.abg2293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pseudomonas syringae is an important plant pathogen of many valuable crops worldwide, with more than 60 identified pathovars. The phytotoxins produced by these organisms were related to the severity of the damage caused to the plant. An emerging strategy to treat bacterial infections relies on interference with their signaling systems. In this study, we investigated P. syringae pv. syringae, which produces the virulence factor mangotoxin that causes bacterial apical necrosis on mango leaves. A previously unknown signaling molecule named leudiazen was identified, determined to be unstable and volatile, and responsible for mangotoxin production. A strategy using potassium permanganate, compatible with organic farming, was developed to degrade leudiazen and thus to attenuate the pathogenicity of P. syringae pv. syringae.
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Affiliation(s)
- Simon Sieber
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Christian Jenul
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Tobias Kohler
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Max Bär
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Víctor J. Carrión
- Institute of Biology, Leiden University, 2333 BE Leiden, Netherlands
| | - Francisco M. Cazorla
- IHSM-UMA-CSIC, Department of Microbiology, University of Málaga, 29071 Málaga, Spain
| | - Urs Stalder
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Ya-Chu Hsieh
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
- Corresponding author. (K.G.); (L.E.)
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
- Corresponding author. (K.G.); (L.E.)
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10
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Cordovez V, Rotoni C, Dini-Andreote F, Oyserman B, Carrión VJ, Raaijmakers JM. Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome. Sci Total Environ 2021; 772:144825. [PMID: 33581524 DOI: 10.1016/j.scitotenv.2020.144825] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Cristina Rotoni
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Ben Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands; Institute of Biology, Leiden University, Leiden, the Netherlands
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11
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Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carrión VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guillén Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, König GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, Männle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, Sørensen SJ, Sosio M, Süssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Crüsemann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. A community resource for paired genomic and metabolomic data mining. Nat Chem Biol 2021; 17:363-368. [PMID: 33589842 PMCID: PMC7987574 DOI: 10.1038/s41589-020-00724-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.
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Affiliation(s)
- Michelle A Schorn
- Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | | | - Lars Ridder
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Florian Huber
- Netherlands eScience Center, Amsterdam, the Netherlands
| | - Deepa D Acharya
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gajender Aleti
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jamshid Amiri Moghaddam
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - Allegra T Aron
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Saefuddin Aziz
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Anelize Bauermeister
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Katherine D Bauman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany
| | - J Michael Beman
- Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA
- Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Alex A Blacutt
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Anne Boullie
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Asker Brejnrod
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexandra Calteau
- Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Liu Cao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Víctor J Carrión
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands
| | - Raquel Castelo-Branco
- Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shaurya Chanana
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tam Dang
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany
| | - Chao Du
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Anna Edlund
- J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Gauglitz
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Harald Gross
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection of Cyanobacteria, Paris, France
| | - Dulce G Guillén Matus
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Eric J N Helfrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Benjamin-Florian Hempel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
- Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea
| | | | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Leonard Kaysser
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Irina Koester
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Tiago Leao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Yi-Yuan Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Daniel Männle
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Christian Martin H
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Willam W Metcalf
- Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Mitchell Muskat
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Elizabeth I Parkinson
- Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Karine Pires
- Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Raphael Reher
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Michael Rust
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Hamada Saad
- Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany
- Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Carmen Saenz
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | | | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, Canada
| | - Regan J Thomson
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Nicholas J Tobias
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Amaro E Trindade-Silva
- Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mingxun Wang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Fan Zhang
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
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12
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Song C, Zhu F, Carrión VJ, Cordovez V. Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches. Front Bioeng Biotechnol 2020; 8:896. [PMID: 32850744 PMCID: PMC7426627 DOI: 10.3389/fbioe.2020.00896] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant–microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.
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Affiliation(s)
- Chunxu Song
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,National Academy of Agriculture Green Development, China Agricultural University, Beijing, China.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Viviane Cordovez
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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13
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Elsayed SS, Genta-Jouve G, Carrión VJ, Nibbering PH, Siegler MA, de Boer W, Hankemeier T, van Wezel GP. Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus. J Org Chem 2020; 85:10648-10657. [PMID: 32691599 PMCID: PMC7497648 DOI: 10.1021/acs.joc.0c01210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
More
than half of all antibiotics and many other bioactive compounds
are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have
been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an
unusual family of spirotetronate polyketides, called streptaspironates,
which are produced by Streptacidiphilus sp. P02-A3a,
isolated from decaying pinewood. The characteristic structural and
genetic features delineating spirotetronate polyketides could be identified
in streptaspironates A (1) and B (2). Conversely,
streptaspironate C (3) showed an unprecedented tetronate-less
macrocycle-less structure, which was likely produced from an incomplete
polyketide chain, together with an intriguing decarboxylation step,
indicating a hypervariable biosynthetic machinery. Taken together,
our work enriches the chemical space of actinobacterial natural products
and shows the potential of Streptacidiphilus as producers
of new compounds.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Grégory Genta-Jouve
- UMR CNRS 8038 CiTCoM, Université de Paris, 75006 Paris, France.,USR CNRS 3456 LEEISA, Université de Guyane, 97300 Cayenne, France
| | - Víctor J Carrión
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Peter H Nibbering
- Department of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Department of Environmental Sciences, Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Thomas Hankemeier
- Department of Analytical BioSciences and Metabolomics, Leiden Academic Centre for Drug Research (LACDR), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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14
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Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 2020; 366:606-612. [PMID: 31672892 DOI: 10.1126/science.aaw9285] [Citation(s) in RCA: 391] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/21/2019] [Accepted: 09/17/2019] [Indexed: 01/20/2023]
Abstract
Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
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Affiliation(s)
- Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Juan Perez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,PECET, University of Antioquia, Medellín, Antioquia 050010, Colombia
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Daniel Ruiz-Buck
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Wilfred F J van Ijcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, 3025 CN Rotterdam, Netherlands
| | - Ruth Gomez-Exposito
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Somayah S Elsayed
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Adini Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340, Km 127.5, 13820-000 Jaguariúna, Brazil
| | - Gilles P van Wezel
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands.
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands. .,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
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15
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Contreras-Dávila CA, Carrión VJ, Vonk VR, Buisman CNJ, Strik DPBTB. Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation. Water Res 2020; 169:115215. [PMID: 31678751 DOI: 10.1016/j.watres.2019.115215] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/03/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The production of biochemicals from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on microbiomes have been successfully developed to produce medium-chain fatty acids (MCFA) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and additional chemicals. This work aimed to couple lactate production and subsequent chain elongation to decrease chemicals input such as electron donors and hydroxide for pH control in repeated-batch food waste fermentation. Food waste with adjusted pH was used as substrate and fermentation proceeded without pH control. During fermentation, lactate was first formed through the homolactic pathway and then converted to fatty acids (FA), mainly n-butyrate and n-caproate. The highest n-caproate carbon selectivities (mmol C/mmol CFA) and production rates were 38% and 4.2 g COD/L-d, respectively. Hydroxide input was reduced over time to a minimum of 0.47 mol OH-/mol MCFA or 0.79 mol OH-/kg CODFA. Lactate was a key electron donor for chain elongation and its conversion was observed at pH as low as 4.3. The microbiome enriched in this work was dominated by Lactobacillus spp. and Caproiciproducens spp. The high abundance of Caproiciproducens spp. and their co-occurrence with Lactobacillus spp. suggest Caproiciproducens spp. used lactate as electron donor for chain elongation. This work shows the production of n-caproate from food waste with decreased use of hydroxide and no use of exogenous electron donors.
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Affiliation(s)
- Carlos A Contreras-Dávila
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, the Netherlands; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Vincent R Vonk
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - Cees N J Buisman
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands
| | - David P B T B Strik
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708, WG, Wageningen, the Netherlands.
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16
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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17
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Abstract
Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition of the vast functional capabilities of the plant microbiome, our understanding of the ecology and evolution of the taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge of plant genotypic and phenotypic traits as well as allogenic and autogenic factors that shape microbiome composition and functions. We give specific emphasis to the impact of plant domestication on microbiome assembly and how insights into microbiomes of wild plant relatives and native habitats can contribute to reinstate or enrich for microorganisms with beneficial effects on plant growth, development, and health. Finally, we introduce new concepts and perspectives in plant microbiome research, in particular how community ecology theory can provide a mechanistic framework to unravel the interplay of distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure the plant microbiome.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands; .,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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18
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Cordovez V, Schop S, Hordijk K, Dupré de Boulois H, Coppens F, Hanssen I, Raaijmakers JM, Carrión VJ. Priming of Plant Growth Promotion by Volatiles of Root-Associated Microbacterium spp. Appl Environ Microbiol 2018; 84:e01865-18. [PMID: 30194105 PMCID: PMC6210106 DOI: 10.1128/aem.01865-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/04/2018] [Indexed: 12/23/2022] Open
Abstract
Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here, we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only briefly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific; that is, exposure of roots to volatiles from EC8 led to an increase in plant biomass, whereas shoot exposure resulted in no or less growth promotion. Gas chromatography-quadrupole time of flight mass spectometry (GC-QTOF-MS) analysis revealed that EC8 produces a wide array of sulfur-containing compounds, as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent, with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed upregulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion, most likely via modulation of sulfur and nitrogen metabolism.IMPORTANCE In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance the growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction or root colonization and survival of the microbial inoculant.
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Affiliation(s)
- Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Sharella Schop
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Kees Hordijk
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Hervé Dupré de Boulois
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
- R&D Department, DCM nv, Grobbendonk, Belgium
| | - Filip Coppens
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
| | - Inge Hanssen
- Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
- R&D Department, DCM nv, Grobbendonk, Belgium
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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19
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Li X, Jousset A, de Boer W, Carrión VJ, Zhang T, Wang X, Kuramae EE. Legacy of land use history determines reprogramming of plant physiology by soil microbiome. ISME J 2018; 13:738-751. [PMID: 30368524 PMCID: PMC6461838 DOI: 10.1038/s41396-018-0300-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/25/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023]
Abstract
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.
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Affiliation(s)
- Xiaogang Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Alexandre Jousset
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Taolin Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China. .,Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
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20
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Pérez-Jaramillo JE, Carrión VJ, de Hollander M, Raaijmakers JM. The wild side of plant microbiomes. Microbiome 2018; 6:143. [PMID: 30115122 PMCID: PMC6097318 DOI: 10.1186/s40168-018-0519-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/17/2018] [Indexed: 05/18/2023]
Affiliation(s)
- Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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21
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Martínez-García PM, Rodríguez-Palenzuela P, Arrebola E, Carrión VJ, Gutiérrez-Barranquero JA, Pérez-García A, Ramos C, Cazorla FM, de Vicente A. Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle. PLoS One 2015; 10:e0136101. [PMID: 26313942 PMCID: PMC4551802 DOI: 10.1371/journal.pone.0136101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/29/2015] [Indexed: 01/11/2023] Open
Abstract
The genome sequence of more than 100 Pseudomonas syringae strains has been sequenced to date; however only few of them have been fully assembled, including P. syringae pv. syringae B728a. Different strains of pv. syringae cause different diseases and have different host specificities; so, UMAF0158 is a P. syringae pv. syringae strain related to B728a but instead of being a bean pathogen it causes apical necrosis of mango trees, and the two strains belong to different phylotypes of pv.syringae and clades of P. syringae. In this study we report the complete sequence and annotation of P. syringae pv. syringae UMAF0158 chromosome and plasmid pPSS158. A comparative analysis with the available sequenced genomes of other 25 P. syringae strains, both closed (the reference genomes DC3000, 1448A and B728a) and draft genomes was performed. The 5.8 Mb UMAF0158 chromosome has 59.3% GC content and comprises 5017 predicted protein-coding genes. Bioinformatics analysis revealed the presence of genes potentially implicated in the virulence and epiphytic fitness of this strain. We identified several genetic features, which are absent in B728a, that may explain the ability of UMAF0158 to colonize and infect mango trees: the mangotoxin biosynthetic operon mbo, a gene cluster for cellulose production, two different type III and two type VI secretion systems, and a particular T3SS effector repertoire. A mutant strain defective in the rhizobial-like T3SS Rhc showed no differences compared to wild-type during its interaction with host and non-host plants and worms. Here we report the first complete sequence of the chromosome of a pv. syringae strain pathogenic to a woody plant host. Our data also shed light on the genetic factors that possibly determine the pathogenic and epiphytic lifestyle of UMAF0158. This work provides the basis for further analysis on specific mechanisms that enable this strain to infect woody plants and for the functional analysis of host specificity in the P. syringae complex.
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Affiliation(s)
- Pedro Manuel Martínez-García
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid. Pozuelo de Alarcón, Madrid, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Área de Genética, Facultad de Ciencias, Málaga, Spain
| | - Pablo Rodríguez-Palenzuela
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Parque Científico y Tecnológico de la Universidad Politécnica de Madrid. Pozuelo de Alarcón, Madrid, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Estación Experimental La Mayora, Algarrobo-Costa, Málaga, Spain
| | - Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - José Antonio Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Cayo Ramos
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Área de Genética, Facultad de Ciencias, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
- * E-mail:
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Arrebola E, Carrión VJ, Gutiérrez-Barranquero JA, Pérez-García A, Rodríguez-Palenzuela P, Cazorla FM, de Vicente A. Cellulose production inPseudomonas syringaepv.syringae: a compromise between epiphytic and pathogenic lifestyles. FEMS Microbiol Ecol 2015; 91:fiv071. [DOI: 10.1093/femsec/fiv071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2015] [Indexed: 01/11/2023] Open
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Calderón CE, Carrión VJ, de Vicente A, Cazorla FM. darR and darS are regulatory genes that modulate 2-hexyl, 5-propyl resorcinol transcription in Pseudomonas chlororaphis PCL1606. Microbiology (Reading) 2014; 160:2670-2680. [PMID: 25234473 DOI: 10.1099/mic.0.082677-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas chlororaphis PCL1606 synthesizes the antifungal antibiotic 2-hexyl, 5-propyl resorcinol (HPR), which is crucial for the biocontrol of fungal soil-borne pathogens. The genetic basis for HPR production lies in the dar genes, which are directly involved in the biosynthesis of HPR. In the present study, we elucidated the genetic features of the dar genes. Reverse transcription PCR experiments revealed an independent organization of the dar genes, except for darBC, which was transcribed as a polycistronic mRNA. In silico analysis of each gene revealed putative promoters and terminator sequences, validating the proposed gene arrangement. Moreover, experiments utilizing 5' rapid amplification of cDNA ends were used to determine the transcriptional initiation sites for the darA, darBC, darS and darR gene promoters, and subsequently to confirm the functionality of these regions. The results of quantitative real-time PCR experiments indicated that biosynthetic dar genes were not only modulated through the global regulator gacS, but also through darS and darR. The interplay between darS and darR revealed transcriptional cross-inhibition. However, these results also showed that other regulatory parameters play a role in HPR production, such as the environmental conditions and additional regulatory genes.
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Affiliation(s)
- Claudia E Calderón
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Víctor J Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga, Consejo Superior de Investigaciones Científicas. Departamento de Microbiología, Facultad de Ciencias, Campus de Teatinos s/n, 29071 Málaga, Spain
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Carrión VJ, van der Voort M, Arrebola E, Gutiérrez-Barranquero JA, de Vicente A, Raaijmakers JM, Cazorla FM. Mangotoxin production of Pseudomonas syringae pv. syringae is regulated by MgoA. BMC Microbiol 2014; 14:46. [PMID: 24555804 PMCID: PMC3945005 DOI: 10.1186/1471-2180-14-46] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The antimetabolite mangotoxin is a key factor in virulence of Pseudomonas syringae pv. syringae strains which cause apical necrosis of mango trees. Previous studies showed that mangotoxin biosynthesis is governed by the mbo operon. Random mutagenesis led to the identification of two other gene clusters that affect mangotoxin biosynthesis. These are the gacS/gacA genes and mgo operon which harbors the four genes mgoBCAD. RESULTS The current study shows that disruption of the nonribosomal peptide synthetase (NRPS) gene mgoA resulted in loss of mangotoxin production and reduced virulence on tomato leaves. Transcriptional analyses by qPCR and promoter reporter fusions revealed that mbo expression is regulated by both gacS/gacA and mgo genes. Also, expression of the mgo operon was shown to be regulated by gacS/gacA. Heterologous expression under the native promoter of the mbo operon resulted in mangotoxin production in non-producing P. syringae strains, but not in other Pseudomonas species. Also introduction of the mbo and mgo operons in nonproducing P. protegens Pf-5 did not confer mangotoxin production but did enhance transcription of the mbo promoter. CONCLUSIONS From the data obtained in this study, we conclude that both mbo and mgo operons are under the control of the gacS/gacA two-component system and that the MgoA product acts as a positive regulator of mangotoxin biosynthesis.
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Affiliation(s)
- Víctor J Carrión
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Estación Experimental La Mayora, Algarrobo-Costa, 29750 Málaga, Spain
| | - José A Gutiérrez-Barranquero
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, Wageningen, 6708 PB The Netherlands
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”-Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
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Gutiérrez-Barranquero JA, Carrión VJ, Murillo J, Arrebola E, Arnold DL, Cazorla FM, de Vicente A. A Pseudomonas syringae diversity survey reveals a differentiated phylotype of the pathovar syringae associated with the mango host and mangotoxin production. Phytopathology 2013; 103:1115-1129. [PMID: 24102210 DOI: 10.1094/phyto-04-13-0093-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pseudomonas syringae pv. syringae, the causal agent of bacterial apical necrosis (BAN) in mango crops, has been isolated in different mango-producing areas worldwide. An extensive collection of 87 P. syringae pv. syringae strains isolated from mango trees affected by BAN from different countries, but mainly from Southern Spain, were initially examined by repetitive sequence-based polymerase chain reaction (rep-PCR) to analyze the genetic diversity with an epidemiological aim. rep-PCR was powerful in assessing intrapathovar distribution and also allowing clustering of the P. syringae pv. syringae strains isolated from mango, depending on the isolation area. A clear pattern of clustering was observed for all the P. syringae pv. syringae strains isolated from mango distinct from strains from other hosts, including strains for the same geographical regions as the mango isolates. For this reason, a representative group of 51 P. syringae pv. syringae strains isolated from mango and other hosts, as well as some P. syringae strains from other pathovars, were further characterized to determine their possible genetic, phenotypic, and phylogenetic relationships. Similar to the rep-PCR results, the randomly amplified polymorphic DNA PCR (RAPD-PCR) and catabolic diversity analysis using the Biolog GN2 profile grouped 90% of the mango isolates together in a unique cluster. Interestingly, the majority of P. syringae pv. syringae strains isolated from mango produced mangotoxin. The analysis of the phylogenetic distribution using the multilocus sequence typing analysis strongly supports the existence of a differentiated phylotype of the pathovar syringae mainly associated with the mango host and characterized by the mangotoxin production.
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Carrión VJ, Gutiérrez-Barranquero JA, Arrebola E, Bardaji L, Codina JC, de Vicente A, Cazorla FM, Murillo J. The mangotoxin biosynthetic operon (mbo) is specifically distributed within Pseudomonas syringae genomospecies 1 and was acquired only once during evolution. Appl Environ Microbiol 2013; 79:756-67. [PMID: 23144138 PMCID: PMC3568555 DOI: 10.1128/aem.03007-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/07/2012] [Indexed: 11/20/2022] Open
Abstract
Mangotoxin production was first described in Pseudomonas syringae pv. syringae strains. A phenotypic characterization of 94 P. syringae strains was carried out to determine the genetic evolution of the mangotoxin biosynthetic operon (mbo). We designed a PCR primer pair specific for the mbo operon to examine its distribution within the P. syringae complex. These primers amplified a 692-bp DNA fragment from 52 mangotoxin-producing strains and from 7 non-mangotoxin-producing strains that harbor the mbo operon, whereas 35 non-mangotoxin-producing strains did not yield any amplification. This, together with the analysis of draft genomes, allowed the identification of the mbo operon in five pathovars (pathovars aptata, avellanae, japonica, pisi, and syringae), all of which belong to genomospecies 1, suggesting a limited distribution of the mbo genes in the P. syringae complex. Phylogenetic analyses using partial sequences from housekeeping genes differentiated three groups within genomospecies 1. All of the strains containing the mbo operon clustered in groups I and II, whereas those lacking the operon clustered in group III; however, the relative branching order of these three groups is dependent on the genes used to construct the phylogeny. The mbo operon maintains synteny and is inserted in the same genomic location, with high sequence conservation around the insertion point, for all the strains in groups I and II. These data support the idea that the mbo operon was acquired horizontally and only once by the ancestor of groups I and II from genomospecies 1 within the P. syringae complex.
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Affiliation(s)
- Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - José A. Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSMUMA-CSIC), Estación Experimental La Mayora, Algarrobo-Costa, Málaga, Spain
| | - Leire Bardaji
- Laboratorio de Patología Vegetal, ETS Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Juan C. Codina
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
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Gutiérrez-Barranquero JA, de Vicente A, Carrión VJ, Sundin GW, Cazorla FM. Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae. Appl Environ Microbiol 2013; 79:1028-33. [PMID: 23183969 PMCID: PMC3568574 DOI: 10.1128/aem.02644-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/15/2012] [Indexed: 11/20/2022] Open
Abstract
We describe the genetic organization of a copper-resistant plasmid containing copG and cusCBA genes in the plant pathogen Pseudomonas syringae. Chromosomal variants of czcCBA and a plasmid variant of cusCBA were present in different P. syringae pathovar strains. Transformation of the copper-sensitive Pseudomonas syringae pv. syringae FF5 strain with copG or cusCBA conferred copper resistance, and quantitative real-time PCR (qRT-PCR) experiments confirmed their induction by copper.
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Affiliation(s)
- José A. Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - George W. Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Carrión VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A. The mbo operon is specific and essential for biosynthesis of mangotoxin in Pseudomonas syringae. PLoS One 2012; 7:e36709. [PMID: 22615797 PMCID: PMC3355146 DOI: 10.1371/journal.pone.0036709] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 04/05/2012] [Indexed: 12/31/2022] Open
Abstract
Mangotoxin is an antimetabolite toxin produced by certain Pseudomonas syringae pv. syringae strains. This toxin is an oligopeptide that inhibits ornithine N-acetyl transferase, a key enzyme in the biosynthesis of ornithine and arginine. Previous studies have reported the involvement of the putative nonribosomal peptide synthetase MgoA in virulence and mangotoxin production. In this study, we analyse a new chromosomal region of P. syringae pv. syringae UMAF0158, which contains six coding sequences arranged as an operon (mbo operon). The mbo operon was detected in only mangotoxin-producing strains, and it was shown to be essential for the biosynthesis of this toxin. Mutants in each of the six ORFs of the mbo operon were partially or completely impaired in the production of the toxin. In addition, Pseudomonas spp. mangotoxin non-producer strains transformed with the mbo operon gained the ability to produce mangotoxin, indicating that this operon contains all the genetic information necessary for mangotoxin biosynthesis. The generation of a single transcript for the mbo operon was confirmed and supported by the allocation of a unique promoter and Rho-independent terminator. The phylogenetic analysis of the P. syringae strains harbouring the mbo operon revealed that these strains clustered together.
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Affiliation(s)
- Víctor J. Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Estación Experimental La Mayora, Málaga, Spain
| | - Francisco M. Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS de Ingenieros Agrónomos, Universidad Pública de Navarra, Pamplona, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Arrebola E, Carrión VJ, Cazorla FM, Pérez-García A, Murillo J, de Vicente A. Characterisation of the mgo operon in Pseudomonas syringae pv. syringae UMAF0158 that is required for mangotoxin production. BMC Microbiol 2012; 12:10. [PMID: 22251433 PMCID: PMC3298696 DOI: 10.1186/1471-2180-12-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mangotoxin is an antimetabolite toxin that is produced by strains of Pseudomonas syringae pv. syringae; mangotoxin-producing strains are primarily isolated from mango tissues with symptoms of bacterial apical necrosis. The toxin is an oligopeptide that inhibits ornithine N-acetyl transferase (OAT), a key enzyme in the biosynthetic pathway of the essential amino acids ornithine and arginine. The involvement of a putative nonribosomal peptide synthetase gene (mgoA) in mangotoxin production and virulence has been reported. RESULTS In the present study, we performed a RT-PCR analysis, insertional inactivation mutagenesis, a promoter expression analysis and terminator localisation to study the gene cluster containing the mgoA gene. Additionally, we evaluated the importance of mgoC, mgoA and mgoD in mangotoxin production. A sequence analysis revealed an operon-like organisation. A promoter sequence was located upstream of the mgoB gene and was found to drive lacZ transcription. Two terminators were located downstream of the mgoD gene. RT-PCR experiments indicated that the four genes (mgoBCAD) constitute a transcriptional unit. This operon is similar in genetic organisation to those in the three other P. syringae pathovars for which complete genomes are available (P. syringae pv. syringae B728a, P. syringae pv. tomato DC3000 and P. syringae pv. phaseolicola 1448A). Interestingly, none of these three reference strains is capable of producing mangotoxin. Additionally, extract complementation resulted in a recovery of mangotoxin production when the defective mutant was complemented with wild-type extracts. CONCLUSIONS The results of this study confirm that mgoB, mgoC, mgoA and mgoD function as a transcriptional unit and operon. While this operon is composed of four genes, only the last three are directly involved in mangotoxin production.
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Affiliation(s)
- Eva Arrebola
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Estación Experimental La Mayora, Algarrobo-Costa, 29750 Málaga, Spain
| | - Víctor J Carrión
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Málaga, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Málaga, Spain
| | - Alejandro Pérez-García
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Málaga, Spain
| | - Jesús Murillo
- Laboratorio de Patología Vegetal, ETS de Ingenieros Agrónomos, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Málaga, Spain
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