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Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics

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Lutz, Stefanie; Thuerig, Barbara; Oberhaensli, Thomas; Mayerhofer, Johanna; Fuchs, Jacques G.; Widmer, Franco; Freimoser, Florian M. and Ahrens, Christian H. (2020) Harnessing the Microbiomes of Suppressive Composts for Plant Protection: From Metagenomes to Beneficial Microorganisms and Reliable Diagnostics. Frontiers in Microbiology, 11, p. 1810.

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Online at: https://www.frontiersin.org/articles/10.3389/fmicb.2020.01810/full

Summary

Soil-borne diseases cause significant yield losses worldwide, are difficult to treat and often only limited options for disease management are available. It has long been known that compost amendments, which are routinely applied in organic and integrated farming as a part of good agricultural practice to close nutrient cycles, can convey a protective effect. Yet, the targeted use of composts against soil-borne diseases is hampered by the unpredictability of the efficacy. Several studies have identified and/or isolated beneficial microorganisms (i.e., bacteria, oomycetes, and fungi) from disease suppressive composts capable of suppressing pathogens (e.g., Pythium and Fusarium) in various crops (e.g., tomato, lettuce, and cucumber), and some of them have been developed into commercial products. Yet, there is growing evidence that synthetic or complex microbial consortia can be more effective in controlling diseases than single strains, but the underlying molecular mechanisms are poorly understood. Currently, a major bottleneck concerns the lack of functional assays to identify the most potent beneficial microorganisms and/or key microbial consortia from complex soil and compost microbiomes, which can harbor tens of thousands of species. This focused review describes microorganisms, which have been isolated from, amended to or found to be abundant in disease-suppressive composts and for which a beneficial effect has been documented. We point out opportunities to increasingly harness compost microbiomes for plant protection through an integrated systems approach that combines the power of functional assays to isolate biocontrol and plant growth promoting strains and further prioritize them, with functional genomics approaches that have been successfully applied in other fields of microbiome research. These include detailed metagenomics studies (i.e., amplicon and shotgun sequencing) to achieve a better understanding of the complex system compost and to identify members of taxa enriched in suppressive composts. Whole-genome sequencing and complete assembly of key isolates and their subsequent functional profiling can elucidate the mechanisms of action of biocontrol strains. Integrating the benefits of these approaches will bring the long-term goals of employing microorganisms for a sustainable control of plant pathogens and developing reliable diagnostic assays to assess the suppressiveness of composts within reach.


EPrint Type:Journal paper
Keywords:long-term, soil-borne disease, Department of Crop Sciences, Crop protection - Phytopathology, compost, organic farming, microbiome, biocontrol, metagenomics, genome assembly, strain collection, mechanism of action
Subjects: Soil > Soil quality
Crop husbandry > Crop health, quality, protection
Research affiliation: Switzerland > Agroscope > ACW - Research Centre Wädenswil
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Plant Protection and Biodiversity
Switzerland > Other organizations
DOI:doi.org/10.3389/fmicb.2020.01810
Deposited By: Thürig, Dr. Barbara
ID Code:38257
Deposited On:05 Aug 2020 09:05
Last Modified:05 Aug 2020 09:05
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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