Abstract
Soil microbiota plays a key role in suppressing soil-borne plant pathogens improving the natural soil suppressiveness. Microbiome disturbance triggers specific perturbation to change and shape the soil microbial communities’ network for increasing suppression against phytopathogens and related diseases. Very important goals have been reached in manipulation of soil microbiota through agronomical practices based on soil pre-fumigation, organic amendment, crop rotation and intercropping. Nevertheless, to limit inconsistencies, drawbacks and failures related to soil microbiota disturbance, a detailed understanding of the microbiome shifts during its manipulation is needed under the light of the microbiome-assisted strategies. Next-generation sequencing often offers a better overview of the soil microbial communities during microbiomes manipulation, but sometime it does not provide information related to the highest taxonomic resolution of the soil microbial communities. This review work reports and discusses the most reliable findings in relation to a comprehensive understanding of soil microbiota and how its manipulation can improve suppression against soil-borne diseases in organic farming systems. Role and functionality of the soil microbiota in suppressing soil-borne pathogens affecting crops have been basically described in the first section of the paper. Characterization of the soil microbiomes network by high-throughput sequencing has been introduced in the second section. Some relevant findings by which soil microbiota manipulation can address the design of novel sustainable cropping systems to sustain crops’ health without use (or reduced use) of synthetic fungicides and fumigants have been extensively presented and discussed in the third and fourth sections, respectively, under the light of the new microbiome-assisted strategies. Critical comparisons on the next-generation sequencing have been provided in the fifth section. Concluding remarks have been drawn in the last section.
Highlights
Plant diseases caused by soil-borne plant pathogens can be effectively suppressed by biotic and abiotic factors of the soil despiteDe Corato Chem
Organic amendment was employed as a part of a more complex strategical picture in controlling more soil-borne pathogens basing on their capability to induce disease suppression [15, 93, 127, 128, 156]
Intensive cropping systems characterized by higher input of synthetic chemicals, lower soil organic matter (SOM) accumulation, scarce humification degree and frequent soil tillage are the primary reasons for soil depletion
Summary
Plant diseases caused by soil-borne plant pathogens (filamentous fungi, oomycetes and bacteria) can be effectively suppressed by biotic and abiotic factors of the soil despiteDe Corato Chem. The integrated agricultural strategies based on the combined use of OAs and BCAs tailored composts and microbial consortia from disease-suppressive composts, and novel bioorganic fertilizers with organic additives (as silicon and chitin) were accepted worldwide for controlling multiple soil-borne pathogens [50, 56, 57, 97, 138, 238]. These practices induce rhizosphere health by beneficial alterations of its microbiota. Very fewer papers regarding the critical revision of the impacts of agronomical practices on agroecosystem health for increasing disease suppression in horticultural farming systems have been found in the literature
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