Fungal biocontrol agents
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While individual Sebacinales strains can interact with roots in the absence of differentiated structures, they can also form specialized interactions with distinctive morphological characteristics on relevant hosts, as in orchid- or ectomycorrhiza symbioses.
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Sebacinales fungi (Basidiomycetes) are a remarkable group of plant mutualists with worldwide occurrence in soils and as endophytes. Although diseases caused by pathogens have been shown to be directly or indirectly reduced by the addition of single or multiple beneficial microbes, how fungal root microbiota members with beneficial functions influence and are influenced by bacterial colonization remains less understood. Several bacterial and fungal isolates have the capacity to directly increase plant biomass via growth hormone production and/or by providing plants with limiting macro- or micro-nutrients. The functions and benefits of root microbiota members in the context of abiotic or biotic stresses have been extensively investigated under laboratory conditions using single microbial strains and, more recently, synthetic bacterial communities (SynComs). By contrast, studies of geographically distinct populations of Arabis alpina and Arabidopsis thaliana (hereafter Arabidopsis) showed that few fungal taxa are prevalent in the root endosphere, and that endophytic fungal communities are strongly influenced by location and climate.
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This latter feature underpins the “bacterial core microbiota” concept, in which strains from specific taxa are commonly selected as endophytes across plant species, soil types, and environmental conditions. Moreover, a number of bacterial taxa (e.g., Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes) consistently occur in the root endosphere of different examined plant species. Microbial diversity and abundance gradually decrease between the soil and vicinity of the root (rhizosphere), and further between the rhizosphere and root internal compartments (endosphere).
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Past studies across a variety of plant species employed environmental sampling or controlled conditions in the field and laboratory to characterize the root microbiota, with an overall greater focus on bacteria than on filamentous fungi. Microbial communities living at the root−soil interface, collectively referred to as the plant root microbiota, have gained centre-stage in pathogen protection. However, as the importance of root-inhabiting pathogenic fungi has often been underestimated, very little is known about the molecular mechanism behind the detrimental interaction of Bs with roots. Root rot normally originates from inoculum carried on the seed or from soil-borne conidia, but the fungus can infect plants at any developmental stage. Cochliobolus sativus, hereafter Bs), the causal agent of spot blotch and common root rot diseases that threaten cereal production in warm regions. A key example of this scenario is represented by the soil-borne plant pathogen Bipolaris sorokiniana (syn. Yet, current tools are becoming environmentally unsustainable or ineffective against rapidly evolving pathogens. Decades of advances in agrochemicals and plant breeding have expanded farmers’ toolkits with fungicides and resistant varieties to limit the detrimental effects of these organisms on crop yield. These threats are expected to increase with global warming. Plant pathogenic fungi limit crop productivity globally.