Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control

Abstract

Phytophthora root rot caused by Phytophthora nicotianae is an economically important disease in pepper crops. The use of suppressive composts is a low environmental impact method for its control. Although attempts have been made to reveal the relationship between microbiota and compost suppressiveness, little is known about the microorganisms associated with disease suppression. Here, an Ion Torrent platform was used to assess the microbial composition of composts made of different agro-industrial waste and with different levels of suppressiveness against P. nicotianae. Both bacterial and fungal populations responded differently depending on the chemical heterogeneity of materials used during the composting process. High proportions (67–75%) of vineyard pruning waste were used in the most suppressive composts, COM-A and COM-B. This material may have promoted the presence of higher relative abundance of Ascomycota as well as higher microbial activity, which have proved to be essential for controlling the disease. Although no unique fungi or bacteria have been detected in neither suppressive nor conducive composts, relatively high abundance of Fusarium and Zopfiella were found in compost COM-B and COM-A, respectively. To the best of our knowledge, this is the first work that studies compost metabolome. Surprisingly, composts and peat clustered together in principal component analysis of the metabolic data according to their levels of suppressiveness achieved. This study demonstrated the need for combining the information provided by different techniques, including metagenomics and metametabolomics, to better understand the ability of compost to control plant diseases.

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae

“…In the fungal community study, Ascomycota and Basidiomycota were the most abundant phyla, in agreement with other studies with similar organic materials [53, 38]. Ascomycota has been observed during different composting processes [34, 36], where most of the microorganisms were saprophytic and lived on dead organic matter that they help to decompose [54].…”

“…Similar results were also observed for different types of composts and peat [34, 35, 36, 38]. Bacterial community from the fortification of compost with the two different Trichoderma strains did not show any important differences in the relative abundance of different phyla compared to non-fortified compost.…”

“…solani infection especially controlled by Pseudomonadaceae [44]. Blaya et al [38] also demonstrated that these genera were found in pepper rhizosphere when suppressive composts were used against P . nicotianae , but not in the ones that did not show suppressive effect.…”

Alpha and Beta-diversity of Microbial Communities Associated to Plant Disease Suppressive Functions of On-farm Green Composts

“…radicis-cucumerinum [31]. In agroindustrial waste composts, it was linked to the control of the Phytophthora root rot on pepper [32] or the muskmelon fusariosis and Phytophthora blight on pepper [33]. However, the composition and the redundant metabolic functions can dramatically affect these properties.…”

Microbiota Characterization of Agricultural Green Waste-Based Suppressive Composts Using Omics and Classic Approaches

“…In this regard, microbiota composition has been well described to be one the main factor in compost for control of plant diseases [34]. L5/6A contained greater relative abundance of Bacteriodetes, Proteobacteria and Actinobacteria, all of them have been well documented to be correlated with plant disease suppression [33,35].…”