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.
Highlights
Phytophthora nicotianae van Breda de Haan (= Phytophthora parasitica Dastur (1896)) stands out among plant pathogens since it is a threat to plant productivity on a global scale for a broadPLOS ONE | DOI:10.1371/journal.pone.0158048 August 4, 2016Omics Approaches and Phytophthora Root Rot Control by Composts range of hosts [1]
Four agro-industrial composts were made from different wastes as follows: Compost A (COM-A): pepper sludge (125 g kg-1), pepper wastes (125 g kg-1), and vineyard pruning wastes (750 g kg-1); Compost B (COM-B): pepper wastes (160 g kg-1), artichoke wastes (160 g kg-1), and vineyard pruning wastes (680 g kg-1); Compost C (COM-C): pepper sludge (190 g kg-1), pepper wastes (20 g kg-1), garlic wastes (20 g kg-1), carrot wastes (350 g kg-1), almond shells (40 g kg-1), and vineyard pruning wastes (380 g kg-1); Compost D (COM-D): artichoke sludge (150 g kg-1), artichoke wastes (264 g kg-1), vineyard pruning wastes (500 g kg-1), and compost (86 g kg-1)
The total organic carbon (TOC) of composts and peat ranged from 273 to 480 g kg-1, with the highest values for peat followed by COM-A, COM-C, COM-B and COM-D (F = 3118; p
Summary
Omics Approaches and Phytophthora Root Rot Control by Composts range of hosts [1]. In Spain and Tunisia, P. nicotianae causes root- and collar- rot in pepper plants (Capsicum annuum L.) and has become a major disease during the last years [3,4,5]. Management of this disease is based on soil fumigation using compounds such as methyl bromide, 1,3-dichloropropene, chloropicrin, metalaxyl and mefenoxam [6]. The banned use of most of these products and their inability to totally control the disease, have prompted the exploration and identification of new approaches
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