Dataset Information

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.

SUBMITTER: Blaya J

PROVIDER: S-EPMC4973912 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Blaya Josefa J Marhuenda Frutos C FC Pascual Jose A JA Ros Margarita M

PloS one 20160804 8

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-industri ...[more]

PMID: 27490955

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Project description:BackgroundPhytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified.ResultsDevelopment of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified.ConclusionsResults support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.

Project description:Phytophthora capsici Leonian (PHC) is a filamentous pathogen oomycete that causes root, fruit, foliar and crown rot over a wide host range, including the economically and nutritionally important summer squash (Cucurbita pepo var. cylindrica L.) crop. PHC chemical control strategies are difficult to adopt, due to the limited number of registered chemicals that are permitted and the scalar harvest system. For these reasons, other strategies, such as the use of waste-based composts that can act as suppressive agents against several soilborne pathogens, have been studied intensively. It is well known that compost's microbiota plays an important role to confer its suppressive ability. In this study, four different composts were analyzed with both 16S rRNA gene and 18S rRNA gene real-time PCR amplification and with 26S gene amplicon-based sequencing; the total abundance of the bacterial and fungal communities was found to be higher compared to literature, thus confirming that the four composts were a good inoculum source for agricultural applications. The core mycobiota was mainly composed of 31 genera; nevertheless, it was possible to observe a clear predominance of the same few taxa in all the composts. The four composts were then tested, at different concentrations (1-10-20% v/v), to establish their ability to confer suppressiveness to the Phytophthora capsici (PHC) - Cucurbita pepo pathosystem in controlled greenhouse pot trials. A total of 12 compost mixtures were considered, and of these, one (Trichoderma-enriched compost at 10% v/v) was able to statistically reduce the disease incidence caused by PHC (by 50% compared to the untreated control). Hence, the microbiota composition of the most effective compost treatment was investigated and compared with untreated and chemical (metalaxyl) controls. Mycobiota sequencing showed genera differences between the three treatments, with relative abundances of several fungal genera that were significantly different among the samples. Moreover, PCA analyses clustered the compost treatment differently from the chemical and the untreated controls. These findings suggest that suppressive activity of a compost is strictly influenced by its microbiota and the applied dosage, but the ability to induce a shaping in the rhizosphere microbial composition is also required.

Dataset Information

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

Publications

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

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