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

Catello Pane,Riccardo Scotti,Giuseppe Celano,Roberto Sorrentino,Antonio Di Matteo,Marcella Molisso,Massimo Zaccardelli

doi:10.3390/agriculture10040113

Abstract

Green waste composts are obtained from agricultural production chains; their suppressive properties are increasingly being developed as a promising biological control option in the management of soil-borne phytopathogens. The wide variety of microbes harbored in the compost ecological niches may regulate suppressive functions through not yet fully known underlying mechanisms. This study investigates alpha- and beta-diversity of the compost microbial communities, as indicators of the biological features. Our green composts displayed a differential pattern of suppressiveness over the two assayed pathosystems. Fungal and bacterial densities, as well as catabolic and enzyme functionalities did not correlate with the compost control efficacy on cress disease. Differences in the suppressive potential of composts can be better predicted by the variations in the community levels of physiological profiles indicating that functional alpha-diversity is more predictive than that which is calculated on terminal restriction fragments length polymorphisms (T-RFLPs) targeting the 16S rRNA gene. However, beta-diversity described by nMDS analysis of the Bray–Curtis dissimilarity allowed for separating compost samples into distinct functionally meaningful clusters and indicated that suppressiveness could be regulated by selected groups of microorganisms as major deterministic mechanisms. This study contributes to individuating new suitable characterization procedures applicable to the suppressive green compost chain.

Highlights

Soil-borne fungal diseases are among the main and most feared factors limiting agricultural production and economic sustainability: they are responsible for severe outbreaks that are difficult to eradicate without the massive use of high-impacting synthetic fungicides
The green waste composts investigated in our study, which varied based in the breakdown of organicbymaterials on the piles; some of them may microorganisms potentially playinvolved a role in Composts are colonized a wide spectrum of Procarya and Eukarya on the plant raw material input, showed a differential pattern of suppressiveness over the two disease suppression
The green waste composts investigated in our study, which varied based in the breakdown of organic materials on the piles; some of them may potentially play a role in assayed pathosystems

Summary

Introduction

Soil-borne fungal diseases are among the main and most feared factors limiting agricultural production and economic sustainability: they are responsible for severe outbreaks that are difficult to eradicate without the massive use of high-impacting synthetic fungicides. Agriculture 2020, 10, 113 eligible habitat for many microbial species with different lifestyles, which impact significantly on yields, quality and healthiness of vegetable crops, with a harmonious use of natural resources, biodiversity and ecosystem processes [3]. These compost-borne microorganisms facilitate many ecosystem functions that generate some fundamental services for people’s well-being [4] and provide regulating services that are noticeable for agriculture sustainability, such as plant nutrient availability, soil regeneration and natural suppression of soil-borne phytopathogens [5]. Compost may act through its microbial components directly towards the pathogen by typical antagonistic mechanisms or on the plant by inducing systemic resistance or stimulating in it an enhanced physiological status [6]

Methods

Results

Discussion

Conclusion