Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells.

Carmen Vida,Antonio De Vicente,Nuria Bonilla,Francisco M Cazorla

doi:10.3389/fmicb.2016.00004

Abstract

This study focused on the microbial profile present in an agricultural soil that becomes suppressive after the application of composted almond shells (AS) as organic amendments. For this purpose, we analyzed the functions and composition of the complex communities present in an experimental orchard of 40-year-old avocado trees, many of them historically amended with composted almond shells. The role of microbes in the suppression of Rosellinia necatrix, the causative agent of avocado white root rot, was determined after heat-treatment and complementation experiments with different types of soil. Bacterial and fungal profiles obtained from natural soil samples based on the 16S rRNA gene and ITS sequencing revealed slight differences among the amended (AS) and unamended (CT) soils. When the soil was under the influence of composted almond shells as organic amendments, an increase in Proteobacteria and Ascomycota groups was observed, as well as a reduction in Acidobacteria and Mortierellales. Complementary to these findings, functional analysis by GeoChip 4.6 confirmed these subtle differences, mainly present in the relative abundance of genes involved in the carbon cycle. Interestingly, a group of specific probes included in the “soil benefit” category was present only in AS-amended soils, corresponding to specific microorganisms previously described as potential biocontrol agents, such as Pseudomonas spp., Burkholderia spp., or Actinobacteria. Considering the results of both analyses, we determined that AS-amendments to the soil led to an increase in some orders of Gammaproteobacteria, Betaproteobacteria, and Dothideomycetes, as well as a reduction in the abundance of Xylariales fungi (where R. necatrix is allocated). The combination of microbial action and substrate properties of suppressiveness are discussed.

Highlights

The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases (Lazarovits et al, 2001; Bailey and Lazarovits, 2003; van Elsas and Postma, 2007; Bonilla et al, 2012b; Pane et al, 2013)
Our previous studies demonstrated that different organic amendments can influence the composition and diversity of soil bacterial communities in avocado plants growing in microcosms after DGGE analysis, showing enhancement of specific populations such as Burkholderia and Frateuria (Bonilla et al, 2012a, 2015)
Among different organic matter tested on avocado crops, composted almond shells (AS; commercial almond shells derived from the almond industry were piled and traditionally composted) exhibited enhancement of soil suppressiveness against R. necatrix (Bonilla et al, 2012a, 2015), the causal agent of avocado white root rot (Pliego et al, 2012)

Summary

Introduction

The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases (Lazarovits et al, 2001; Bailey and Lazarovits, 2003; van Elsas and Postma, 2007; Bonilla et al, 2012b; Pane et al, 2013). The soils that become suppressive soils provide an environment in which plant disease development is reduced, even in the presence of a virulent pathogen and a susceptible host (Hadar and Papadopoulou, 2012) This phenomenon could be induced as a direct result of the activity of microorganism consortia that are naturally established on soil after application of the amendment (Weller et al, 2002). Employing genomic approaches to understand which changes occur in soil could be a good alternative strategy to decipher the profiling of soil microbiota (Garbeva et al, 2004)

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