Nuria Bonilla

Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils

Background and aimsThe avocado-producing area of southern Spain includes conventional orchards and organic orchards that use different organic amendments. To gain insight into the effects of these amendments, physicochemical properties and microbial communities of the soil were analysed in a representative set of commercial and experimental orchards.MethodsThe population size of several groups of culturable microorganisms was determined by plating on different selective media. Bacterial community structure was studied by denaturing gradient gel electrophoresis (DGGE)ResultsCommercial composts showed the largest effects, especially the animal compost, enhancing the population sizes of some microbial groups and affecting bacterial community structure in superficial and deep soil layers. Moreover, animal and vegetal compost, manure and blood meal addition are related to high bacterial diversity in the superficial soil layer.ConclusionsAll of the organic amendments used in this study affect soil properties in one or more of the characteristics that were analysed. Culturable microbial population data revealed the most evident effects of some of the organic treatments. However, molecular analysis of soil bacterial communities by DGGE allowed the detection of the influence of all of the analysed amendments on bacterial community composition. This effect was stronger in the superficial layer of the avocado soil.

Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

ABSTRACT One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially.

Biological control of avocado white root rot with combined applications of Trichoderma spp. and rhizobacteria

This study tested the effectiveness of single and combined applications of Trichoderma and rhizobacterial strains to control white root rot (WRR) caused by Rosellinia necatrix in avocado plants. Three Trichoderma, two T. atroviride and one T. virens monoconidal strains and four bacterial strains (Bacillus subtilis, Pseudomonas pseudoalcaligenes and two P. chlororaphis) were assayed to determine their compatibilities in vitro. In addition, the effects of the bacterial filtrates were evaluated against the Trichoderma strains and reciprocally; these filtrates were applied alone or in combination to determine their effectiveness against R. necatrix. Individual control agents or combinations of them were applied to avocado plants that were artificially inoculated with a virulent R. necatrix strain. Compatibility between the combined Trichoderma applications and the bacterial strains was observed and these combinations significantly improved the control of R. necatrix during the in vitro experiments. A relative protective effect of some Trichoderma and bacteria was observed on the control of avocado WRR when they were applied singly. The combinations of T. atroviride strains with bacterial strains P. chlororaphis and P. pseudoalcaligenes showed a better control of avocado WRR, whereas the rest of Trichoderma and bacteria combinations also reduced significantly the level of disease and induced a delay at the onset of disease with respect to avocado plants inoculated either with Trichoderma or bacteria.

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

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.