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. 2015 May 15;81(10):3405-18.
doi: 10.1128/AEM.03787-14. Epub 2015 Mar 13.

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

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

Nuria Bonilla et al. Appl Environ Microbiol. .
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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.

Figures

FIG 1
FIG 1
Effect of the organic amendments on avocado plant growth during 9 months of assay. Comparison between amended and unamended control treatment in plant height, trunk cross-sectional area, and growth of lateral branches of noninoculated plants in the two greenhouse experiments. Different letters mean significant differences between treatments (ANOVA, P < 0.05). UC, unamended control; AS, almond shells; PW, pruning waste; YW, yard waste.
FIG 2
FIG 2
Effect of the organic amendments on avocado white root rot. Time course of the disease index, calculated by evaluation of the aerial symptoms of white root rot in the inoculation assays. (A) Assay 1; (B) assay 2. Symbols: ■, unamended control; ▲, almond shells; ●, pruning waste; ◆, yard waste.
FIG 3
FIG 3
Effect of organic amendments on the chemical properties of the soil. Scatter plot based on PCA of the soil chemical properties of the assay 2. The symbols refer different treatments: ■, unamended control; ▲, almond shells; ●, pruning waste; ◆, yard waste. The data for the chemical composition of the amended soils and the correlation of chemical parameters to ordination axes derived from PCA analysis are available in Tables S1 and S2 in the supplemental material.
FIG 4
FIG 4
Effect of organic amendments on culturable microorganisms. The population densities of fast-growing heterotrophic bacteria, pseudomonads, sporulating bacteria, actinomycetes, and fungi were assessed by plate counts. Different lowercase letters indicate significant differences (ANOVA, P < 0.05). UC, unamended control; AS, almond shells; PW, pruning waste; YW, yard waste.
FIG 5
FIG 5
Effect of organic amendments on the metabolic profiles of the microbial community. Scatter plots were prepared based on PCA of normalized OD data of Biolog Ecoplates. (A) Bulk soil of the assay 1; (B) bulk soil of the assay 2; (C) rhizosphere of the assay 2. Symbols: ■, unamended control (UC); ▲, almond shells (AS); ●, pruning waste (PW); ◆, yard waste (YW).
FIG 6
FIG 6
Effect of organic amendments on soil bacterial communities. (A, C, and E) PCR-DGGE fingerprints of bacterial 16S rRNA gene fragments. One replicate from each pot (named A, B, and C) of the different treatments were loaded in the same gel. (B, D, and F) Cluster dendrograms based on Pearson correlation coefficient and UPGMA algorithm showing similarity between 16S DGGE profiles. Numbers at the nodes represent cophenetic correlation values in percent. (A and B) Bulk soil of the assay 1; (C and D) bulk soil of the assay 2; (E and F) rhizosphere of the assay 2. UC, unamended control; AS, almond shells; PW, pruning waste; YW, yard waste. The codes of numbers and letters marked on the DGGE bands from panels A, C, and E correspond to the band codes of 16S rRNA gene sequences shown in Table 4.

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