Soil amendments for management of Phytophthora root rot in avocado and their impact on the soil microbiome

Qurrat U Farooq

The use of microbial agents to control plant diseases has many advantages Unlike chemical fungicides, they do not induce plant resistance to disease or damage the environment. The ability of different soil additives and fungicides to control Phytophthora root rot was compared in three experiments using potted avocado plants under glasshouse conditions. It also investigates the impact of soil additives and phosphite on soil microbiome. Avocado plants were grown in pots using soil from an avocado orchard. To simulate ‘orchard soil’ conditions several additives (chicken manure, wood mulch, and mulch from beneath 20-year-old trees in an avocado orchard) were added to the pots. In experiment 1, the effect of two microbial soil conditioners, one organic conditioner, two mineral conditioners, two fungicides and one herbicide were investigated. On the basis of this experiment, the effect of organic conditioner was compared with a soil microbial conditioner, two mineral conditioner and phosphite in a second experiment. In the third experiment, the effect of organic mulches, a silicate based mineral mulch and phosphite were compared again. For microbiome study, soil and roots were collected for metabarcoding study, soil samples were collected for RNA study at the time of harvest. Despite of substantial root damage in some of treatments, Phytophthora added had no damaging effects on shoots in all three experiments. The degree of root damage resulting from treatments was assessed from total and fine root dry weights along with visual root damage. Silicate based mineral mulch reduced the Phytophthora damage to the similar extent to that obtained by phosphite in all the three experiments. No significant loss in weight of total roots were found in the presence of the organic mulches alone or combined with the probiotic or mineral conditioners. In two of three experiments, a significant drop in fine root dry was observed in all treatments except silicate based mineral mulch and phosphite. No significant increase in root protection was observed using a combined application of silicate based mineral mulch and phosphite. A microbial conditioner was beneficial in only one experiment. Metabarcoding study of microbiome reveals, diversity and species richness of soil bacteria were significantly higher in rhizosphere soil treatments with mineral mulch or phosphite compared to soils with only organic mulches. There were more differences between inoculated and non-inoculated plants in mineral mulch than any other treatments suggesting that changes to the bacterial biome may be linked to the disease control. Significantly, the relative abundance of actinobacteria was higher, and that of proteobacteria less in rhizosphere soil with mineral mulch or phosphite treatments, than in the other treatments, whether or not P. cinnamomi was present. Metatranscriptomics analysis showed that more differentially expressed genes were found between mineral mulch and phosphite. The rhizosphere of mineral mulch was dominant by more firmicutes and less proteobacteria, opposite in case with phosphite. The most dominant firmicutes found were from family Bacillaceae and proteobacteria were from families Pseudomonadaceae and Rhizobiaceae family. Greater expression of starch and sucrose metabolism, amino acid biosynthesis, tryptophan metabolism, secondary metabolites biosynthesis was found in plants treated with silicate based mineral mulch when compared to those treated with phosphite. This study showed under glasshouse conditions, addition of microbial based soil conditioners does not protect the plant from Phytophthora root rot. However, silicate based mineral mulch gave a significant level of control, comparable to the fungicide, phosphite. Analysis of the soil microbiome revealed changes in bacterial groups in treatments with silicate based mineral mulch and phosphite. The taxa involved were same as previously reported to contain pathogen antagonists. Metatranscriptomics showed fewer differentially gene expression than expected from similar published studies on disease suppression.

Soil amendments for management of Phytophthora root rot in avocado and their impact on the soil microbiome

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