Differential selection pressure exerted by root rot disease on the microbial communities in the rhizosphere of avocado (Persea americana Mill.)

Despite the high economic impact of root rot disease, knowledge regarding the rhizosphere microflora of avocado trees affected by root rot is limited. Metagenomics was applied to identify the difference in the rhizosphere microflora of avocado trees with and without visible symptoms of root rot. Approximately, 446,970 common gene catalogues differed between them, confirming that root rot affected the bacterial and fungal communities in the rhizosphere. The proportion of bacterial genera, namely, Labilithrix, Sorangium, Sandaracinus and Pedosphaera showed a decrease while Phenylobacterium, Rhizomicrobium, Candidatus Solibacter and Silvibacterium genera were increased by root rot. The proportion of fungal genera, namely, Pseudogymnoascus, Moelleriella, Mortierella, Lepidopterella, Babjeviella, Lachancea, Macrophomina, Pneumocystis, Sugiyamaella and Cyphellophora showed an increase while Cryptococcus, Verticillium, Bipolaris, Pyrenochaeta, Rhizophagus, Cenococcum and Neonectria genera were inhibited by root rot. Moreover, the proportion of the top 10 bacteria in the rhizosphere of symptomatic trees was significantly higher, and that of the top 10 fungi was significantly lower, compared to the asymptomatic trees. Principal component analysis based on abundance analysis and function prediction showed that in symptomatic trees, the bacterial community was more concentrated, while the fungal community was more dispersed. The differences in the responses of bacterial and fungal genera suggested that the pathogenic fungi exert varying selection pressure on the microflora. Moreover, root rot affected the metabolism of carbohydrates, lipids and amino acids in bacteria, and the global and overview maps, carbon metabolism and processing of genetic and environmental information in fungi, which might result in differential selection pressure.