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The avocado root phytobiome: microbial community structure under abiotic and biotic stress

Sharifa Crandall: California State University Monterey Bay

<div>Phytophthora root rot, caused by the plant pathogen <em>Phytophthora cinnamomi</em> (Pc) can adversely affect the health of avocado (<em>Persea americana</em>) trees, especially when soil salinity is high. However, diagnosing the effect of biotic and abiotic stressors requires time consuming and costly laboratory tests. Previous research shows that bacteria and fungi are prevalent in roots as part of a plant’s phytobiome; and the composition and structure of microbial communities change under varying environmental conditions. Identifying the microbes present under stressed environments could rapidly and accurately diagnose avocado health at affordable costs. The primary objective of our research was to screen for root microbes that can serve as indicators of plant stress for avocado trees growing in California. A total of 117 avocado root and soil samples were taken from 18 orchards along the central and southern coast region of California. Soil salinity ranged from 0.68 dS/m to 5.28 dS/m across all sites. Real-time PCR results indicate that 34% of the samples tested positive for Pc. Novel next-generation DNA sequencing was used to identify bacteria and fungi species that are associated with plant stress. Results will prove useful to screen for microbial candidates that may be used in future Pc biocontrol experiments.</div>