Using next-generation sequencing technology for pathogen discovery

Blueberries are woody perennials that, with proper care, can produce a crop each year for decades. In some fields in New Jersey, fruit yields and plant health are declining without definitive cause. Microbial communities in the soil can directly or indirectly affect plant health. Thus, determining what soil organisms are associated with decline, might provide clues for developing approaches to remediation. Soils were collected from the rhizosphere of blueberry plants in healthy and ‘decline-associated’ fields. DNA was extracted from the soils and target regions (16S for bacteria, ITS for fungi, and 18S for nematodes) were amplified by PCR and sequenced. Taxonomic determinations of the soil microorganisms were based on sequence similarity using BLAST. Preliminary data showed the bacterial community was dominated by the Proteobacteria, with no distinct differences between the soil types. FUNGuild was used to assign the fungal taxa to ecological guild. Most of the fungi detected were saprotrophs, but a substantial number of potential plant pathogens were also identified. We identified more than 70 nematode genera and of those genera detected, only three were classified by NEMAGuild to be plant parasites. Follow up studies are needed to confirm the presence and potential impact of bacterial, fungal, and nematode phyla that may be associated with decline.