Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations.

Assessment of pathogen diversity in agricultural fields is essential for informing management decisions and the development of resistant plant varieties. However, many population genomic studies have relied on culture-based approaches that do not provide quantitative assessment of pathogen populations at the field-level or the associated host microbiome. Here, we applied whole-genome shotgun sequencing of microbial DNA extracted directly from the washings of pooled leaf samples, collected from individual tomato and pepper fields in Alabama that displayed the classical symptoms of bacterial spot disease caused by Xanthomonas spp. Our results revealed that while the occurrence of both X. perforans and X. euvesicatoria within fields was limited, evidence of co-occurrence of up to three distinct X. perforans genotypes was obtained in 7 of 10 tomato fields sampled. These population dynamics were accompanied by the corresponding type 3 secreted effector repertoires associated with the co-occurring X. perforans genotypes, indicating that metapopulation structure within fields should be considered when assessing the adaptive potential of X. perforans. Finally, analysis of microbial community composition revealed that co-occurrence of the bacterial spot pathogens Pseudomonas cichorii and Xanthomonas spp. is common in Alabama fields and provided evidence for the non-random association of several other human and plant opportunists.

A Multivirus Epidemic of Tomatoes in Alabama.

During 1992, a multivirus epidemic reduced tomato production by as much as 25% in the major tomato-growing region of Alabama. Estimated yield losses of 100% resulted from the epidemic in over 250 ha in two counties of North Alabama. Cucumber mosaic cucumovirus (CMV), alone or in combination with potato potyvirus Y (PVY) and/or tobacco etch potyvirus (TEV), was responsible for the crop failure. CMV was detected alone or in combination with PVY and/or TEV in over 70% of the samples tested and was present in 90% of the fields surveyed. In 1993, 21 tomato fields were monitored weekly from transplanting through harvest for CMV, PVY, TEV, tobacco mosaic tobamovirus, and tomato spotted wilt tospovirus. All 5 viruses were detected, with CMV occurring most frequently. Incidence of CMV at the 61% level or higher was found in 16 of the 21 fields surveyed. Tomatoes transplanted in April and May were least effected and had relatively low virus incidence until late in their development. Tomatoes transplanted in June and July were infected at an earlier age, had the highest virus incidence, were the most severely affected, and suffered the greatest loss in yield. In 1994,Aphis gossypii, the cotton aphid, was the most common virus vector found during an aphid monitoring/virus spread study. Populations of A. gossypii peaked in late June, immediately preceding a period of rapid CMV incidence and spread.