Purpose: We profiled the surface bacterial communities of cucumber fruit, tomato fruit, and tomato leaves in the days surrounding two rainstorms to investigate the influence of rain on the microbiome of these high risk crops.
Methods: Cucumber fruit (n=24) and tomato leaf (n=35) and fruit (n=35) samples were collected from a Maryland organic farm on 5 dates surrounding 2 rain events (12.45 mm and 3.56 mm). DNA was extracted from surface washes, and 16S rRNA gene sequencing was performed using Illumina MiSeq v3. Data was quality filtered and analyzed using QIIME v. 1.8.
Results: At a sampling depth of 15,540 sequences per sample, approximately 1,055 OTUs (97% similarity) were identified for each sample. A significant influence of collection date on microbial community composition was observed on cucumbers (R2=0.225, P=0.002), with 4 days pre-rain and 1 day post-rain samples hosting significantly different communities (P=0.002); 4 day post-rain samples were indistinguishable from the two other time points. A weaker, but still significant, effect of sampling date was observed on tomato fruit communities (R2=0.12, P=0.003) but not tomato leaf-associated communities (R2=0.06, P=0.43). Both cucumber and tomato fruit-associated communities showed a temporary increase in Betaproteobacteria immediately following rain, which was partially reversed by 4 days post-rain.
Significance: This study demonstrated a shift in the structure of cucumber and tomato fruit surface-associated bacterial communities following a rain event. The susceptibility of plant hosts to pathogen colonization could be enhanced by these weather-induced shifts in microbial species dominance, and this shift may be more dramatic on fruits.