Seasonal Community Succession of the Phyllosphere Microbiome

Abstract

The leaf microbiome is influenced by both biotic and abiotic factors. Currently, we know little about the relative importance of these factors in determining microbiota composition and dynamics. To explore this issue, we collected weekly leaf samples over a 98-day growing season from multiple cultivars of common bean, soybean, and canola planted at three locations in Ontario, Canada, and performed Illumina-based microbiome analysis. We find that the leaf microbiota at the beginning of the season is very strongly influenced by the soil microbiota but, as the season progresses, it differentiates, becomes significantly less diverse, and transitions to having a greater proportion of leaf-specific taxa that are shared among all samples. A phylogenetic investigation of communities by reconstruction of unobserved states imputation of microbiome function inferred from the taxonomic data found significant differences between the soil and leaf microbiome, with a significant enrichment of motility gene categories in the former and metabolic gene categories in the latter. A network co-occurrence analysis identified two highly connected clusters as well as subclusters of putative pathogens and growth-promoting bacteria. These data reveal some of the complex ecological dynamics that occur in microbial communities over the course of a growing season and highlight the importance of community succession.

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

“…Primer set 799f/1193r revealed 438 ± 24 OTUs in the bulk soils compared to 383 ± 122 in the A. pseudoplatanus rhizosphere, suggesting that this chloroplast mismatch primer, which was effective in reducing chloroplast amplification for A. pseudoplatanus , comes at a trait-off in the number of OTUs detected and overall coverage and phylum spectrum. Previously, primer set 799f and 1193r was shown to effectively reduce chloroplast amplification from A. thaliana rhizosphere and root endophytic tissues ((Bulgarelli et al, 2012), (Schlaeppi et al, 2014)), seed endophytes (Truyens et al, 2015), and soybean, canola, and common bean leaves (Copeland et al, 2015). Interestingly, in our study, primer set 967f/1391r was also effective in reducing the co-amplification of chloroplast targets from A. pseudoplatanus rhizosphere samples (only 38 reads detected or <0.1%) while maintaining a higher overall coverage compared to 799f/1193r, suggesting it is a promising primer for bacterial community analyses of sycamore trees and potentially other plant species.…”

The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen

“…Burkholderia, Pseudomonas and Methylophilus are among the major genera reported in the phylloplane of A. thaliana and other plants (Vorholt, 2012;Reisberg et al, 2013;Bodenhausen et al, 2014). Obviously, the physical and biochemical properties of the plant leaf surface, as well as environmental factors determine the composition of the microbes it harbours (Vorholt, 2012;Copeland et al, 2015).…”

Understanding and exploiting plant beneficial microbes

“…Studies of successional dynamics of plant microbiota suggest that upon emergence, initial seed microbiomes rapidly give way to different, soil-derived communities that are still changing days following emergence [40]. Throughout the growing season, this soil-derived community undergoes continuous succession in both above-ground [41,42] and below-ground [43] fractions of the plant. Thus, even if PGP inoculants colonize the plant initially, their persistence over time is not guaranteed.…”