Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome

Abstract

Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.

Transient interactions and influence among bacteria in field-grown Arabidopsis thaliana tissues

“…The high fraction of positive relationships suggests that competitive interactions do not stabilize plant bacterial communities as they do in models of the human gut microbiome (9). A preponderance of positive interactions is perhaps not surprising given that we considered bacteria only; broader surveys of the plant microbiome indicate that negative interactions are more common between kingdoms than within them (8,10). Positive correlations between bacterial ASV abundances might arise from metabolic cooperation (11), a confounding non-bacterial microbe (10) or a confounding abiotic factor (12).…”

Parasites as niche modifiers for the microbiome: A field test with multiple parasites

“…While we interrogated relationships between parasites and the fungal microbiome, there 396 is growing evidence that bacterial and fungal microbiota associate with different factors (Elhady 397 et al, 2017;Bergelson, Mittelstrass, & Horton, 2019). For example, while we found that a 398 biotrophic parasite had no relationship with fungal microbiome diversity, recent work 399 investigating the bacterial microbiome of wheat found that leaves infected with a parasite 400 infecting as a biotroph had higher bacterial diversity than uninfected leaves (Seybold et al, 401 2019).…”

Investigating microbial associations from sequencing survey data with co‐correspondence analysis

“…Technological advances now make it possible to acquire NGS data on different taxonomic groups simultaneously for the same samples (Fierer et al, ) and lead to analysis of a pair of tables (i.e., OTU composition for the same sampling sites for two different taxonomic groups). To analyse such a pair of tables, common practice consists of merging the two tables into a single one and then applying network analysis (e.g., Banerjee et al, ; Kueneman et al, ; Ma et al, ) and/or multivariate analysis (Bergelson, Mittelstrass, & Horton, ; Cannon et al, ). However, this data aggregation is unsuitable especially when NGS data sets, which are a function of sequencing depth (Ni, Yan, & Yu, ), are standardized by dividing read counts by the total number of reads in each sample.…”