Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Abstract

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

“…In addition, our observation of several ASVs with differential abundance patterns across greenhouse blocks in both treatments suggests that random or dispersal forces also shaped rhizosphere community assembly, as previously noted in Arabidopsis phyllospheres and across meter-scale field plots in rhizospheres of several Brassica cultivars ( 26 , 27 ). Alternatively, subtle and unmeasured variations in temperature or other factors across different areas of the greenhouse may play a role (particularly for block 6, which sat directly underneath a heater; see Fig.…”

“…Population-level spatiotemporal variability has also been observed, such as in a reporter assay where the activity of a root-associated Pseudomonas aligned with expected rhizodeposition patterns during root growth ( 25 ). Not only guided by host influences, the assembly of plant-associated bacterial communities is to an extent shaped by stochastic forces across small spatial or temporal scales ( 26 – 28 ).…”

Artificial Intelligence for Earth System Predictability (AI4ESP) (2021 Workshop Report)

“…This experimental finding motivated development of a new theoretical modeling framework published by Song et al (2020) that defined a new model parameter that quantifies the impacts of thermodynamics on biogeochemical reactions. Additional field sampling was then conducted through the WHONDRS consortium to identify spatial and temporal patterns across diverse systems, and the resulting data were used to simulate intersystem biogeochemical process variability using the KBase modeling platform (e.g., Napieralski and Roden 2020; Klasek et al 2021). The ModEx cycle is ongoing in this example and extends into the AI/ML space, as ML analyses of the WHONDRS data/metadata are currently being used to plan the next WHONDRS sampling campaign, the outcomes of which will in turn be used to refine watershed model parameters.…”