Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract

Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

“…A similar pattern has been well established elsewhere, in that the bacterial and fungal community structures in the rhizosphere differed from those in bulk soil in rice and wheat fields (Edwards et al, 2015;Zhang et al, 2017). Roots may select for specific microbial communities by releasing root exudates into the rhizosphere (Edwards et al, 2015;Zhang et al, 2017;Ceja-Navarro et al, 2021). The change in protist diversity might have arisen from the subsequent enrichment and depletion of some protists going from the bulk soil to soybean rhizosphere.…”

“…However, a comprehensive understanding of the diversity and ecological functioning of rhizospheric protists of soybean still eludes us. The development of new molecular markers and databases allows us to understand the rhizospheric protist community (Ceja-Navarro et al, 2021).…”

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines

“…The rhizosphere effect has been well documented ( 25 , 35 , 36 ) wherein the rhizosphere exhibits changes in bacterial richness compared to the bulk soil. Given the rhizosphere effect is consistent and drastic, there must be deterministic selection processes at work.…”

Fighting climate change: soil bacteria communities and topography play a role in plant colonization of desert areas

“…The connectivity of each node was determined based on its within‐module connectivity (Zi) and among module connectivity (Pi), and used to classify the nodes based on their topological roles that they play in the network. The general classification was based on categories defined in four categories: module hubs (highly connected nodes within modules, Zi >2.5 and Pi <0.62), and peripherals (nodes connected in modules with few outside connections, Zi <2.5 and Pi <0.62) (Ceja‐Navarro et al ., 2021).…”