Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field

Abstract

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genuslevel clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere), we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent arbuscular mycorrhizal (AM) fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, followed by the soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize–cabbage rotation

“…This result is unsurprising because microbial communities including fungi are known to be influenced by crops and land use history, including crop rotations. This is also the case with eukaryotic communities; for instance, protist communities were changed by fertilization 44 and depth 45 , and unique communities of eukaryotes 46 – 49 , including protists 50 – 53 and nematodes 54 , 55 , were formed in different types of soils, including agricultural soils. Furthermore, the taxonomic variations in β-diversities were almost comparable among the three different growth stages of crops except for prokaryotic variations in field_2 soils cropping maize at the early stage (Fig.…”