Nematode and protist community responses in soil to land use conversion from conventional to organic farming

Soil organisms at higher trophic positions in the food web, such as nematodes or protists, play a key role in shaping the composition and functioning of soil communities. However, intensive agriculture can put these organisms under pressure and restoring communities of soil organisms will be vital for a more sustainable functioning of agricultural soils. Here, we examine how changing land use from conventional to organic farming influences the composition and diversity of belowground nematodes and protists. We collected soil samples from 68 organic and conventional farmers’ fields on clay and sandy soils and used 18S sequencing to determine soil community composition and diversity. In order to test effects of time since conversion from conventional to organic management, we used organically farmed soils that had been converted at time periods varying from 1 to 25 years ago, each being paired with a nearby conventional field in order to account for local environmental differences in climate and soil conditions. The ASV richness and Shannon diversity of protists was lowest in organic fields and while protist community composition differed between organic and conventional fields in clay soils, effects were relatively minor. Similarly, Shannon diversity of nematodes was lower in organic fields at clay soil, but there was no difference in nematode community composition and species richness between conventional and organic fields. Progressing time since conversion to organic management impacted community composition for both nematodes and protists in clay soils and led to an increased protist richness and diversity in both clay and sandy soils. However, we found a similar trend for the conventional fields if we assigned them the age of the paired organic field, suggesting that the observed shifts may not have been driven by time since conversion alone, but also by other hitherto unidentified factors. Although pH, soil organic matter content, and microbial biomass were not related to time since conversion, they could explain functional and taxonomic community composition of both nematodes and protists. Shifts in the relative abundance of feeding/functional groups of protists and nematodes were variable and depended on soil and management type. We conclude that conversion from conventional to organic management influenced protist and nematode diversity and community composition, but effects were relatively minor and dependent on sand versus clay soil. Further studies are needed to determine functional implications of the shifts in protist and nematode community composition for functioning of the organic versus conventionally farmed soils. • Chronosequences were established to study the duration of organic management. • Protist and nematode diversity was lower in organic fields on clay soils. • On clay soils, protist communities differed between conventional and organic fields. • Community shifts occurred over time in both conventional and organic fields. • Time since conversion may not be the only factor driving community composition.