Metabarcoding of nematode communities for soil quality evaluation

Nematodes are abundant and diverse in nearly any soil, and directly and indirectly contribute to important soil functions such as nutrient cycling, decomposition, and pest and pathogen regulation. In addition, nematode communities have been shown to be sensitive to agricultural management such as tillage and organic matter additions. As such, soil nematode are promising indicators for soil quality. Morphological assessment of nematode communities and indices such as the maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI) have been used for soil quality evaluations. Molecular methods to study community composition and diversity offer advantages compared to traditional methods in terms of cost, time, resolution and throughput. Thus far, the use of molecular data to calculate indices has not received much attention. In the present study we used molecular methods to: i) assess the effects of soil management on nematode qPCR counts, alpha- and beta- diversity, and food web indices; ii) identify nematode taxa specific to certain soil management, and iii) investigate the relationship between nematode community parameters with soil chemical, physical and biological parameters. We assessed nematodes communities with metabarcoding in 10 European long-term field experiments to study the effect of tillage (conventional vs reduced) and organic matter addition (low vs high).