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A full-length SSU rRNA-based workflow for high-resolution monitoring of nematode communities reveals direct and indirect responses to plant-based manipulations
Nematodes are considered an informative taxonomic group to assess soil health, but their routine use in soil assessments requires a method that accurately identifies nematode communities in high-throughput and preferably at a high taxonomic resolution (genus/species level).
Microscopic characterization of nematodes communities is labour intensive and requires ample taxonomic expertise, and is therefore not optimal as community characterization method. Typical DNA-based identification (qPCR or short-read sequencing) of these communities is efficient and can be performed in high-throughput, but these techniques rarely provide a reliable high taxonomic resolution. In our new publication, we describe a workflow (see figure) to characterize nematode communities at mostly species level by full SSU rRNA (18S) sequencing with Nanopore sequencing devices. Then, we put our method into practice to study the effect of various cover crops on nematode communities. This workflow facilitates the high resolution characterization of nematodes communities in high-throughput and can therefore be used as a valuable tool in soil health assessments.