Environmental DNA is more effective than soil-pit hand sorting in evaluating earthworm biodiversity responses to more regenerative agricultural management

Abstract

Regenerating soil biodiversity is vital to help reverse declines in the health of agricultural soils caused by intensification, and to support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecotypes and species delivering specific beneficial soil functions. However, conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowing ecotypes). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with hand-sorting from standard soil-pits. The experiment comprised four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm population responses had been recorded by hand-sorting for the first two years and our goal was to assess these in the third year and to compare them both by hand and with the use of eDNA. The eDNA method found the same 8 species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We demonstrate that eDNA can overcome some of the significant barriers and limitations to monitoring earthworm diversity and recommend its wider use both to better understand the earthworm population benefits of different soil management practices, and to guide agricultural policy and practice decisions affecting soil health.