The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes. (April 2018)

• Record Type: Journal Article
• Authors: Griffiths, B.S.; de Groot, G.A.; Laros, I.; Stone, D.; Geisen, S.
• Is Part Of: Ecological indicators. Volume 87(2018)
• Page Start: 43
• Page End: 46
• Publication Date: 2018-04
• Subjects: Biodiversity -- DNA extraction -- Metabarcoding -- Microscopy -- Molecular approaches -- Nematodes -- Standardisation; Environmental monitoring -- Periodicals; Environmental management -- Periodicals; Environmental impact analysis -- Periodicals; Environmental risk assessment -- Periodicals; Sustainable development -- Periodicals; 333.71405
• DOI: 10.1016/j.ecolind.2017.12.002
• Languages: English
• ISSNs: 1470-160X

Abstract

Graphical abstract: Highlights: Molecular approaches are replacing the morphological identification of soil fauna. There is still a choice to first extract the fauna and then the DNA or to directly extract DNA from soil. We compared all three approaches for soil nematodes. Not only did taxonomic composition vary between all three methods, the community results indicated different soil quality. High-throughput sequencing increases resolution, but standardisation is required to give more meaningful information. Abstract: Molecular approaches are offering a supplement to, or even the possibility of replacing morphological identification of soil fauna, because of advantages for throughput, coverage and objectivity. We determined ecological indices of nematode community data from four sets of duplicate soil cores, based on morphological identification of nematodes after elutriation from 200 g soil and high throughput sequencing (HTS) targeting nematodes both after being elutriated from soils and DNA extracted directly from 10 g soil. HTS (at genus and species level) increased the taxonomic resolution compared to morphology (at family level). DNA extracted from elutriated nematodes identified more nematode taxa than when extracted from soil, due to an enrichment in nematode sequences. Each method also gave a different ecological footprint for the nematode community. Standardisation to previously determined indices based on morphological identification is needed in order to provide more meaningful information about soil quality and for ecological monitoring.