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

TY - JOUR

T1 - The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes

AU - Griffiths, B.S.

AU - de Groot, G. Arjen

AU - Laros, I.

AU - Stone, D.

AU - Geisen, S.

N1 - 6534, TE;

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - Biodiversity, DNA extraction, Metabarcoding, Microscopy, Molecular approaches, Nematodes, Standardisation

KW - international

U2 - 10.1016/j.ecolind.2017.12.002

DO - 10.1016/j.ecolind.2017.12.002

M3 - Article

SN - 1470-160X

VL - 87

SP - 43

EP - 46

JO - Ecological Indicators

JF - Ecological Indicators

ER -