Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion

TY - JOUR

T1 - Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion

AU - Geisen, S.

AU - Snoek, B.

AU - Ten Hooven, F.C.

AU - Duyts, H.

AU - Kostenko, O.

AU - Bloem, Janneke

AU - Martens, H.J.

AU - Quist, C.W.

AU - Helder, Johannes

AU - van der Putten, W.H.

N1 - 6492, TE; Data archiving: data archived in Dataverse

PY - 2018

Y1 - 2018

N2 - Below‐ground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR‐based nematode identification techniques are well available, but high‐throughput sequencing (HTS) might be more suitable for non‐targeted nematode community analyses.We compared effectiveness of qPCR‐ and HTS‐based approaches with morphological nematode identification while examining how climate warming‐induced plant range expansion may influence below‐ground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is a range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach.HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant‐feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances.Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost‐effective, in‐depth methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.

AB - Below‐ground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR‐based nematode identification techniques are well available, but high‐throughput sequencing (HTS) might be more suitable for non‐targeted nematode community analyses.We compared effectiveness of qPCR‐ and HTS‐based approaches with morphological nematode identification while examining how climate warming‐induced plant range expansion may influence below‐ground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is a range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach.HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant‐feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances.Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost‐effective, in‐depth methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.

KW - national

U2 - 10.1111/2041-210X.12999

DO - 10.1111/2041-210X.12999

M3 - Article

SN - 2041-210X

VL - 9

SP - 1366

EP - 1378

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

IS - 6

ER -