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

Stefan Geisen*, L.B. Snoek, Freddy C. ten Hooven, Henk Duyts, Olga Kostenko, Janneke Bloem, Henk Martens, Casper W. Quist, Johannes A. Helder, Wim H. van der Putten

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

Abstract

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.
Original languageEnglish
Pages (from-to)1366-1378
JournalMethods in Ecology and Evolution
Volume9
Issue number6
DOIs
Publication statusPublished - Jun 2018

Fingerprint

soil nematodes
community response
range expansion
nematode
Nematoda
soil
Centaurea stoebe
methodology
method
Centaurea jacea
relative abundance
soil food webs
Slovenia
sampling
global warming
rhizosphere

Keywords

  • Biodiversity
  • High-throughput sequencing
  • Microscopy
  • Molecular approaches
  • Nematodes
  • QPCR
  • Soils

Cite this

@article{c9dee2084c9e44ea94d90c38ee0878eb,
title = "Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion",
abstract = "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.",
keywords = "Biodiversity, High-throughput sequencing, Microscopy, Molecular approaches, Nematodes, QPCR, Soils",
author = "Stefan Geisen and L.B. Snoek and {ten Hooven}, {Freddy C.} and Henk Duyts and Olga Kostenko and Janneke Bloem and Henk Martens and Quist, {Casper W.} and Helder, {Johannes A.} and {van der Putten}, {Wim H.}",
year = "2018",
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doi = "10.1111/2041-210X.12999",
language = "English",
volume = "9",
pages = "1366--1378",
journal = "Methods in Ecology and Evolution",
issn = "2041-210X",
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Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion. / Geisen, Stefan; Snoek, L.B.; ten Hooven, Freddy C.; Duyts, Henk; Kostenko, Olga; Bloem, Janneke; Martens, Henk; Quist, Casper W.; Helder, Johannes A.; van der Putten, Wim H.

In: Methods in Ecology and Evolution, Vol. 9, No. 6, 06.2018, p. 1366-1378.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

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

AU - Geisen, Stefan

AU - Snoek, L.B.

AU - ten Hooven, Freddy C.

AU - Duyts, Henk

AU - Kostenko, Olga

AU - Bloem, Janneke

AU - Martens, Henk

AU - Quist, Casper W.

AU - Helder, Johannes A.

AU - van der Putten, Wim H.

PY - 2018/6

Y1 - 2018/6

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 - Biodiversity

KW - High-throughput sequencing

KW - Microscopy

KW - Molecular approaches

KW - Nematodes

KW - QPCR

KW - Soils

U2 - 10.1111/2041-210X.12999

DO - 10.1111/2041-210X.12999

M3 - Article

VL - 9

SP - 1366

EP - 1378

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

IS - 6

ER -