Abstract
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.
Highlights
Nematode communities are highly diverse and include the most abundant animals in any environment (Ettema, 1998)
As high-throughput sequencing (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
We show significantly positive correlations between all methods when focusing on seven functionally diverse nematode taxa targeted by qPCR and between most taxa recovered by HTS and MorphoID
Summary
Nematode communities are highly diverse and include the most abundant animals in any environment (Ettema, 1998). Well-developed extraction methods enable collection of nematodes from soil, plant roots and shoots, routinely followed by morphological identification to feeding guilds, based on their distinct mouthparts (Yeates, Bongers, De Goede, Freckman, & Georgieva, 1993). Nematode identification approaches vary from detecting single plant parasites in soil or plant materials for export purposes (Vervoort et al, 2012) to entire community composition-oriented studies for monitoring purposes (Bongers, 1990; Bongers & Ferris, 1999; Chen, Daniell, Neilson, O’Flaherty, & Griffiths, 2010; Neher, 2001; Ritz & Trudgill, 1999). A fraction of 100–150 individuals within individual samples are identified to determine the nematode community structure, which usually takes skilled morphological identification experts more than 1 hr for completion (Griffiths, de Groot, Laros, Stone, & Geisen, 2018). Morphological analyses of environmental nematode samples are constrained by taxonomic resolution, time and, money (Griffiths et al, 2018)
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