High-throughput sequencing and conventional morphotyping show different soil nematode assemblages but similar community responses to altitudinal gradients on Mt. Ibuki, Japan

•We examined nematode assemblages by morphological and molecular approaches.•Both methodological approaches showed a similar taxon richness.•Thirty-nine percent of nematode genera were common in both analyses.•Nematode communities corresponded to elevations regardless of the analyses.•Metabarcoding is effective tool to determine the nematode assemblage patterns. The progress of molecular techniques has provided opportunities to comprehensively understand the assemblage patterns of nematode communities in various natural ecosystems. However, we still do not clearly understand whether molecular techniques result in similar assemblage patterns for nematode communities as those generated by conventional morphological analyses. We compared the community structures of soil nematodes depicted by morphological and high-throughput sequencing (HTS) analyses at five different altitudes on Mt. Ibuki, central Japan. Diversity and community composition of soil nematodes were examined from soils in coniferous Japanese cedar (Cryptomeria japonica) forests at altitudes of 200 m, 500 m, and 800 m, in a broad-leaved Shirasawa maple (Acer shirasawanum) forest at an altitude of 1100 m, and in an alpine grassland (Boehmeria silvestrii and Cirsium sp.) at an altitude of 1350 m, by identification with morphotyping or Ion Torrent PGM sequencing. Seventy genera of nematodes were detected; 51 by the HTS method and 46 by the morphological method. Of these, only 27 genera (39 %) were commonly detected in both methods. In non-metric multidimensional scaling ordinations, the nematode communities derived from the two methods were distinctly segregated, but exhibited relatively similar distribution patterns according to environmental gradients within each method. The results indicated that HTS and conventional morphotyping could depict different nematode community structures, but similar community responses to environmental gradients. Thus, HTS analysis can be an effective tool to determine the nematode assemblages responding to environmental changes.