Effects of ecosystem disturbance on nematode communities in calcareous and red soils: Comparison of taxonomic methods.

Soil nematode communities have been traditionally characterized through morphological examination, which is time-consuming and demands highly trained specialist in order to deliver reproducible results. In order to tackle these problems, molecular approaches have been developed for the characterization of soil nematode communities, and yet, their accuracy is controversial. In this study, we compared the characterization of soil nematode communities by the morphological method and by two molecular methods (that differed in primers and high-throughput sequencing platforms). Soil nematodes communities were quantified from four different land-use types (cropland, natural grass-shrubland, orange orchard, and semi-natural pine forest), encompassing 2 soil types (calcareous soil and red soil) with and without anthropogenic disturbance. Our results showed that the characterization of soil nematode community differed substantially between methodologies at both genus and trophic group level. We therefore argue that currently available molecular methodologies may not be accurate for quantitative evaluation of soil nematode communities as a standalone technique, and rather, the needs to be considered as complementary approaches. In order to match the precision with widely used microbial 16S rRNA techniques, we suggest that refinements in both primers sequences and quality alongside quantity of public-available sequences are needed. In addition, a large proportion of nematodes in the natural ecosystems could not be identified by the molecular methods, which indicates the need for enriching nematode sequences in GenBank. With respect to land-use effects, nematode abundances were higher in the highly disturbed cropland and orchard than in the undisturbed grass-shrubland and pine forest, perhaps because external inputs (inorganic or organic fertilizers) were added to the disturbed but not to the undisturbed systems. In each soil type, the absence of disturbance caused a shift in the soil decomposition pathway from bacterial-mediated to fungal-mediated. The cropland had higher nematode generic diversity and lower maturity and faunal structure than the grass-shrubland in the calcareous soil. The orchard had lower nematode diversity and higher maturity and faunal structure than the pine forest in the red soil. Altogether, these differences between disturbed and undisturbed ecosystems for each soil type might be due to different responses of low and high trophic groups to the input of chemical and organic fertilizer to the cropland and orchard, respectively. • Primer and quantitative ability are important issues of molecular methods for nematode. • Nematode abundances were higher in disturbed than undisturbed ecosystems. • Reduced disturbances promoted fungal-mediated pathway. [ABSTRACT FROM AUTHOR]