Suitability of molecular taxonomy for assessing polluted sediments using the NemaSPEAR[%] index

•Nematodes as ubiquitous organisms are well-suited for biomonitoring approaches.•The molecular-based NemaSPEAR[%] index can distinguish between an acceptable and unacceptable sediment quality.•The use of metabarcoding for biomonitoring was demonstrated.•Congruence between molecular-based index and morphological biomass-based data higher than with abundance-based morphological data. Assessing the ecological consequences of marine and freshwater contamination is an important use of biological indicators. The NemaSPEAR[%] index is a nematode-based index for the evaluation of sediment quality and an expedient complement to macroinvertebrate-based indicator systems, especially for fine, cohesive sediments. While the NemaSPEAR[%] index in its original form is morphologically based, in this study the nematode communities of 38 locations with known sediment contamination were analyzed by light microscopy and metabarcoding to demonstrate the validity of a molecular-taxonomy-based NemaSPEAR[%] index. The results showed that the molecular-based index can reliably distinguish between sites of good, moderate, and bad pollution status. Moreover, a greater congruence with molecular read abundances were obtained after the morphology-based NemaSPEAR[%] index was corrected for differences in the biomass of different nematode species. However, incomplete reference databases hamper a full congruence between the species inventories recorded in morphological and molecular datasets. Another source of variability is the substantial difference in the biomass (and thus also of gene copies) of different species, thus evidencing a bias in abundance-based calculations of the NemaSPEAR[%] index. Despite these limitations, the molecular approach provides an expertise-free means of reliable bioindication using one of the most abundant and diverse components of benthic macroinvertebrate communities. Moreover, due to the ubiquity of nematodes, application of the index can be extended to wastewater, biofilm, and other lotic and lentic waters that require regular monitoring.