Because of their challenging taxonomy, arthropods are traditionally underrepresented in biological inventories and monitoring programs. However, arthropods are the largest component of biodiversity, and no assessment can be considered informative without including them. Arthropod immature stages are often discarded during sorting, despite frequently representing more than half of the collected individuals. To date, little effort has been devoted to characterising the impact of discarding non-adult specimens on our diversity estimates. Here, we use a metabarcoding approach to analyse spiders from white oak communities in the Iberian Peninsula collected with standardised protocols, to assess (1) the contribution of juvenile stages to local diversity estimates, and (2) their effect on the diversity patterns inferred across communities. We further investigate the ability of metabarcoding to inform on abundance. We obtained 363 and 331 species as adults and juveniles, respectively. Species represented only by juveniles represented an increase of 35% with respect to those identified from adults in the whole sampling. Differences in composition between communities were greatly reduced when immature stages were taken considered, especially across latitudes. Moreover, our results revealed that metabarcoding data are to a certain extent quantitative, but some sort of taxonomic conversion factor may be necessary to provide accurate informative estimates. Although our findings do not question the relevance of the information provided by adult-based inventories, they also reveal that juveniles provide a novel and relevant layer of knowledge that, especially in areas with marked seasonality, may influence our interpretations, providing more accurate information from standardised biological inventories.

In a recent paper, “Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. Not only is this terminology based on categories that are often difficult to assign and uninformative, but it ignores what is in our opinion the most important distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based approaches are valuable to improve understanding of the biological communities and for biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) metabarcoding for assessing the structure and distribution of fish communities by analysing sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each site was sampled twice, before and after a major rain event in a five-week period and fish diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, including endemic, introduced, and previously unrecorded species for this basin. Spatio-temporal variation of fish assemblages was detected, richness during the first campaign was nearly twice as high as in the second sampling round; though peaks of diversity were primarily associated with only four locations. No correlation between β-diversity and longitudinal distance or presence of dams was detected, but low species richness observed at sites located near dams indicates that these anthropogenic barriers might have an impact on local fish diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these sections should be further evaluated as putative “eDNA reservoirs” for rapid monitoring. By uncovering spatio-temporal changes, unrecorded biodiversity components, and putative anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to access.