Determining the species compositions of local assemblages is a prerequisite to understanding how anthropogenic disturbances affect biodiversity. However, biodiversity measurements often remain incomplete due to the limited efficiency of sampling methods. This is particularly true in freshwater tropical environments that host rich fish assemblages, for which assessments are uncertain and often rely on destructive methods. Developing an efficient and nondestructive method to assess biodiversity in tropical freshwaters is highly important. In this study, we tested the efficiency of environmental DNA (eDNA) metabarcoding to assess the fish diversity of 39 Guianese sites. We compared the diversity and composition of assemblages obtained using traditional and metabarcoding methods. More than 7,000 individual fish belonging to 203 Guianese fish species were collected by traditional sampling methods, and ~17 million reads were produced by metabarcoding, among which ~8 million reads were assigned to 148 fish taxonomic units, including 132 fish species. The two methods detected a similar number of species at each site, but the species identities partially matched. The assemblage compositions from the different drainage basins were better discriminated using metabarcoding, revealing that while traditional methods provide a more complete but spatially limited inventory of fish assemblages, metabarcoding provides a more partial but spatially extensive inventory. eDNA metabarcoding can therefore be used for rapid and large-scale biodiversity assessments, while at a local scale, the two approaches are complementary and enable an understanding of realistic fish biodiversity.

Deforestation and mining are recognized as major threats to Amazonian biodiversity, but, in addition to the well known impacts of clear cutting and industrial mining, the impact of cryptic threats such as illegal smallscale gold-mining and reduced impact logging remain little known. Here, we quantify the impact of those cryptic disturbances on a set of 201 sites dispersed throughout French Guiana. The fish assemblages of 139 pristine forest sites were compared to 16 sites subjected to reduced impact logging (i.e. selective logging), 24 sites with ongoing small-scale gold-mining and 22 sites formerly mined for gold. Controlling for the environmental variability between sites showed the significant structuring effect of all disturbances on fish taxonomic structure, with a marked impact of gold-mining. This effect was of strong magnitude and remained significant after mining activity ceased. In contrast, the reduced impact logging effect remains of low magnitude, although significant. From a functional point of view, gold-mining drives species assemblages towards a decrease in the richness of small-sized stream habitat specialist species and favours larger ubiquitous species living in both streams and rivers. Reduced impact logging effect was slighter, and negatively affected only the richness of phytophagous species. These results, encompassing a variety of hydrographic basins, unambiguously show the detrimental effect of small-scale gold-mining on fish assemblages as well as the slight effect of reduced impact logging. Since gold-mining is one of the most widespread threats throughout the Amazonian region, particular care should be given to controlling this, often illegal, activity.