Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding

Abstract

23The biodiverse Neotropical ecoregion remains insufficiently assessed, poorly managed, and 24 threatened by unregulated human activities. Novel, rapid and cost-effective DNA-based 25 approaches are valuable to improve understanding of the biological communities and for 26 biomonitoring in remote areas. Here, we evaluate the potential of environmental DNA (eDNA) 27 metabarcoding for assessing the structure and distribution of fish communities by analysing 28 sediments and water from 11 locations along the Jequitinhonha River catchment (Brazil). Each 29 site was sampled twice, before and after a major rain event in a five-week period and fish 30 diversity was estimated using high-through-put sequencing of 12S rRNA amplicons. In total, 31 252 Molecular Operational Taxonomic Units (MOTUs) and 34 fish species were recovered, 32including endemic, introduced, and previously unrecorded species for this basin. Spatio-33 temporal variation of fish assemblages was detected, richness during the first campaign was 34 nearly twice as high as in the second sampling round; though peaks of diversity were primarily 35 associated with only four locations. No correlation between β-diversity and longitudinal 36 distance or presence of dams was detected, but low species richness observed at sites located 37 near dams indicates that these anthropogenic barriers might have an impact on local fish 38 diversity. Unexpectedly high α-diversity levels recorded at the river mouth suggest that these 39 sections should be further evaluated as putative "eDNA reservoirs" for rapid monitoring. By 40 uncovering spatio-temporal changes, unrecorded biodiversity components, and putative 41 anthropogenic impacts on fish assemblages, we further strengthen the potential of eDNA 42 metabarcoding as a biomonitoring tool, especially in regions often neglected or difficult to 43 access. 44

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

“…For these reasons, we used MOTUs curated by a combination of a clustering algorithm and conservative abundance-based post-clustering filters. While uncurated MOTUs are prone to overestimate real diversity [50] and a given MOTU can represent several species within one cluster or several MOTUs belonging to one species, MOTUs with conservative curation have been shown to reflect the true level of fish diversity across scales in streams [51,52]. Additionally, some species share the same barcode sequence due to insufficient genetic differentiation on such a small mitochondrial marker [49].…”

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

“…In addition to the above ten case studies conducted in various freshwater environments, MiFish eDNA metabarcoding methods have been applied to biodiversity monitoring in the Duck and Clinch Rivers, Tennessee, USA (Paine 2019); Lake Michigan, USA (Jurecki 2020); Jequitinhonha River catchment, Brazil (Sales et al 2020b); St. Laurence and Rupert Rivers, Canada (Boivin-Deslile et al 2020;Berger et al 2020); Lake Kasumigaura in Ibaraki, central Japan (Kondo et al 2016); agricultural waterway in Saitama, central Japan (Kimochi et al 2020); two rivers in Hokkaido and Hyogo, Japan (Akamatsu et al 2018); 14 rivers in Sado Island, Niigata, Japan (Koseki 2019); a small river in Okinawa, southern Japan (Sato et al 2018); an urban stream in Suwon City, Korea (Song et al 2019); four Korean rivers (Alam et al 2020); the middle and lower reaches of the Yangtze River, China (Nian et al 2020); and irrigation water from two agro-ecological regions of Sri Lanka (Gamage et al 2020). Furthermore, effects of seasonal thermal stratification and fish habitat preferences on the vertical distributions of eDNA were investigated in the Experimental Lakes Area, north-western Ontario, Canada (Littlefair et al 2020).…”