Study Area and data collection
The study was conducted on the Approuague River (French Guiana) at Saut
Mathias, an area that includes both rapids and slow-flowing sections,
located 90 kilometers from the river’s mouth (4°18′N, -52°34′W). Since
2008, this site has been subject to annual fishing surveys as part of a
water quality surveillance program in accordance with the European WFD.
These surveys use a standardized protocol involving multiple nets with
different mesh sizes (ranging from 15 to 35mm) overnight to inventory
species diversity and abundance. Over 13 years (2008-2022, excluding
2016, 2018, 2019, and 2021), WFD surveys were conducted during 11 annual
campaigns at this site identifying a total of 51 fish species belonging
to 20 families (Table S1). However, the average number of species
recovered per year is much lower (23.3, sd = 3.17) due to a strong
inter-annual variability (54.6% of species turnover between consecutive
years) (Figure S1). The most recent WFD campaign (2022) recorded 23
species (13 families). To obtain the most comprehensive inventory of
local fish communities, we conducted an extensive 10-day survey in
October 2021 (dry season) (hereafter refereed as the ‘deep inventory’)
using various fishing techniques and gear, including nets, traps,
fishing rods, and cast nets, to capture a broad range of species (n=70,
with mean body length ranging from 2 and 75 cm). Each fish captured was
measured and identified by taxonomic experts.
At the same time, Freshwater decapods were collected over three days
using two complementary sampling methods, conducted alongside the deep
inventory. Active sampling with landing nets was used to captureEurhyrinchus sp., Macrobrachium brasiliense, andMacrobrachium carcinus in shallow areas along the riverbank.Macrobrachium olfersii was collected using both landing nets and
baited traps, while Macrobrachium amazonicum was exclusively
captured using traps. In order to avoid potential DNA contamination that
could interfere with metabarcoding analyses, traps were baited with
commercial chicken-flavored cat food pellets. Baited traps were set at
night with two collection times. This sampling strategy resulted in the
collection of 116 shrimp specimens (Table 1), which were stored in
ethanol at ambient temperature until analysis in the laboratory.