Introduction
Tropical freshwater ecosystems harbour the most taxonomically diverse
fish communities on the planet (Pelicice et al., 2017), which fulfill a
wide range of critical functions such as nutrient recycling and seed
dispersal (Lévêque et al., 2008; Toussaint et al., 2016; Vitule et al.,
2017), while providing essential services like food provision and water
quality regulation (Collen et al., 2014; Hoeinghaus et al., 2009; Longin
et al., 2021; Pelicice et al., 2023). Despite their great ecological and
societal value, neotropical freshwater fish are experiencing alarming
biodiversity loss over recent decades due to multiple threats induced by
human activities, including deforestation, flow regulation,
overexploitation, non-native species introduction, and pollution
(Antunes et al. 2016; Barlow et al. 2018). In many countries, the lack
of adequate monitoring tools and reliable data hampers efforts to
develop effective conservation stategies, contributing to an increasing
homogenization of fish communities and modifications of species
assemblages through local extinctions and species introductions (Barlow
et al., 2018; Pelicice et al., 2017; Su et al., 2021).
To understand and quantify the impact of human pressures on freshwater
ecosystems, it has become urgent to accuratly assess fish assemblages
across various spatial and temporal scales. However, traditional methods
for conducting fish inventories in tropical freshwaters (e.g. using
gillnets, longlines or biocides) are costly and destructive (Allard et
al., 2016; Araújo et al., 2009). They are also heavily reliant on the
presence of taxonomic experts, particularly in highly diversified areas
such as tropical rivers, characterized by complexes of closely related
species, where morphological identification of specimens can be
extremely challenging. Another strong limitation of traditional
inventory net-based methods is their selectivity and limited capacity to
detect small or rare species that may have a strong contribution to
ecosystem functioning (Mouillot et al., 2013, 2014).
In recent years, environmental DNA (eDNA) metabarcoding has allowed the
emergence of promising non-invasive and cost-efficient tools for
biodiversity monitoring (Takahashi et al., 2023). While the analysis of
water, soil, or sediment eDNA is now widely adopted, researchers are
increasingly investigating the potential of « natural samplers » for
local scale biomonitoring, based on living organisms that, through
feeding, aggregate the DNA of species in their immediate environment
(Siegenthaler et al. 2019). Ideal natural samplers should be abundant,
widely distributed, easy to collect, and feed opportunistically on a
wide taxonomic range of prey. (Boyer et al. 2015). For example, several
studies have used the blood DNA of hematophagous insects (Kocher et al.,
2017; Massey et al., 2022) or the feces of generalist predators
(Nørgaard et al., 2021) to inventory flora and fauna in terrestrial
environments. In aquatic environments, filter-feeding organisms such as
sponges or mussels have been investigated as natural samplers for marine
biodiversity to capture a wide range of eDNA from supsended particules
in the water colum ( Weber et al. 2023; Mariani et al. 2019; Gallego et
al. 2024). Similarly, the dietary DNA of small detritivorous
invertebrates have shown promise for providing insight into local fish
assemblages (Cordone et al., 2022; Siegenthaler et al., 2019).
Here, we investigated whether freshwater detritivorous shrimp can serve
as “natural samplers” for assessing the local composition of highly
diverse fish assemblages in neotropical riverine ecosystems, comparing
their effectiveness with traditional monitoring methods. Our study
focused on the fish communities of large rivers in French Guiana, a
territory almost entirely covered by primary rainforest and
characterized by a very dense hydrographic network that supports over
400 fish species, equivalent to the entirety of Western Europe (Le Bail,
2012). These ecosystems face increasing anthropogenic pressures,
particularly from small-scale gold mining and logging activities, which
have been shown to significantly alter local fish assemblages (Allard et
al., 2016; Cantera, Coutant, et al., 2022; Coutant et al., 2023). In
this context, French Guiana must comply with European regulations aiming
at developing surveillance programs on water quality (Water Framework
Directive 2000/60/EC, hereafter WFD) and requires the development of
effective and non-invasive tools to complement or replace current
inventory methods.
We developed a multi-marker metabarcoding approach to analyze the
dietary DNA (dDNA, hereafter) of several abundant and widely distributed
species of shrimp, which can be easily captured using traps along the
riverbanks. These small scavenger crustaceans have restricted home
ranges (Hirt et al., 2017) and exhibit a highly versatile feeding
regime, ranging from feces to fish carcasses (da Cruz et al., 2021;
Silveira De Melo & Nakagaki, 2013). As a result, they concentrate
surrounding DNA in their digestive tracts, making them well suited as
samplers for assessing local biodiversity. To obtain the most
comprehensive and robust picture of fish assemblages, the dDNA was
analysed using three mitochondrial markers (12S rRNA and cytochrome c
oxidase 1 [COI] gene) that differ in taxonomic resolution and
coverage (Polanco F. et al., 2021; Quéméré et al., 2021). We compared
the taxonomic diversity and inferred size range of fish assemblages
recovered through dDNA with those recorded after 10 days of intensive
fishing with gillnets, cast nets and traps, as well as with data
obtained from the standardized WFD fish monitoring protocol
traditionally used in French Guiana.
Given the opportunistic feeding strategy of shrimp and their diverse
microhabitats, we expected that dDNA analysis would reveal a greater
number of fish species compared to traditional WFD monitoring methods,
likely being more effective at identifying rare or cryptic species.
Additionally, dDNA analysis is expected to be less biased toward larger
species than gillnet-based fishing methods. From a methodological
perspective, we also anticipated that the use of multiple markers would
help overcome PCR biases and provide a more complete picture of fish
diversity compared to a single-marker approach.