Diversity and site occupancy of fish communities
The identification of 31 taxa by eDNA metabarcoding represented more
taxa than expected. Higher fish detectability by eDNA metabarcoding
compared to conventional methods has been found in riverine as well as
lacustrine environments (Hänfling et al., 2016; Li et al., 2019a;
McDevitt et al., 2019; Olds et al., 2016; Pont et al., 2018). In each
reservoir, some taxa were detected for the first time by eDNA
metabarcoding, demonstrating the sensitivity of this method.
All conventional methods (i.e. boat electrofishing, fyke-nets,
gillnetting and seine netting) are selective, thus there are several
reasons for species underestimation with these tools (Kubečka et al.,
2009). Small-bodied species, such as European bitterling (Rhodeus
amarus ) in Klíčava and stone loach in Žlutice, were most probably
overlooked in structured benthic habitats. Even species with medium body
size, such as white bream in Klíčava and Žlutice, could be misclassified
to the more common freshwater bream with similar appearance (especially
juveniles) or disguised as hybrids (Kottelat & Freyhof, 2007). The
other explanation is small population size in a water body and occurence
in a specific habitat (Balasingham et al., 2017). Bullhead, Eurasian
minnow (Phoxinus phoxinus ) and salmonids are restricted to
relatively small, structured and shallow parts of tributaries, which are
difficult habitats to sample by conventional methods. Typically netting
is used, but net diameters, mesh sizes and used material determine the
catch (Prchalová et al., 2009b; Říha et al., 2008). Large fish can
escape from small nets or break through fragile nets, whereas small fish
can escape through larger mesh sizes. Bleak, a common species in Římov,
was probably recently introduced in Žlutice (maybe with piscivorous fish
stocking), as the first record in gillnets was in 2019 (Blabolil,pers. obs. ).
eDNA metabarcoding is acknowledged as a highly sensitive method for
detection of invasive and endangered species (Lawson Handley, 2015). Of
the seven non-native species we detected, prussian carp and topmouth
gudgeon have invasive potential in the Czech Republic (Pergl et al.,
2016). Spread of these species can be facilitated by outflowing water
from ponds and therefore early and reliable detection is imperative to
help protect native fishes. Pumpkinseed was detected only in main part
of Římov and will require immediate action to prevent further spread as
it is naturally reproducing in the reservoir. Grass carp
(Ctenopharyngodon idella ), Hypophthalmichthys spp.,
rainbow trout (Oncorhynchus mykiss ) and Salvelinus spp.
are dependent on artificial stocking, but grass carp andHypophthalmichthys spp. are undesirable in reservoirs. Grass carp
reduce submerged vegetation and Hypophthalmichthys spp. filter
zooplancton in the water column, supporting phytoplankton. Therefore,
early eDNA detection of undesirable species should trigger their
elimination, similar to eradication management of common carp
(Cyprinus carpio ) in Tasmania (Furlan et al., 2019) and topmouth
gudgeon in the UK (Robinson et al., 2019).
Three taxa were classified as regionally Extinct as current populations
are dependent on artificial stocking. Common carp is the most popular
game fish in the Czech Republic and stocked in ponds across the country
(Boukal et al., 2012). Ponds in catchments are the most probable source
of individuals found in the studied reservoirs. Coregonus spp.
and Acipenser spp. were detected only in Římov. Ponds occur in
this catchment as well as fish hatcheries breeding this species
(Pstruhařství ČRS Kaplice, Ltd.) that are directly connected to the
inflowing river. Potential escapees from pools is therefore plausible
(Naylor et al., 2001). The European eel is categorised as Extinct in the
Wild because migration of juveniles upstream is impossible and high
mortality of adults during downstream spawning migration through dams
with hydro turbines (Trancart et al., 2019). European eel eDNA detection
in Klíčava and Římov could help initiate construction of suitable dam
bypasses and/or capture of spawning stock and transport downstream past
the dam.
The crucian carp (Carassius carassius ) was the only Critically
Endangered species we detected and typically occurs in small ponds
(Harper et al., 2019a), but here was exclusively detected from the side
inflow to Římov. In this particular case, it is very probable that eDNA
originated upstream in a pool, the closest one being around 670 m from
the sampling locality. This suggests that populations of endangered
species could be identified through eDNA transport. Vulnerable taxa are
rare in the reservoirs associated with tributaries (Eurasian minnow,
grayling and Lampetra spp.) or submerged macrophytes (tench
[Tinca tinca ]), but these species can be considered as
indicators of ecological quality and diverse habitats (Blabolil et al.,
2017b, Šmejkal et al., 2014). The category of Near Threatened species is
important as these species could be at high risk of extinction in the
near future and therefore population assessment should follow any eDNA
detections. Finally, most of the species we detected were classified as
Least Concern, suggesting that conditions were suitable for common
species.
The cumulative number of detected taxa was highest (29) in Římov
(largest reservoir) and lowest (16) in Klíčava (smallest reservoir). Our
observation confirms a general increase of fish diversity with the area,
volume and catchment size of a water body (Mehner et al., 2005).
However, the number of taxa in individual samples was much lower,
typically in single units. This confirms the observation from previous
studies that eDNA is not homogeneously distributed in lentic habitats
and reflects local species presence (Harper et al., 2019a; Lawson
Handley et al., 2019; Li et al., 2019b). We observed greater taxon
detection in autumn compared to summer, which may be due to prolonged
eDNA persistence at colder temperatures (Collins et al., 2018; Lawson
Handley et al., 2019). Summer sampling is more likely to reflect
contemporary species distribution and activity compared to colder
conditions that preserve eDNA and facilitate transport, and could
provide more accurate information on changes in species activity (e.g.
downstream migration for wintering, Jonsson & Gravem, 1985) as well as
eDNA flushed from upstream. These results provide further evidence that
spatial and temporal replication in eDNA surveys is required for
reliable estimates of species richness (de Souza et al., 2016; Djurhuus
et al., 2020; Hänfling et al., 2016; Lawson-Handley et al., 2019; Li et
al., 2019b).
Despite this spatiotemporal heterogeneity, we found semi-quantitative
abundance estimates from eDNA metabarcoding in reservoirs (i.e. site
occupancy) were highly correlated with abundance categories based on
long-term fish surveys, which corroborates previous studies in UK lakes
(Hänfling et al., 2016; Lawson Handley et al., 2019). The majority of
fish in our studied reservoirs were of riverine origin, but the most
plastic species, such as freshwater bream and roach, prevailed and
occupied new niches of more or less standing water (Blabolil et al.,
2016). Although the pelagic zone was more homogeneous compared to the
structured littoral zone with different bottom substrate, vegetation,
slope, Bray-Curtis dissimilarity values were lower (indicating higher
similarity) for littoral samples compared to pelagic samples. This may
be due to the lower number of taxa per sample in pelagic habitats
resulting in more dissimilar samples. Studies in other geographic
regions also found more species in the littoral compared to the pelagic
zone (Lawson Handley et al., 2019; Zhang et al., 2019). Overall, more
taxa per sample resulted in higher similarity as shown in tributary
samples.