Introduction
High quality water sources are essential for ecosystem service
provisioning under global change, including climate and pollution (Baron
et al., 2002). One effective way to maintain high quality water sources
is water storage in reservoirs that have been created for drinking,
agriculture and industrial purposes, flood protection, recreation, and
hydropower generation among others (Labadie 2004). Despite the key
importance of reservoirs, research has typically focused on natural
water bodies whereas artificial or heavily modified water bodies are
often neglected (Straškraba 2005). Deep reservoirs are prime, widespread
examples of aquatic heterogeneous ecosystems with hydrological
characteristics that are intermediate between lakes and rivers, and
include lacustrine, transitional and riverine components (Wetzel 2001).
Deep temperate reservoirs are hydrologically complex environments where
seasonal variation in temperature and flow conditions affects
stratification and mixing patterns of the water column. River inflows
along with an intricate outflow dam system further modify reservoir
hydrodynamics and often result in currents and intrusion of water to
deeper strata (Ford, 1990, Straškrabová et al., 1994). In summer, stable
thermal stratification occurs with higher temperature (>20
°C) in the epilimnion and lower temperature (4 °C) associated with
higher water density in the hypolimnion. Summer stratification is
followed by autumn mixing of the entire water column, with gradual
cooling to temperatures around or below 4 °C. During winter, the
hypolimnion contains water of the highest density with temperature close
to 4 °C, and surface water has lower density with possible ice coverage.
The stability of the water column in winter depends on weather
conditions (e.g. ice cover, wind, precipitation) and water level
manipulations. In canyon-shaped reservoirs, spatial heterogeneity is
also associated with longitudinal gradients (Thornton et al., 1990).
Nutrient rich tributaries support phytoplankton production, which
decreases towards the dam (Rychtecký & Znachor, 2011). A transition
between the littoral and pelagic zones represents an additional source
of reservoir spatial heterogeneity as the littoral zone differs in many
aspects from more homogeneous pelagic habitats (Říha et al., 2015).
Littoral habitats can be complex with macrophyte, rock and root
configurations, or simple (e.g. sandy or muddy beaches), creating
diverse environments affecting species composition, abundance and
spatial distribution of the whole trophic web, from phyto- and
zooplankton to fish (Prchalová et al., 2009a).
Fish have both direct and indirect effects on all trophic levels and are
well-adapted to the various environmental conditions of heterogeneous
temperate freshwaters. Therefore, they are often used as ecological
indicators (EC, 2000). The long lifespan of many species also means that
fish communities reflect changes over decadal timescales (Blabolil, et
al., 2017b). Reliable assessment of fish community composition in
reservoirs has typically required a combination of various sampling
methods. However, established sampling methods are relatively laborious,
expensive, sometimes destructive, taxonomically biased, and their
application is case-specific, thus these limitations often result in
poor accuracy and precision (Kubečka et al., 2009). In Europe,
gillnetting is commonly used to assess fish populations, but this type
of fish survey is extremely invasive (Blabolil, et al., 2017a).
Therefore, efforts should be invested in the implementation of
less-invasive and more universal monitoring strategies. Traditionally,
visual census and hydroacoustics have been used for non-invasive
surveys, but both have limitations. The accuracy of visual census
depends on water clarity (Holubová et al., 2019), whereas hydroacoustics
application is constrained by water depth and results do not provide
species composition (Baran et al., 2017). Recently, environmental DNA
(eDNA) metabarcoding has come to the fore as an innovative method for
aquatic biodiversity biomonitoring (Taberlet et al., 2018).
eDNA refers to genetic material released by organisms into their
environment, which can be captured and analyzed to enable non-invasive,
highly sensitive species detection (Taberlet et al., 2018). Aquatic
ecosystems are particularly suited to eDNA analysis as water is an
effective medium for deposition and transport of intracellular or
extracellular organismal DNA from aquatic, semi-aquatic and terrestrial
organisms (Deiner et al., 2016; Harper et al., 2019b). All water bodies
can be easily sampled to collect eDNA, including temporary pools
(Bylemans et al., 2019), rivers (Deiner et al., 2016), ponds (Harper et
al., 2019a), large heterogeneous lakes (Lawson Handley et al., 2019) and
marine environments (Djurhuus et al., 2020). eDNA metabarcoding is an
especially powerful and cost-efficient approach for biomonitoring as it
allows whole communities to be screened (Hering et al., 2018). During
metabarcoding, eDNA is PCR-amplified using broad-range primers and
sequenced on a high-throughput sequencing platform (Deiner et al.,
2017). However, species composition and distribution inferred from eDNA
metabarcoding must account for environmental conditions that influence
eDNA dynamics. Various factors affect eDNA persistence and degradation,
such as temperature, ultraviolet (UV) light intensity, and oxygen
concentration, that in turn determine microbial action and metabolic
activity of aquatic organisms (Barnes et al., 2014). The spatial
distribution of eDNA in a given water body can be influenced by species’
habitat preferences and activity (de Souza et al., 2016), oxygen and
trophic conditions (Lawson Handley et al., 2019), or water movements
caused by inflows and outflows, precipitation, wind, convective currents
etc. (Jeunen et al., 2019). Background data characterizing environmental
conditions and their possible links to eDNA dynamics are desperately
needed, but are often not provided in published studies (Nicholson et
al., 2020; Ruppert et al., 2019).
The aim of our study was to use eDNA metabarcoding to assess the fish
communities in three Czech Republic reservoirs across two seasons. We
compared species composition at multiple sites characterizing the
spatial gradient in each of the reservoirs. We also tested the
relationship between eDNA site occupancy and scores derived from
conventional sampling for each taxon. Finally, we analyzed the
relationship between species diversity and reservoir spatial
heterogeneity.