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Fish stock monitoring is an important element for the sustainable management of inland water resources. A scarcity of data and the lack of systematic monitoring for Lake Trichonis precludes an up-to-date assessment. To assess the current status of pelagic fish stock, a hydroacousting survey was conducted for the first time in Lake Trichonis, Greece. In October 2019, the lake was acoustically surveyed with two, horizontally and vertically mounted, 120 kHz transducers during day and night. A decreasing gradient in pelagic fish density from the western to the eastern shores of the lake was observed. Fish density was significantly higher in the intermediate layers of the water column, in the eastern region, compared to the western region. The lake appears to host primarily communities of small-sized fish (TL: 0&ndash, 5 cm), whereas larger fish (TL: 5&ndash, 50 cm) are a small minority of the total fish stock. The overall average estimated fish length was approximately 2.4 cm. The adoption of routine inland fish stock monitoring through hydroacoustic methods could be a promising step in the effort to improve the understanding of unique inland water ecosystems with minimum impact on endemic species, as well as to mitigate human impact and achieve long-term sustainable management.

Sampling of benthic fish is complicated, especially in deep inland water bodies with a structured bottom. The catches were compared of rapidly spreading round goby (Neogobius melanostomus) using small fykes nets and benthic gillnets in three artificial lakes in The Netherlands over a two year period. Round gobies were captured at all depth layers in each sampled lake. Significantly larger individuals were captured in gillnets compared to fyke nets. Reference sampling in littoral areas captured a wide range in size of round gobies with beach seines. With fyke nets, the highest catches were usually achieved in the shallowest and deepest depth strata. Gillnets catch decreased at deeper layers. Both methods are passive sampling tools and did not provide the absolute catch per bottom area, however relative density estimates of round gobies at different depths or habitats are possible. Round gobies showed a significant size bias associated with capture method. Because it is important to understand the biology and ecology of invasive species like round goby, the combination of small fyke nets and gillnets appears to be a good solution to sample a variety of ranges in deep or/and structured benthic habitats.

Monitoring of biota in heterogeneous ecosystems requires sampling in different habitats and across environmental gradients. The resulting multivariate community data are typically aggregated into one or several indicator values for the entire ecosystem, but the relationship between the robustness of such indicators and sampling effort, including the identification of minimum acceptable sampling designs, is not fully understood. We address this issue for multi-mesh gillnet sampling of freshwater fish communities in deep-valley reservoirs, using data from 29 detailed annual surveys in eight reservoirs in the Czech Republic that account for the inherent longitudinal and depth gradients and the qualitatively different benthic and pelagic habitats. We evaluate the performance of eight sampling scenarios, created by variously reducing the full dataset. To this end, we use 31 fish-based, community-, size- and species-level indicators calculated separately for benthic and pelagic habitats, and fit the relationships between the indicator values based on the reduced and full sampling design using Bayesian generalized linear models. The ability of reduced data to estimate the “true” indicator value across the entire dataset, expressed as the adjusted R 2 value of the best model for the given indicator, increased with sampling effort. However, the relationships differed between indicators: R 2 values were higher for abundance-based than for biomass-based indicators. We identified three suitable reduced sampling designs: (1) sampling the entire longitudinal profile in the epilimnion, yielding on average the highest R 2 values (0.97), (2) same as before but limited to one sampling layer closest to the surface (R 2 = 0.91), and (3) sampling all depth strata at the farthest points of the longitudinal gradient ( i.e. , dam and tributary, R 2 = 0.83). These results demonstrate that, in order to obtain robust estimates of fish community indicators, current gillnet sampling protocols can be optimized to reduce effort and minimize unwanted fish mortality.

Horizontally-aligned, fixed and mobile, transducers are routinely deployed at depths of 0.5–0.75 m to survey the surface layer of waterbodies for fish. However, simulations and measurements demonstrate that a smooth surface can cause serious errors in the target strength (TS) and split-beam angular position estimates. Errors in TS up to 10 dB and depth position up to 0.5 m were observed. Simulations suggested that multi-path signal propagation interfered with the direct path of that signal. Furthermore, when a standard target (calibration copper sphere) was moved away from the transducer at fixed depths, the estimated TS and depth of the target started to oscillate as a function of range. The amplitude increased with increasing range. The frequency decreased from the oscillation start until a certain range where the oscillation stopped. The region of oscillation depended on both the transducer and target depth. Horizontal observations of known fish echoes behaved similarly. Experiments in a lake showed that the influence from the surface disappeared when the surface became rippled due to wind.

Information about fish distribution and abundance in the upper part of the water column are often fundamental for both research and management. However, this information is extremely hard to obtain using conventional hydroacoustic methods. For this reason, the mobile hydroacoustic upward-looking system (38 kHz split-beam echosounder) in combination with a passive sampling method (gillnets) was tested to investigate the fish community (fish larger than 8 cm total length) in the upper 3 m of water column of the Řimov Reservoir (Czech Republic) during the growing season. We found most fish located in the depth layer closest to the surface down to 1 m – 50–78 % by acoustics (layer 0.3; 1 m) and 55-–1 m) and 55–71 % by gillnets. The size structure of both methods was generally similar, but the acoustic results contained a higher proportion of small fish (

DIDSON acoustic cameras provide a way to collect temporally dense, high-resolution imaging data, similar to videos. Detection of fish targets on those videos takes place in a manual or semi-automated manner, typically assisted by specialised software. Exploiting the visual nature of the recordings, tools and techniques from the field of computer vision can be applied in order to facilitate the relatively involved workflows. Furthermore, machine learning techniques can be used to minimise user intervention and optimise for specific detection and tracking scenarios. This study explored the feasibility of combining optical flow with a genetic algorithm, with the aim of automating motion detection and optimising target-to-background segmentation (masking) under custom criteria, expressed in terms of the result. A 1000-frame video sequence sample with sparse, smoothly moving targets, reconstructed from a 125 s DIDSON recording, was analysed under two distinct scenarios, and an elementary detection method was used to assess and compare the resulting foreground (target) masks. The results indicate a high sensitivity to motion, as well as to the visual characteristics of targets, with the resulting foreground masks generally capturing fish targets on the majority of frames, potentially with small gaps of undetected targets, lasting for no more than a few frames. Despite the high computational overhead, implementation refinements could increase computational feasibility, while an extension of the algorithms, in order to include the steps of target detection and tracking, could further improve automation and potentially provide an efficient tool for the automated preliminary assessment of voluminous DIDSON data recordings.

Ecological quality assessment of non-natural water bodies is, in contrast to natural systems, less developed and requires determining biological indicators that reliably reflect environmental conditions and anthropogenic pressures. This study was motivated to propose fish indicators appropriate for assessment of reservoir ecosystems in central Europe. We analysed changes in water quality, total biomass and the taxonomic, trophic and size composition of fish communities along the longitudinal axes of four elongated, deep-valley reservoirs. Due to high nutrient inputs from their catchments, the reservoirs exhibited pronounced within-system gradients in primary productivity and water transparency. Although fish communities were similar among the reservoirs and dominated by few native species, the community structure and biomass systematically changed along the longitudinal axes of the reservoirs. The biomass and proportion of planktivores/benthivores in the fish community were highest at eutrophic sites near the river inflow and declined substantially towards deep, more oligotrophic sites close to the dam. The biomass and proportion of piscivores significantly increased downstream within the reservoirs alongside improving water quality. At species level, perch Perca fluviatilis and bream Abramis brama responded most sensitively, although in opposite directions, to the longitudinal environmental gradient. The major longitudinal changes in fish community characteristics were found to be consistent between pelagic and benthic habitats. The results of this study suggest that fish communities are appropriate indicators of eutrophication and can be used for ecological quality assessment of non-natural lentic water bodies, such as reservoirs. Moreover, our results underline the necessity to consider within-system gradients in water quality and the fish community when planning sampling programmes for deep-valley reservoirs.

Fish otoliths are conservative structures that are widely used on fishery science for multiple purposes. Despite its relevance in the research field, little is known about the ontogeny and inter-population effects on the otolith of freshwater fish. In this study we used otoliths from 1800 European perch (Perca fluviatilis) individuals from 9 different populations to analyze the ontogenetic and inter-population differences on the otolith shape using six morphometric indices. The relationship between fish and otolith length was fitted using three different regression models (linear, power and logistic) to identify the best allometric relationship. Our results show that there are strong ontogenetic and interpopulation differences in P. fluviatilis otolith shapes. We also show that the relationship between the fish and otolith length follows a logistic curve. The ontogenetic differences on otolith shape might be related to extrinsic factors (diet shift and intra and interspecific competition) in each ecosystem, given that the reservoirs are different and no clear pattern on the otolith shapes can be distinguished among populations. Our results imply that the available back-calculation models may not always provide accurate estimates of P. fluviatilis length and that a model that takes into account the real allometric relationship for the species can improve the fish length estimations of back-calculated fish lengths for the European perch.

The effect of target strength oscillations, generated by surface or bottom-induced sound multi-pathing, can cause serious errors in estimates of fish biomass in horizontal acoustic surveys of extremely shallow inland waters (depth 1.7–2 m). In this study, the oscillations were shown to occur in both windy and calm weather conditions, and depended on the target’s depth and range from a transducer. In calm weather the oscillations were more pronounced and targets that were located close to the water surface and further from the transducer were most affected. Errors in target strength reached up to an 8 dB difference from the theoretical value. Fish abundance and size structure estimates are likely to be affected even more than biomass estimates. To avoid boundary-induced errors in target strength, simulations of fish biomass surveys demonstrated that the data-processing range should be limited to 10 m from the transducer for surveys conducted in extremely shallow waters.

We conducted multiple small (2011–2012) and one large sampling campaign (2013) at selected profiles along the Elbe River. With the data we were able to outline spatial and temporal variability of methane concentration, oxidation and emissions in one of the major rivers of Central Europe. The highest methane concentrations were found in human-altered riverine habitats, i.e., in a harbor (1,888 nmol L−1), in a lock and weirs (1409 ± 1545 nmol L−1), and in general in the whole “impounded” river segment (383 ± 215 nmol L−1). On the other hand, the lowest methane concentrations were found in the “lowland” river segment (86 ± 56 nmol L−1). The methane oxidation rate was more efficient in the “natural” segment (71 ± 113 nmol L−1day−1, which means a turnover time of 49 ± 83 day−1) than in the “lowland” segment (4 ± 3 nmol L−1day−1, which means a turnover time of 39 ± 45 day−1). Methane emissions from the surface water into the atmosphere ranged from 0.4 to 11.9 mg m−2 day−1 (mean 2.1 ± 0.6 mg m−2 day−1) with the highest CH4 emissions at the Meissen harbor (94 kg CH4 year−1). Such human-altered riverine habitats (i.e., harbors and similar) have not been taken into consideration in the CH4 budget before, despite them being part of the river ecosystems, they may be significant CH4 hot-spots. The total CH4 diffusive flux from the whole Elbe was estimated to be approximately 97 t CH4 year−1.

Chaoborus larvae inhabit frequently the water column of lakes, when they can be mistaken for small fish. Because larvae ascend up to the blind zone of downward-looking echo sounding at night, quantitative acoustic estimation of them is possible only with upward-looking approach. For this reason, the mobile hydroacoustic upward-looking system (120 and 38 kHz split-beam echosounder) in combination with a direct catch method (trawling) was tested to investigate the night community of invertebrates and juvenile fish in the surface layer of the Římov reservoir (Czech Republic). In the target strength range of invertebrates (smaller than -59 dB), the 38 kHz echosounder recorded only a small proportion of targets while the 120 kHz echosounder recorded distinct peaks corresponding to high densities of Chaoborus (target strength, TS range -70 to -60 dB, average TS -66 to -64 dB). At 120 kHz frequency, the TS distribution of smaller cohort of juvenile fish ( 1.5 ind.m-3.

Round goby is generally accepted to be a typical benthic dwelling fish species both in its native and invasive ranges. Nevertheless, mid-water night trawling in the Biesbosch reservoirs (The Netherlands) identified pelagic occurrence of invasive round goby juveniles, which is the first observation of pelagic utilization in Europe. Subsequent diet analysis revealed the presence of benthic and also pelagic zooplanktonic prey in the digestive tracts of investigated fish, which further confirmed active feeding in the pelagial. Round goby juveniles almost completely avoided the surface water layer and their maximum density always occurred below 6 m in all reservoirs. The observed size spectrum (8–58 mm standard length) included the largest pelagic round goby to ever be mentioned in the scientific literature. Our data also showed that round goby prevailed over other species soon after its invasion into the reservoirs, with native species disappearing from the fry community. This study documents the first evidence of the pelagic occurrence and feeding of round goby juveniles, and confirms the importance of pelagic habitats for early stages of this invasive species in European lentic systems.

Understanding spatial distribution of organisms in heterogeneous environment remains one of the chief issues in ecology. Spatial organization of freshwater fish was investigated predominantly on large-scale, neglecting important local conditions and ecological processes. However, small-scale processes are of an essential importance for individual habitat preferences and hence structuring trophic cascades and species coexistence. In this work, we analysed the real-time spatial distribution of pelagic freshwater fish in the Římov Reservoir (Czechia) observed by hydroacoustics in relation to important environmental predictors during 48 hours at 3-h interval. Effect of diurnal cycle was revealed of highest significance in all spatial models with inverse trends between fish distribution and predictors in day and night in general. Our findings highlighted daytime pelagic fish distribution as highly aggregated, with general fish preferences for central, deep and highly illuminated areas, whereas nighttime distribution was more disperse and fish preferred nearshore steep sloped areas with higher depth. This turnover suggests prominent movements of significant part of fish assemblage between pelagic and nearshore areas on a diel basis. In conclusion, hydroacoustics, GIS and spatial modelling proved as valuable tool for predicting local fish distribution and elucidate its drivers, which has far reaching implications for understanding freshwater ecosystem functioning.

Citation: Žák, J., Jůza, T., Blabolil, P., Baran, R., Bartoň, D., Draštík, V., Frouzová, J., Holubová, M., Ketelaars, H. A. M., Kočvara, L., Kubečka, J., Mrkvička, T., Muška, M., Říha, M., Sajdlová, Z., Šmejkal, M., Tušer, M., Vašek, M., Vejřík, L., Vejříková, I., Wagenvoort, A. J., J. 2018 Invasive round goby Neogobius melanostomus has sex dependent locomotor activity and is under-represented in catches from passive fishing gear compared with seine catches. J. Fish Biol. 93:147–152. DOI: 10.1111/jfb.13646 Invasive

Methane (CH4) is an important atmospheric trace gas mostly released from wet anoxic soils and sediments. While many studies have focused on relatively homogenous environments like rice fields and lake sediments, the changing contribution of heterogeneous sediments e.g. along the longitudinal profile of a rivers has not been covered very frequently. Here we investigated sediment samples from 11 locations of the Elbe River. Sediments were incubated to measure methanogenic/methanotrophic potentials and contribution of individual methanogenic pathways using isotope analysis of δ13C. Additionally, we determined the diversity of the methanogenic communities (analysis of T-RFLP targeting the mcr-A gene in the sediment samples), while abundances of archaea, methanogens and methanotrophs were determined by qPCR. The CH4 production was detected in six samples (out of 11 examined) and ranged from 0.12 to 644.72 nmol gDW−1 d−1. Methanotrophy was found in all examined sediment samples and ranged from 654 to 10,875 nmol gDW−1 d−1. Abundance of methanogens and methanotrophs (Mcr-A and pmo-A gene copy numbers) was not significantly different and quite stable around 106 to 107 copies gDW−1. The group specific qPCR showed high fluctuations, while the highest counts were reported for Methanomicrobiales and Methanosarcinales (105 to 108 copies per gram dry sediment), followed by Methanobacteriales (103 to 105 copies per gram dry sediment). A significant proportion of unidentified methanogens was found in almost every locality. Isotope analysis of δ13C showed that (CH4) is produced mainly by hydrogenotrophic methanogens. We see no trend in the studied parameters along the Elbe River. The molecular data showed no spatial characteristics, while we found hotspots of the measured CH4 processes (CH4 production and oxidation) due to other local driving factors (e.g. carbon content). Thus, out results indicate that the observed variability of the CH4 production and oxidation rates is only indirectly linked to the presence or quantities of different microbial guilds.

For ethical reasons and animal welfare, it is becoming increasingly more important to carry out ecological surveys with a non-invasive approach. Information about fish distribution and abundance in the upper water column is often fundamental. However, this information is extremely hard to obtain using classical hydroacoustic methods. We developed a rigid frame system for pushing upward looking transducers of the scientific echo sounder (38 and 120 kHz) in front of the research vessel. The efficiency of the new approach for monitoring juvenile fish at night was investigated by comparing the results with a quantitative fry trawl in the Římov Reservoir in the Czech Republic. The experimental setup enabled comparisons for the 0–3 m and 3–6 m depth layers, which are utilized by almost all juvenile fish in summer. No statistically significant differences in the estimated abundance of juveniles were found between the two sampling methods. The comparison of abundance estimates gathered by the two frequencies were also not significantly different. The predicted mean lengths from acoustic sampling and the trawl catches differed by less than 10 mm in all comparisons. Results suggest that mobile hydroacoustic upward-looking systems can fill the methodological gap in non-invasive surveying of surface fishes.

The assessment of ecological quality in freshwater ecosystems is a key issue in many countries, but conditions for the development of assessment methodologies are often country-specific. This study proposes a simple methodology for the assessment of the ecological potential of reservoirs based on fish communities using a dataset covering major environmental and pressure gradients in reservoirs in the Czech Republic. Fish data obtained by gillnet sampling were correlated with a proxy of eutrophication as a key indicator of anthropogenic pressure for selecting appropriate fish-based indicators, establishing scoring criteria and developing the index of ecological quality. Expert judgement was also used to select potential fish indicators. Nine indicators were selected for the final fish-based index, fulfilling the criteria required by the Water Framework Directive. Two steps were used to validate the fish-based index quantification of its inter annual stability and sensitivity analysis of individual indicators. Finally, the index was compared to a previously developed general index for Central and Western Europe. Our study demonstrates that a combination of expert judgement and strict validation methods can result in an informative assessment of the ecological conditions, which can help identify conservation and restoration priorities. © P. Blabolil.

We investigated the change in benthic fish communities in three artificial lakes of the Biesbosch area in the Netherlands between two time periods: before and after the invasion of round goby (Neogobius melanostomus). Native ruffe (Gymnocephalus cernua), the dominant species in benthic gillnet and littoral beach seining catches before the invasion, almost completely disappeared in all lakes only 2 years after the invasion. We found a significant increase in 0 + perch (Perca fluviatilis) and, in some lakes, pikeperch (Sander lucioperca) abundance in gillnet catches after invasion. In the post-invasion period, the 0 + fish community was dominated by perch, and the older fish community was dominated by round goby. The species richness of 0 + fish increased in the post-invasion period owing to the invasion of gobiids. However, it did not change for older fish between periods. Our results clearly show that, owing to a similar benthic lifestyle and high niche overlap, ruffe was the only species negatively influenced by the round goby invasion. The competitive superiority of round goby over ruffe is so strong that the once-dominant species of the overall benthic fish community collapsed after only a few years of coexistence.