Distribution Of Aquatic Organisms Research Articles

Quantifying the Detection Sensitivity and Precision of qPCR and ddPCR Mechanisms for eDNA Samples.

Environmental DNA (eDNA) detection employing quantitative PCR (qPCR) and droplet digital PCR (ddPCR) offers a non-invasive and efficient approach for monitoring aquatic organisms. Accurate and sensitive quantification of eDNA is crucial for tracking rare and invasive species and understanding the biodiversity abundance and distribution of aquatic organisms. This study compares the sensitivity and quantification precision of qPCR and ddPCR for eDNA surveys through Bayesian inference using latent parameters from both known concentration (standards) and environmental samples across three teleost fish species assays. The results show that ddPCR offers higher sensitivity and quantification precision, particularly at low DNA concentrations (< 1 copy/μL reaction), than qPCR. These findings highlight the superior performance of ddPCR for eDNA detection at low concentrations, guiding researchers towards more reliable methods for effective species monitoring. Additionally, this study indicates that a two-step (detection and concentration) model increased the precision of qPCR results, useful for enhancing the robustness of eDNA quantification. Furthermore, we investigated the lower limit of quantification for ddPCR, providing insights on how such limit can be extended, which could also be applied to qPCR.

Water Temperature Model: A Case Study in Alagoinhas-BA

In recent years, climate change has generated disturbances at both local and global scales, directly impacting the water temperature of rivers. Temperature fluctuations have become a common occurrence in river water, where after experiencing heating, the return to its natural temperature is gradual. Consequently, temperature changes affect various internal processes within rivers, including nutrient consumption, food availability, and dissolved oxygen concentration. These alterations subsequently impact the growth and distribution of aquatic organisms. This article focuses on the physical variables derived from a model characterized by limited computational complexity. The final structure of the model consists of a single ordinary differential equation, which is linearly dependent on air and water temperature, as well as flow rate. Additionally, to handle data sequences such as time series more efficiently than traditional Recurrent Neural Networks (RNNs), we employ a Long Short-Term Memory (LSTM) neural network.

Effects of freshet events on early life stages of fish and macroinvertebrates in a highly turbid estuary of Iberian Peninsula

The present study investigates effects of three different types of freshet events (varying in intensity, duration, and period of discharge) on the early life stages of fish, macroinvertebrates inhabiting in the water column, and the environmental conditions within the hiperturbid estuary of the Guadalquivir River. Freshet events compressed the salinity gradient and increased turbidity; during the most intense freshet event, the oxygen concentration also decreased. These environmental changes had significant effects on the abundance and distribution of aquatic organisms, reducing the nursery area from 40 km upstream to 20 or 10 km, depending on the freshet. Recovery of physicochemical conditions was relatively rapid (within one or two weeks) for less intense freshets, while the most intense event showed only partial recovery even one month later. Biological responses varied among species and time periods. Pelagic species (e.g., anchovies) were flushed out of the estuary. The populations of these species can show a posterior reintroduction and a recovery to levels similar to before the freshet, or a nonrecovery, probably depending on larval supplied from the offshore stock. In contrast, benthic and estuarine species (e.g., gobies, mysids), were just displaced downstream during the freshets. In the most intense freshet event, which occurred before the high recruitment period of these species (early spring), their abundances increased significantly, exceeding the levels of normal years (without freshets). This suggests that, depending on the intensity and the period in which the freshet occur, they could act as attraction signals for certain species. In general, estuarine and benthic species, such as gobies and other macroinvertebrates, coped better with freshets than pelagic marine migrant species, such as anchovies. However, the estuary and its estuarine organisms showed high resilience to environmental fluctuations.

Vertical distribution patterns of zooplankton across a gradient of fish predation in boreal lakes

Abstract Different physical factors such as solar radiation and wind impose strong vertical gradients in lake water columns and have important consequences on the distribution of aquatic organisms, from bacteria to fish. The heterogeneous vertical distribution of zooplankton in lakes is a clear example of a pattern related to these vertical gradients. Although the vertical distribution of zooplankton is probably controlled by multiple factors including light, resources, and predation, we still lack an integrated view of the interplay among these potential drivers, which are most often analysed separately. Moreover, most studies focussed on temperate lakes in which both phytoplankton resources and predation risk from fish are highest in the epilimnion, whereas only a few investigated boreal lakes, where phytoplankton is often more abundant in the metalimnion than in the epilimnion and cold‐stenothermic fishes prey on zooplankton below the warm epilimnetic layers. Here we investigated zooplankton vertical distribution in the epi‐ and metalimnetic waters of 17 boreal lakes that varied in fish predation, resource quantity and quality, and optical properties. The lakes were sampled at midday and midnight at five different depths in the well‐lit epi‐ and metalimnetic layers, where the strongest gradient in light (and predation risk) were expected. We used a multi‐model inference approach combined with linear modelling to examine the relative effects of physical factors (light attenuation, temperature and moon phase), resources (chlorophyll‐a and polyunsaturated fatty acids), and predation (fish and Chaoborus) on depth selection in four zooplankton taxa. All taxa showed a heterogeneous vertical distribution that in most cases had a clear diel migration pattern. Both predation and resources (food and temperature gradient) were associated with vertical depth selection by zooplankton, but each taxon had different responses to each factor. Vertebrate predators were associated with the vertical distribution of Daphnia, Calanoida, and Cyclopoida, but—unexpectedly—all these taxa reduced their diel vertical migration patterns in the presence of fish. Invertebrate predators were better correlated with the distribution of Cyclopoida, which tended to be shallower when Chaoborus was abundant. Food abundance seemed important for Holopedium glacialis and Calanodia, while the temperature gradient was partly associated with both Daphnia spp. and Calanoida distribution. Finally, we found an intriguing, albeit weak, positive association between the vertical distribution of Cyclopoida and that of food quality. These results showed that taxa less vulnerable to predators such as H. glacialis perform inverse DVM, and that this is at least partly related to moon phase rather than to fish predation. They also suggest that boreal lakes colonised by stenothermic planktivorous fish behave differently from the classical DVM paradigm, given that visual predators do not have access to fully lit layers.

Features of the spatial structure of the macro- and meiobenthos community of the lagoon ecosystem of Kislaya Bay head (Gulf of Kandalaksha, White sea)

The spatial and species structure of meio- and macrobenthos communities of the Kislaya Bay (Gulf of Kandalaksha, White Sea) lagoon ecosystem was analysed. A total of 32 species of benthic organisms (including 11 species of invertebrate larvae) and 9 species of seagrasses and algae were found. Eumeiobenthos groups were identified to the level of large taxa (nematodes, harpacticoids, ostracods, turbellaria). The highest total biomass of macrobenthos organisms was mainly observed in the lower horizon of the littoral zone and at the exit from the lagoon (high biomass of Mytilus edulis populations). For meiobenthos biomass was the highest in the middle and upper littoral horizons and in the bayhead. This may indicate a complementary distribution of meio- and macrobenthos: the role of meiofauna grew where macrobenthos development was somewhat inhibited. An analysis of the similarity of meio- and macrobenthos of different habitats revealed differences in the species structure of communities between the three littoral horizons – upper, middle, and lower. Communities of the lower and middle horizons of the littoral zone exhibited a greater similarity of the species structure than communities of the upper horizon. The differences in the structural characteristics of the community lengthwise – with increasing water salinity, are less pronounced (especially when compared with the corresponding structural changes in meio- and macrobenthos in the Chyornaya River estuary). This is probably due to the milder salinity conditions in the lagoon versus the Chyornaya River estuary, lower impact of this factor on the distribution of aquatic organisms and, accordingly, smaller change in the species structure of the community lengthwise – from the bayhead towards the sea.

Combined effect of temperature and a reference toxicant (KCl) on Daphnia middendorffiana (Crustacea, Daphniidae) in a high-mountain lake

Climate change has direct effects on aquatic systems where increased water temperature leads to range shifts and changes in the distribution of aquatic organisms. The effects of climate change on aquatic ecosystems are expected in all biomes, and in Alpine environments in particular. Anthropogenic pressure (e.g., chemical pollution) besides climate change impact on the state and quality of aquatic systems in which climate change and environmental contaminants can interact. To better understand the effect of increases in temperature and environmental pollution on high-mountain lakes, we performed an ecotoxicological assay on Daphnia middendorffiana collected during summer 2021 in a high-mountain lake (Upper Balma Lake, Cottian Alps, 2212 m a.s.L.). Samples were exposed to two temperature values (15 °C and 20 °C), potassium chloride (KCl) as the reference toxicant, and D. magna as the model organism for comparison. Findings showed immobilization after exposure to KCl in both species, but exposure to non-optimal water temperature (20 °C and 15 °C for D. middendorffiana and D. magna, respectively) enhanced this effect. The mean half-maximal effective concentration (EC50; 24 h) for D. middendorffiana was significantly lower than that recorded for D. magna exposed to 20 °C (KCl) (46.9 mg/L vs 255 mg/L). A significantly higher EC50 (273.4 mg/L; 24 h) was recorded for D. middendorffiana exposed to 15 °C (KCl) compared to D. magna (EC50 50.6 mg/L; 24 h). Our findings suggest that the combined effects of temperature and chemical pollution may severely affect the occurrence of D. middendorffiana, which occupies a central position in the food webs of high-mountain lakes in the Alps.

Air temperatures over-predict changes to stream fish assemblages with climate warming compared with water temperatures.

Studies predicting how the distribution of aquatic organisms will shift with climate change often use projected increases in air temperature or water temperature. However, the assumed correlations between water temperature change and air temperature change can be problematic, especially for mountainous, high elevation streams. Using stream fish assemblage data from 1,442 surveys across a mountain-plains gradient (Wyoming, USA; 1990-2018), we compared the responsiveness of thermal guilds, native status groups, and assemblage structure to projected climate warming from generalized air temperature models and stream-specific water temperature models. Air temperature models consistently predicted greater range shift differences between warm-water and cold-water species, with air temperatures predicting greater increases in occurrence and greater range expansions for warm-water species. The "over-prediction" of warm-water species expansions resulted in air temperature models predicting higher rates of novel species combinations, greater increases in local species richness, and higher magnitudes of biotic homogenization compared with water temperature models. Despite differences in model predictions for warm-water species, both air and water temperature models predicted that three cold-water species would exhibit similar decreases in occurrence (decline of 1.0% and 1.8% of sites per 1°C warming, respectively) and similar range contractions (16.6 and 21.5 m elevation loss per 1°C warming, respectively). The "over-prediction" for warm-water species is partially attributable to water temperatures warming at slower rates than air temperatures because local, stream-scale factors (e.g., riparian cover, groundwater inputs) buffer high elevation streams from rising air temperatures. Our study provides the first comparison of how inferences about climate-induced biotic change at the species- and assemblage-levels differ when modeling with generalized air temperatures versus stream-specific water temperatures. We recommend that future studies use stream-specific water temperature models, especially for mountainous, high elevation streams, to avoid the "over-prediction" of biotic changes observed from air temperature variables.

An underwater video system to assess abundance and behavior of epibenthic Mysis

AbstractThe application of remote video technologies can provide alternative views of in situ behavior and distribution of aquatic organisms that might be missed with traditional net‐based techniques. We describe a remote benthic video camera system designed to quantify epibenthic density of the macroinvertebrate Mysis diluviana. We deployed the camera multiple times during the day and night at a 60‐m depth site in Lake Champlain and quantified Mysis density from the footage using basic methods and readily available software. Density estimates from the video were on average 43 times higher than concurrent estimates from benthic sled tows, suggesting sleds may be inefficient at sampling mysids. Deployment caused initial scattering of individuals, resulting in low densities immediately after deployment that slowly increased. On some occasions, Mysis densities on video fluctuated greatly over several hours, consistent with organisms that have a patchy distribution on the lake bottom. The camera system provided novel insights on behavior and distribution of Mysis on benthic habitats, demonstrating potential for use as a tool to study partial diel vertical migration and predator–prey interactions.

A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems.

The use of environmental DNA (eDNA) to determine the presence and distribution of aquatic organisms has become an important tool to monitor and investigate freshwater communities. The successful application of this method in the field, however, is dependent on the effectiveness of positive DNA verification, which is influenced by site-specific environmental parameters. Factors affecting eDNA concentrations in aquatic ecosystems include flow conditions, and the presence of substances that possess DNA-binding properties or inhibitory effects. In this study we investigated the influence of different environmental parameters on the detection success of eDNA using the invasive goby Neogobius melanostomus. In a standardized laboratory setup, different conditions of flow, sediment-properties, and fish density were compared, as well as different potential natural inhibitors such as algae, humic substances, and suspended sediment particles. The presence of sediment was mainly responsible for lower eDNA detection in the water samples, regardless of flow-through or standing water conditions and a delayed release of eDNA was detected in the presence of sediment. Humic substances had the highest inhibitory effect on eDNA detection followed by algae and siliceous sediment particles. The results of our study highlight that a successful application of eDNA methods in field surveys strongly depends on site-specific conditions, such as water flow conditions, sediment composition, and suspended particles. All these factors should be carefully considered when sampling, analyzing, and interpreting eDNA detection results.

Impacts of Thermal Stratification on the Hydrochemistry and Dissolved Inorganic Carbon in a Typical Karst Reservoir in Summer

Thermal stratification leads to significant stratification characteristics of hydrochemistry and aquatic organisms in reservoirs, and thus affects the biogeochemical cycle in the reservoir. This study aims to understand physico-chemical properties and dissolved inorganic carbon change processes and its factors in a karst groundwater-fed reservoir, Dalongdong Reservoir, located in Shanglin County, Guangxi Zhuang Autonomous Region, China. The eight sampling points were placed along the direction of the water flow on June 19-21, 2015. The results show that: ① The reservoir exhibited obvious thermal stratification in the summer. There were significant differences in physical and chemical parameters, such as pH and conductivity (Spc) between the epilimnion and thermocline; ② The dissolved oxygen (DO) and chlorophyll a (Chl-a) content from the surface to the bottom did not show a single decreasing trend, but the maximum value occurred 2.5 m or 5 m below the surface; ③ From the surface to the bottom, dissolved inorganic carbon (DIC) concentrations showed an increasing trend with the average DIC concentration of 2.03 mmol·L-1 in the epilimnion and the average DIC concentration of 4.18 mmol·L-1 at the bottom of the thermocline. The value of stable carbon isotope (δ13CDIC) was more positive in the epilimnion than in the thermocline, where δ13CDIC gradually became partially negative with water depth. Possible reasons of these results include: ① The significant differences in temperature, distribution of aquatic organisms, and strength and direction of metabolisms in different water layers due to thermal stratification; ② The DIC variations in the epilimnion were mainly affected by the carbonate precipitation process and phytoplankton photosynthesis, thereby affecting the DIC stable isotope fractionation. DIC was mainly controlled by biological respiration and the organic matter decomposition process in the thermocline.

Structure and dynamics of aquatic organisms in the littoral zone of Petrokrepost Bay (Lake Ladoga)

The study of spatiotemporal distribution of aquatic communities was conducted in the shallow part of littoral zone of Petrokrepost Bay of Lake Ladoga for three years (from 2010 to 2012). The study covered three types of habitats gradually changing as depth increased: the littoral reed beds, zone of emergent vegetation, dominated by Potamogeton perfoliatus , and unvegetated zone (sand). The morphometric description and characteristics of macrophytes in Petrokrepost Bay are presented. It is shown that different habitats which are closely located (within hundreds of meters) are more similar in terms of aquatic species composition than the same habitats separated by tens of kilometers. The following aspects have been studied: spatial heterogeneity in the distribution of aquatic organisms; active and passive circadian horizontal and vertical migrations of mesoplankton, benthos, bacterio- and phytoplankton, and protozoa. The set of abiotic and biotic factors affecting the distribution of different groups of aquatic organisms has been detected.

Effects of environmental and spatial variables on lotic ostracod metacommunity structure in the Iberian Peninsula

The heterogeneous distribution of aquatic species in lotic environments has been studied little in terms of metacommunity theory. Previous empirical tests have found significant spatial and environmental effects in pond and lake communities, but this has not yet been clearly established for stream networks. We conducted a multi-season survey of mountain streams in the Iberian Peninsula. We recorded GIS and in situ environmental data and collected biological samples to determine ostracods and macroinvertebrates and identified 41 ostracod species, the most common belonging to genera Herpetocypris, Sarscypridopsis, and Ilyocypris. A generalized linear model analysis showed that thermal range, alkalinity, slope, and the Iberian Average Score Per Taxon (IASPT) macroinvertebrate biotic index negatively influenced ostracod presence, whereas the Iberian Bio-Monitoring Working Party (IBMWP) biotic index and nitrite concentration had a positive effect. Conductivity, mean air temperature, slope, and IBMWP were the most statistically significant environmental factors affecting ostracod species distribution according to a canonical correspondence analysis, together with large-scale spatial factors identified with a principal coordinates neighbour matrix (PCNM) analysis. Both environment and space, although markedly overlapping, contributed significantly to the explanation of ostracod metacommunity structure. We conclude that both colonisation histories and environmental adaptations affect the patterns of distribution of aquatic organisms in riverine environments, extending beyond intra-basin connectivity.

Statistical analysis of structural variations of benthic communities and testing the hypothesis of river continuum

Statistical methods for assessing the spatial distribution of benthic communities in different parts of watercourses have been considered as applied to lowland rivers of the Lower Volga region. The applicability domains are described for different response models, gradient analysis, and random skewers methods, which are used to analyze the distribution of aquatic organisms in bottom sediments. Stationarity and autocorrelation criteria for the description of generalized characteristics of macrozoobenthos communities are analyzed. The problems of identification of statistically significant isolated zones at whose boundaries the succession change of the species composition of aquatic organisms are discussed. The results of nonparametric dispersion analysis of species similarity matrices, the formation of dendrites, and the search for barriers between individual areas are given (based on Delaunay triangulation and Monmonier’s maximal-diversity algorithm).

Intraspecific morphological variation in a freshwater crustacean Aegla plana in southern Brazil: effects of geographical isolation on carapace shape

Freshwater ecosystems are characterized by a high spatial complexity. This heterogeneity affects the distribution of aquatic organisms in riverine landscapes. Morphological variation in natural populations is driven by evolutionary forces. In crustaceans, morphological variations have been observed between different basins, environments, or developmental sequences along their geographical distribution. In this study, we assessed the possible effects of spatial scale on the phenotype of Aegla plana Buckup and Rossi, 1977 using geometric morphometrics. We examined 110 adult specimens from three river basins in southern Brazil. We used 13 morphological landmarks for the dorsal view of the carapace; the coordinates were superimposed using a generalized Procrustean analysis. We used a multivariate analysis to test the morphological variation in crabs from different basins, and we employed the Mantel test to assess the relationship of spatial and environmental factors with the principal components matrix for the carapace shape. Populations from different river basins differed significantly in carapace centroid size. Carapace shapes also differed significantly among the river-basin populations, and the interaction between sex and populations was also significant. The environmental and geographical matrices were correlated with the carapace shape matrix. This morphological variation shows an association with the geographical distribution of microbasins, which suggests a biogeographical effect on the distribution of A. plana.

The distribution of zoobenthic organisms as the water level decreases in a small river

The influence of water level changes on the distribution of aquatic organisms in the channel of a small river was studied. A decrease in the water level leads to the migration of animals to deeper habitats. A further decrease in the water level results in the concentration of benthic organisms in other streams. Aquatic organisms able to survive for a long time were found on the wet bottom sediments at dried parts of the river channel.

River behavior on megafans and potential influences on diversification and distribution of aquatic organisms

Megafans are partial cones of river sediment usually laid down by a single switching river, characterized by areas on the order of 10 3–10 5 km 2, smooth plains, and slopes of <1°. Astronaut handheld imagery acquired since the early 1980s has permitted the first global geomorphic survey of megafans. Using examples mainly from South America, and based on stream behaviors common in megafans, seven models that appear to have implications for the distribution and diversification of aquatic organisms are presented. River behaviors that appear significant for the fragmentation and age of aquatic habitats on megafans include river switching (models 1.1–1.4) and the disconnection of the megafan river from the main river of the basin (models 2–4). Each model has a habitat fragmentation and a habitat combining mode. In their vicariant mode, models 1.1 and 1.2 involve longer periods of time. Models 1.3 and 1.4 involve the relatively instantaneous merging of aquatic populations from neighboring megafan rivers or neighboring major basins. Models 2–4 involve longer-term dynamics with the potential for speciation. We identify the following levels of diversity related to scales of stream operation: intrafan diversity, or local populations and among local populations; interfan diversity, or among local populations and species; and interbasin diversity, or species and biotas.

Potential Changes in Aquatic Biota in the Period of Global Climate Warming

The results of investigations of water bodies subjected to constant many-year thermal pollution are proposed to use for the prediction of the consequences of climate warming. General tendencies in changes in the aquatic biota and the distribution of aquatic organisms under the effect of thermal pollution are established by analyzing the materials collected at different cooling ponds of nuclear and thermal power stations.

Foraging in a Lethal Environment: Fish Predation in Hypoxic Waters of a Stratified Lake

Development of low oxygen conditions (hypoxia) in bottom waters of stratified lakes has a profound effect on the distribution of aquatic organisms. Fish avoid hypoxic waters by moving into oxygenated water and suffer massive die—offs when migration is not possible. However, central mudminnows (Umbridae: Umbra limi) were captured regularly in severely hypoxic bottom waters of a lake in northern Wisconsin, USA. Caging experiments confirmed the lethality of this environment to mudminnows. The presence of freshly ingested phantom midge larvae (Diptera: Chaoborus) in the stomachs of mudminnows during the day coupled with the observation that Chaoborus are restricted to hypoxic waters during the day indicate that mudminnows routinely ventured into a lethal environment to forage. This conclusion was supported by caging experiments whereby mudminnows denied access to hypoxic water during the day did not contain Chaoborus in their stomachs. In laboratory experiments, ingestion of air bubbles enhanced the ability of mudminnows to forage in hypoxic water, but even in the absence of surface access, mudminnows readily foraged in hypoxic waters. These data help explain reports of other fish venturing into hypoxic waters and suggest that foraging in hypoxic waters may be common among some fishes when food abundance is low in surface waters.

Effects of algal turf canopy height and microscale substratum topography on profiles of flow speed in a coral forereef environment

Water motion can be an important variable affecting the recruitment, metabolism, growth rates, feeding efficiency, and distribution of aquatic organisms. Recent studies suggest that flow speed may be an important factor regulating primary productivity of reef algal turf communities. We measured profiles of flow speed over algal turfs with different canopy heights and over algal turfs growing on substrata that varied in microtopography. Profiles over sea urchin‐grazed algal turfs with low canopy heights and algal turfs growing on topographical high points indicate that the boundary layer is dominated by turbulent eddies. In contrast, flow over algal turfs with higher canopy heights and those growing within depressions in the substratum is influenced more by viscous forces that may lead to diffusion‐limited metabolism of these algal communities. These data demonstrate that flow speeds over coral reef algal turfs exhibit spatial variation over small spatial scales and temporal variation that is dependent on ambient flow speeds. Our results predict microscale variation in algal turf metabolism and suggest that photosynthetic rates of this component are likely to be below maximum capacity for a significant portion of the time.