Estuarine Fish Research Articles

Flood effects on estuarine fish are mediated by seascape composition and context

Estuaries are crucial feeding, nursery and resting sites for fish but can also be subject to the impacts of severe flooding. The environmental features of estuaries can mediate how they respond to these impacts. For example, the size, configuration, and context of estuarine habitats across seascapes affects the value of patches for fish, and so fish assemblages at sites with a greater habitat extent or closer to the mouth of an estuary may rebound more quickly from flooding. We investigated how a once in 100-year flood event affected fish assemblages at approximately 600 sites across 13 estuaries and six estuarine habitats (bare sediments, log snags, mangrove forests, rocky structures, saltmarsh and seagrass meadows) in southeast Queensland, Australia, and determined whether flood impacts were mediated by the position of sites within the broader estuarine seascape. Sites were surveyed annually in 2020/2021 (pre-flood) and 2022 (6 months post-flood) using underwater videography. Flooding modified the structure of the fish community and reduced the abundance of fish targeted by local fisheries in all six habitats. Crucially, flood effects on fish were greater at sites near more expansive urbanisation in some ecosystems, but lower at sites nearer to the estuary mouth. Maximising the extent of natural habitats across estuaries can mediate the effects of floods and should be priorities for restoration and management plans seeking to maintain biodiversity and fisheries productivity in the face of increasing climate-related disturbances.

Does salinity mediate the toxicity of perfluorooctanesulfonic acid (PFOS) in an estuarine fish?

Perfluorooctanesulfonic acid (PFOS) is detected in estuarine environments, where salinity levels fluctuate regularly. We investigated the effects of salinity on the toxicity of PFOS in embryos and larvae of Cyprinodon variegatus. We crossed six PFOS treatments (0, 1–10,000 μg/L) with two salinities (10, 30 ppt). Larvae exposed to the highest concentration of PFOS under high salinity accumulated over twice the amount of PFOS compared to larvae maintained under low salinity. Embryonic survival was unaffected by PFOS, salinity, or their interaction. PFOS delayed time to hatch and increased salinity reduced time to hatch regardless of PFOS treatment; however, no salinity by PFOS interactions were observed. Conversely, PFOS and salinity interacted in the larval stage, with decreased survival at 30 ppt salinity. This is one of the first studies evaluating interactive effects of PFOS and high salinity and highlights the importance of assessing PFAS toxicity across life stages.

Acute toxicity testing of 6PPD-quinone on the estuarine-dependent sport fish, Sciaenops ocellatus.

Recently, large-scale fish kills in the Pacific Northwest were linked to tire wear particles (TWPs) left on roadways, with the lethality attributed to 6PPD-quinone. which has a median lethal concentration of <1 µg/L for selected salmonids. However, there remains a paucity of 6PPD-quinone toxicity values developed for estuarine fish species, which is particularly significant because estuaries receiving inflows from highly urbanized watersheds are especially vulnerable to TWP contamination. Therefore, the present study aimed to determine the toxicity of 6PPD-quinone to an economically and ecologically important estuarine-dependent fish-red drum (Sciaenops ocellatus). Here, we examined the relative sensitivities of three early life stages within red drum: embryonic, larval, and post-settlement for 24-72 hours, depending on the life stage. Exposure concentrations ranged from 10 μg/L to 500 μg/L. We also assessed the sub-lethal impacts of 6PPD-quinone exposure on development during embryonic and larval stages, including body and organ sizes. Our results indicate that red drum are not acutely sensitive to 6PPD-quinone at each early life stage tested. We also found that yolk-sac larvae did not exhibit sub-lethal morphological impacts in a dose-dependent manner, regardless of exposure during embryonic and larval stages. These data are the first to assess the impacts of 6PPD-quinone on estuarine-dependent non-model fishes.

Estuarine front dynamics drive ichthyoplankton assemblage in the tidal freshwater zone of the Río de la Plata, South America

Frontal zones are critical in the retention and dispersal of ichthyoplankton. This study evaluates the response of ichthyoplankton assemblage to frontal zone dynamics in one of the world's largest estuaries, the Río de la Plata, South America. Surveys were conducted between October 2014 and December 2017 in a nearshore habitat of the tidal freshwater zone of the estuary. Ichthyoplankton was collected using conical nets, and physico-chemical variables were registered in situ. The frontal zone dynamics were evaluated through the turbidity front (TF) location, determined by satellite imagery. Although most larval taxa belonged to the freshwater category, the estuarine category had the highest abundances. The highest species richness and abundance occurred during spring and summer, linked to the season and proximity of spawning areas. The dynamics of the TF emerged as the primary driver of interannual variability in ichthyoplankton assemblages within the tidal freshwater zone. A seaward shift of the TF correlated with a reduction in total abundance and the prevalence of freshwater larvae, whereas a retraction of the TF location corresponded to an increased abundance of marine larvae in the tidal freshwater zone. These interannual shifts in TF location and fish larvae assemblages were closely tied to significant variations in river discharges resulting from the ENSO events during the study period. The findings suggest that marine and estuarine fish eggs exhibit effective retention near the frontal zone and the outer regions of the estuary. In contrast, larvae from these categories disperse along the main axis of the estuary in response to the displacement of the frontal zone. Finally, we discuss into the role of the frontal zone in the Río de la Plata as a pivotal environmental cue for fish larvae, influencing their behavior to regulate dispersal patterns.

A rapid and simple procedure for the whole-mount bone staining of small fish

ABSTRACT The cartilage and bone structure has provided insightful knowledge about evolution and ecology of fish, which is an important component of biological oceanography. However, the whole-body bone staining is a lengthy and complicated process that typically takes five days to several months, and the improvement of the conventional method has been one of the important issues in this field. Here we report a quick and easy whole-mount bone staining method for small fish, in which a newly designed fixative is applied. Compared to conventional methods, this novel protocol is a straightforward process that could be adopted for small estuarine fish and other small vertebrates.

Atorvastatin causes developmental and behavioral toxicity in yellowstripe goby (Mugilogobius chulae) embryos/larvae via disrupting lipid metabolism and autophagy processes

Atorvastatin (ATV) is one of the most commonly prescribed lipid-lowering drugs detected frequently in the environment due to its high use and low degradation rate. However, the toxic effects of residual ATV in the aquatic environment on non-target organisms and its toxic mechanisms are still largely unknown. In the present study, embryos of a native estuarine benthic fish, Mugilogobius chulae, were employed to investigate the developmental and behavioral toxic effects of ATV including environmentally relevant concentrations. The aim of this study was to provide a scientific basis for ecological risk assessment of ATV in the aquatic environment by investigating the changes of biological endpoints at multiple levels in M. chulae embryos/larvae. The results showed that ATV had significantly lethal and teratogenic effects on M. chulae embryos/larvae and caused abnormal changes in developmental parameters including hatch rate, body length, heart rate, and spontaneous movement. ATV exposure caused oxidative stress in M. chulae embryos/larvae subsequently inhibited autophagy and activated apoptosis, leading to abnormal developmental processes and behavioral changes in M. chulae embryos/larvae. The disruptions of lipid metabolism, autophagy, and apoptosis in M. chulae embryos/larvae caused by ATV exposure may pose a potential ecological risk at the population level.

Bioaccumulation and trophic transfer of per- and polyfluoroalkyl substances in a subtropical mangrove estuary food web

Mangrove estuaries are an important land-sea transitional ecosystem that is currently under various pollution pressures, while there is a lack of research on per- and polyfluoroalkyl substances (PFAS) in the organisms of mangrove estuaries. In this study, we investigated the distribution and seasonal variation of PFAS in the tissues of organisms from a mangrove estuary. The PFAS concentrations in fish tissues varied from 0.45 ng/g ww to 17.67 ng/g ww and followed the order of viscera > head > carcass > muscle, with the highest tissue burden found in the fish carcass (39.59 ng). The log BAF values of PFDoDA, PFUnDA, and PFDA in the whole fish exceeded 3.70, indicating significant bioaccumulation. The trophic transfer of PFAS in the mangrove estuary food web showed a dilution effect, which was mainly influenced by the spatial heterogeneity of PFAS distribution in the estuarine environment, and demonstrated that the gradient dilution of PFAS in the estuary habitat environment can disguise the PFAS bio-magnification in estuarine organisms, and the larger the swimming ranges of organisms, the more pronounced the bio-dilution effect. The PFOA-equivalent HRs of category A and B fish were 3.48–5.17 and 2.59–4.01, respectively, indicating that mangrove estuarine residents had a high PFAS exposure risk through the intake of estuarine fish.

Particle separation mechanisms in suspension-feeding fishes: key questions and future directions

Key unresolved questions about particle separation mechanisms in suspension-feeding fishes are identified and discussed, focusing on areas with the potential for substantial future discovery. The published hypotheses that are explored have broad applicability to biological filtration and bioinspired improvements in commercial and industrial crossflow microfiltration processes and microfluidics. As the first synthesis of the primary literature on the particle separation mechanisms of marine, estuarine, and freshwater suspension-feeding fishes, the goals are to enable comparisons with invertebrate suspension-feeding processes, stimulate future theoretical and empirical studies, and further the development of biomimetic physical and computational fluid dynamics models. Of the eight particle separation mechanisms in suspension-feeding fishes, six have been proposed within the past twenty years (inertial lift and shear-induced migration, reduction of effective gap size by vortices, cross-step filtration, vortical flow along outer faces of gill raker plates, ricochet filtration, and lateral displacement). The pace of discovery is anticipated to continue accelerating. Multidisciplinary collaboration and integration among biologists and engineers (including chemical, mechanical, biomedical, and filtration engineering) will result in new perspectives to identify patterns and potential unifying mechanisms across the breadth of suspension-feeding fish taxa, morphology, and function.

A Cross-Decadal Change in the Fish and Crustacean Community of Lower Yaquina Bay, Oregon, USA

Natural environmental change, anthropogenic development, and inter-annual variability can affect the ecology of estuarine fish and invertebrates. Yaquina Bay, Oregon, a well-studied estuary, has undergone intense development, as well as deep-draft dredging during the latter half of the 20th century, resulting in the alteration of ~45% of the lower estuary’s natural shoreline. In 1967, the United States Environmental Protection Agency (USEPA) conducted a 21-month survey of Yaquina Bay to characterize the demersal fishes and epibenthic crustaceans that occupy the bay. From 2003 to 2005, we conducted a 25-month survey to replicate that work and provide a comparative snapshot of the demersal fish and epibenthic crustacean community in the bay. A comparison of the trawl survey datasets reveals a 91% decline in total catch per unit effort (CPUE) between surveys, as well as a decline in multiple measures of biodiversity. Furthermore, the fishes and crustaceans of Yaquina Bay have experienced a shift in species dominance from demersal fishes in the late 1960s to epibenthic crustaceans in the 2000s, marked most notably by a nine-fold increase in the Dungeness crab CPUE. While this work does not establish a causal relationship between changes in the demersal communities of this West Coast estuary and human or natural events, it does document substantial changes in both the diversity and total abundance of animals in that community over a three-plus decade period of development and environmental variability. Hence, this forms a second baseline for continued long-term monitoring.

How the Water-Sediment Regulation Scheme in the Yellow River affected the estuary ecosystem in the last 10 years?

The Yellow River, renowned as the most sediment-laden river globally, grapples with sediment deposition issues compromising reservoir functionality and elevating downstream riverbeds, posing threats to human life and property safety. In response, the Water-Sediment Regulation Scheme (WSRS) has been innovatively implemented to address these challenges. While effectively mitigating sediment deposition, WSRS has concurrently disrupted the equilibrium of the estuarine ecosystem. This paper addresses the understudied but crucial topic of the interannual impact of WSRS on the estuarine ecosystem. Drawing upon physical, chemical, and biological data gathered through field surveys conducted before, during, and after WSRS from 2011 to 2022, the analysis delves into the interannual changes in the estuarine environment, fish eggs and larvae abundance, and species diversity under the influence of WSRS. The findings reveal an interannual decreasing trend in terrestrial material input due to WSRS, juxtaposed with an interannual increasing trend in fish eggs and larvae around the estuary, as well as the species diversity index. Notably, these trends became more pronounced post-2014. Compared to pre-2014, nutrient concentrations experienced a ~20 % decrease, chlorophyll-a concentration increased by 44 %, fish eggs proliferated approximately 1 time, and the species diversity index transitioned from a declining trend to an ascending trajectory. After 12 years of continuous WSRS implementation, the impact on the estuarine ecosystem has demonstrably diminished. This research aims to furnish reference experience and scientific basis for water and sediment regulation in major rivers around the world in terms of estuarine ecology.

Can environmental factors increase oxidative responses in fish exposed to polycyclic aromatic hydrocarbons (PAHs)?

Relations among polycyclic aromatic hydrocarbons (PAHs), biomarkers of oxidative stress (lipid peroxidation, glutathione, and glutathione S-transferase activity), and the possible influence of environmental factors (temperature, pH, and salinity) were assessed in situ for specimens of Ramnogaster arcuata, a native estuarine fish. PAH levels found in the muscular tissue of R. arcuata ranged from 0.7 to 293.4 ng g−1 wet weight with petrogenic and pyrolytic inputs. Lipid peroxidation in the liver showed positive correlations (P < 0.05) with total PAHs (r = 0.66), 3-ring (r = 0.66) and 4-ring PAHs (r = 0.52) and glutathione in muscle (r = 0.58). Significant positive correlations (P < 0.05) were also evidenced between muscular glutathione with total (r = 0.62) and 3-ring PAHs (r = 0.75). Hepatic glutathione S-transferase negatively correlated with 4-ring PAHs (r = −0.58). These correlations suggest that lipid peroxidation and muscular glutathione could be good biomarkers for complex mixtures of PAHs, and hepatic glutathione S-transferase could be a suitable biomarker for 4-ring PAHs. Furthermore, significant correlations (P < 0.05) of environmental factors with PAH levels and biomarkers were observed, especially pH with 3-ring PAHs (r = −0.65), lipid peroxidation (r = −0.6), glutathione in the liver (r = −0.73) and muscle (r = −0.75); and temperature with 2-ring PAHs (r = −0.75) and glutathione in muscle (r = 0.51). The data suggest an influence of physicochemical parameters which could be driving a shift in PAH toxicity in R. arcuata. These results are essential for an integrated understanding of ecotoxicology and could help to predict environmental effects in present and future scenarios of ocean warming and acidification.

Migratory history of the threespine stickleback Gasterosteus aculeatus in western Ireland

Microchemical analysis of trace elements in otoliths and bio-mineralised earstones of teleost fishes is an emerging approach to analysing the environmental migratoryand life histories of fish species. The migration history of the three-spine stickleback (Gasterosteus aculeatus) collected in western Ireland was examined using calcium (Ca) and strontium (Sr) concentrations in otoliths. The otolith Sr:Ca values fluctuated with the habitat. The habitat use and migration history of G. aculeatus can be categorised into two types, as determined by the mean value and life history transect of the otolith Sr:Ca; that is, freshwater and estuarine residents, whereas there were no anadromous sticklebacks which is believed to be a typical migration pattern in the species. The otolith Sr:Ca profiles of the freshwater resident fishes exhibited constantly low Sr:Ca values, averaging 0.41–0.58 × 10−3 from the core towards the edge. However, the otolith Sr:Ca profiles of the estuarine resident fishes exhibited constantly high Sr:Ca values from the core towards the edge without a clear transition point from low to high Sr:Ca values, as found in the anadromous fish, averaging 1.82–4.26 × 10−3. The present study is the first published confirmation that 100 % of sticklebacks living in coastal habitats in Ireland > have an estuarine resident migratory pattern, constantly residing in marine environments or brackish water throughout their lifespan and not in freshwater environments in Ireland.

Accumulation, tissue distribution, health hazard of microplastics in a commercially important cat fish, Silonia silondia from a tropical large-scale estuary

The current knowledge regarding the presence of microplastics (MPs) in the digestive tracts of fish, particularly the non-edible parts, provides limited assistance in assessing the risk to human health and establishing guideline values for policy-making purposes. Therefore, we conducted the first investigation into MPs within the commercially significant catfish species S. silondia, form a major tropical estuary assessing their accumulation, characteristics, and associated risks in various tissues, particularly the consumable muscle. A sum of 132 MPs were identified, and the mean abundance of MPs were 7.40 ± 4.12 item/DT, 3.20 ± 1.69 item/gill and 2.60 ± 1.65 item/muscle found in digestive tract (DT), gill and muscle of the fish, respectively. The strong relationships of MPs among three different tissues (y = 0.6069x - 22.69, R2 = 0.7589) indicated the pathways and how MPs were influenced by the physiology of organisms. The prevalence of MPs in fish muscle demonstrated their trophic transmission to humans. Moreover, fishes with higher weight had higher MPs in their gill, and DT. The dominant type, color and size of MPs were fibrous (89.67%), violet (41%) and &amp;lt; 0.5 mm sized (94%), respectively. The high percentage of fibers suggests that they might have come from ropes, fishing nets or sewage. FTIR chemical composition analyses of microplastics (MPs) identified three primary polymer types: PET (44.5%), PE (33.3%), and PP (22.2%) in fish. These polymers are commonly associated with packaging materials, household wastes and plastic pipes. Contamination level assessment by CF (CF = 2.76) and PLI (PLI &amp;gt; 1) indicated moderately to highly contaminated fish with MPs ingestion. While the complete understanding of the direct negative effects of microplastics (MPs) on human health remains elusive, their presence in estuarine fish raises concerns for both human and ecosystem health. The findings will be useful for assessing the hazards to human health from exposure to MPs and for creating effective risk management plans to reduce those risks.

Evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient.

Identification of the key biotic and abiotic drivers within food webs is important for understanding species abundance changes in ecosystems, particularly across ecotones where there may be strong variation in interaction strengths. Using structural equation models (SEMs) and four decades of integrated data from the San Francisco Estuary, we investigated the relative effects of top-down, bottom-up, and environmental drivers on multiple trophic levels of the pelagic food web along an estuarine salinity gradient and at both annual and monthly temporal resolutions. We found that interactions varied across the estuarine gradient and that the detectability of different interactions depended on timescale. For example, for zooplankton and estuarine fishes, bottom-up effects appeared to be stronger in the freshwater upstream regions, while top-down effects were stronger in the brackish downstream regions. Some relationships (e.g., bottom-up effects of phytoplankton on zooplankton) were seen primarily at annual timescales, whereas others (e.g., temperature effects) were only observed at monthly timescales. We also found that the net effect of environmental drivers was similar to or greater than bottom-up and top-down effects for all food web components. These findings can help identify which trophic levels or environmental factors could be targeted by management actions to have the greatest impact on estuarine forage fishes and the spatial and temporal scale at which responses might be observed. More broadly, this study highlights how environmental gradients can structure community interactions and how long-term data sets can be leveraged to generate insights across multiple scales.

Metabarcoding is (usually) more cost effective than seining or qPCR for detecting tidewater gobies and other estuarine fishes.

Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered northern tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining took twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding has gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining remains the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions.

Fish fauna and environmental factors in river estuaries of small and medium-sized rivers on islands significantly influenced by warm currents.

River estuaries are influenced by terrestrial and marine areas, and have a unique environment that is constantly fluctuating. They are also important habitats for biodiversity conservation. Tanegashima Island is significantly influenced by the Kuroshio Current. Although nearby Yakushima Island has been recognized as a World Natural Heritage site and information on many species has been collected, there is little information on species inhabiting the river estuaries of Tanegashima Island. In this study, the river estuarine ichthyofauna of 26 small and medium-sized rivers on Tanegashima Island was surveyed and a total of 2758 individuals of 29 species and one genus belonging to 15 families were collected. The fish fauna of the river estuaries of Tanegashima Island were classified into three groups, namely the river estuaries where coastal terraces are underdeveloped and drowned valleys are formed, the river group where the riverbed gradient at the mouth is high, and other river groups. Environmental factors selected as being important for ordination of fish fauna were the altitude of the headstreams at the watershed scale, the gradient of the river estuarine area, and the presence or absence of rapids in the estuary. The importance of the geohistorical factor of drowned valley formation, in addition to habitat and watershed scale environmental factors, as a factor on river estuarine fish fauna is an important finding for future conservation of local biota diversity.

Occurrence of larval fishes sampled by drifting light traps in the lower reaches of a South African estuary.

The tidal occurrence of larval fishes was investigated in the permanently open Kowie Estuary on the warm-temperate coast of South Africa. Larval fishes were sampled in the mouth region using two drifting light traps deployed on the ebb and flood tides every second night for two consecutive 14-day periods, coinciding with the dark moon phase. A total of 553 larval fishes were caught, representing nine families and 26 species, of which Blenniidae and Clupeidae dominated. The prevalence of different estuarine association fish guilds was also tide-specific. Marine and estuarine species, such as Omobranchus woodi, were more dominant during flood tides, while marine straggler species, such as Sardinops sagax, which are not dependent on estuaries, were dominant on the ebb tide. Marine estuarine-dependents were only present during flood tides, potentially indicating ingress and entrainment within the estuary. The results confirm that light trap catches yield a different composition of species compared to towed ichthyoplankton net studies. Additionally, drifting light traps allow for better targeting of species with a phototactic response and reduction of incidental catch. Consequently, a mixture of gear is encouraged for more comprehensive surveys of larval fish occurrence.

Sampling design modifications to a fishery-independent monitoring survey balance the maintenance of long-term data with emerging management needs and funding limitations

Development of Florida’s marine Fisheries-Independent Monitoring (FIM) program began in 1985, and it initiated long-term monitoring in Tampa Bay in 1989 with the purpose of providing timely fishery-independent data and analyses to fishery managers for the conservation and protection of the species that support Florida’s fisheries. Over time, the program expanded sampling in other Florida estuaries. Data from this monitoring program are integral to the assessment and management of numerous state and federally managed fishes, so long-term consistency is of paramount importance, but sampling design modifications have been necessary over time. This review presents three case studies in which the estuarine component of the FIM program was changed to address emerging data needs in management of Florida’s fishery resources, while maintaining standardization and consistency with long-term surveys statewide. In the first case study, survey changes increased the amount of data on juvenile common snook, Centropomus undecimalis, on the Gulf of Mexico and Atlantic coasts and improved indices of abundance, survival estimates, and age-length keys for state management purposes. In the second case study, the FIM program improved estimates of abundance of juvenile reef fishes by initiating a complementary survey that expanded FIM sampling to new regions of the Florida Gulf coast and targeted a unique habitat (polyhaline seagrass beds along estuarine shoal habitats) not previously sampled in the standard long-term survey. In the third case study, the FIM program addressed a data limitation for regional management of spotted seatrout, Cynoscion nebulosus, by initiating seasonal sampling in western Florida. In each case study, the standard long-term survey design was modified to include sampling of new and unique areas and habitats, providing valuable data on estuarine fish assemblages that support analyses at the broader, ecosystem level. Survey amendments were designed to maintain standardization and consistency, all with limited additional funding. The success of these survey modifications was the result of several key factors: mission-focused programmatic goals, geographically dispersed laboratories, standardized protocols, ongoing critical analysis of the data, grant award success, and high-level data management. Although each case study originated with a survey expansion, all were followed by survey reductions or streamlining, so expansion and reduction scenarios are presented in this review. Regardless of these modifications, the mission of the FIM program remains the same: to provide timely data and analysis for the use of fishery managers, including state and federal partners.

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches.

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Studies on the Spatial Distribution and Abundance of Selected Estuarine Fish Species in the Indus Delta Creek System Sindh, Pakistan

Studies on the Spatial Distribution and Abundance of Selected Estuarine Fish Species in the Indus Delta Creek System Sindh, Pakistan