Editor’s Choice Articles

Short-term captivity is widely used in experimental studies but may unintentionally alter host-associated microbiomes, potentially confounding biological interpretation of experimental outcomes. Here, we evaluated the effects of 35 days of captivity on the gut microbiome of Fundulus heteroclitus collected from Long Island Sound (Milford, CT, USA) using 16S rRNA gene sequencing. Comparisons between Field Control (FC) and short-term Captive Treatment (CT) groups revealed a marked reduction in microbial diversity under captive conditions. Observed richness decreased approximately five-fold (Field Control: 1026 features; Captive Treatment: 221 features), and Shannon diversity declined from 8.89 to 5.93. Beta diversity analyses based on UniFrac distances demonstrated clear separation between groups, indicating substantial shifts in community composition. Taxonomic profiling revealed reduced community complexity in captive fish, with increased dominance of Proteobacteria and loss of diverse environmental taxa. Predicted enrichment of pathways associated with stress response, altered respiration, and metabolic flexibility in captivity reflects inferred functional potential rather than direct functional activity. Given the use of pooled samples with limited biological replication, these findings should be interpreted as strong community-level patterns rather than population-level inference. Collectively, these results indicate that short-term captivity alters the F. heteroclitus gut microbiome. Full article

Fast, reliable detection methods are paramount in the fight against the spread of aquatic invasive species (AIS), and eDNA techniques provide many benefits over traditional sampling methods. AIS are spreading rapidly around the world, reshaping ecosystems, outcompeting native species, and experiencing explosive population growth. Some sources cite the Laurentian Great Lakes as the most heavily invaded freshwater system in the world. The advantages of using eDNA technology for AIS detection include: (1) it is often more sensitive, (2) it can cover much more area, (3) it is less destructive, (4) it does not require trapping of threatened species, and (5) it can be done with considerably less taxonomic training. This study was implemented to test the utility of a commercially available metabarcoding assay against a targeted, qPCR approach for the detection of four AIS in Lake Erie. We sampled eight localities monthly throughout the summer of 2024 using both techniques. Our target AIS were the bloody red shrimp Hemimysis anomala, the fishhook waterflea Cercopagis pengoi, the water flea Daphnia lumholtzi, and the gammarid scud Echinogammarus ishnus. We found that the targeted, qPCR approach was more successful at AIS detection for our four target organisms than the specific, commercially available metabarcoding assay that was used. Full article

Whale sharks (Rhincodon typus) predominantly inhabit the epipelagic layer, yet dives to at least 1928 m have been reported. Even so, current understanding of the species’ true maximum dive depth is constrained by the technological limitations of depth sensors of commercially available satellite tags, which are generally rated to a maximum depth of 2000 m. Here, we report a new maximum depth range of 1978–2527 m inferred from a Wildlife Computers custom-calibrated SPLASH10-346C finmount tag (2500 m capability), deployed on a 7 m juvenile male whale shark in the Coral Sea, Australia. This extends the currently accepted depth limit by 50–599 m. Full article

Monoenoic fatty acids (MUFAs), defined by the presence of a single carbon–carbon double bond within a long aliphatic chain, constitute a structurally diverse and ecologically significant class of lipids widely distributed in aquatic organisms. In marine and freshwater environments, MUFAs are fundamental components of membrane phospholipids and storage lipids, where mono-unsaturation modulates melting point, lipid packing, and bilayer dynamics, enabling homeoviscous adaptation to fluctuations in temperature, pressure, salinity, and oxygen availability. Positional and geometric isomerism (e.g., cis-Δ5, Δ7, Δ9, Δ11, Δ13, and trans forms) further enhances biochemical diversity, providing sensitive chemotaxonomic markers and indicators of trophic transfer across food webs. In addition to common straight-chain monoenes, rare methyl-branched, cyclopropane-containing, and acetylenic derivatives occur in specialized aquatic taxa, reflecting evolutionary adaptation and ecological niche differentiation. Computational QSAR analyses suggest that monoenoic fatty acids and their unusual analogues occupy bioactivity spaces associated with lipid metabolism regulation, vascular and inflammatory modulation, antimicrobial defense, and membrane stabilization. This review integrates structural chemistry, biosynthesis, ecological distribution, trophic dynamics, and predicted biological activity of monoenoic fatty acids in aquatic systems, highlighting their dual role as adaptive membrane constituents and as biologically active mediators linking molecular lipid architecture to hydrobiological function and environmental change. Full article

The Water Framework Directive 2000/60/EC requires the assessment of the ecological quality in all surface waters using biological indices, yet the effective application of these indices often demands extensive and long-term monitoring data. Oxidative stress biomarkers offer a promising complementary approach, as they can detect early biochemical responses of organisms to environmental degradation. In this study, we evaluated the suitability of two oxidative stress biomarkers—malondialdehyde (MDA) levels and DNA damage—in the gonads of a freshwater fish species, the Prussian carp Carassius gibelio (Bloch, 1782) as indicators of ecological condition in lakes of differing environmental quality. Fish were sampled from four lakes (Doirani, Vegoritida, Volvi, Petron; Northern Greece) representing a gradient of physicochemical and ecological quality. Both MDA concentrations and DNA damage showed significant (p < 0.05) differences among lakes. However, only DNA damage in the gonads was significantly (p < 0.05) associated with lake ecological quality as determined by the Greek Lake Fish Index (GLFI), with higher biomarker responses observed in lakes of poorer status. These findings demonstrate that oxidative stress biomarkers in C. gibelio reflect variations in lake ecological quality and may serve as sensitive, early-warning tools for biomonitoring and pollution assessment in freshwater ecosystems. Full article

Meiofaunal assemblages are crucial components of benthic ecosystems, significantly contributing to organic matter cycling and energy transfer. However, baseline quantitative data from some upwelling systems remain limited. This study characterizes the abundance, vertical distribution, and secondary production of meiofauna at a coastal upwelling station off southern Peru (14°16′ S) for July 2006 (Neutral conditions) and May 2007 (moderate La Niña, LN), using four-replicated sediment cores sectioned into 0–1, 1–2, 2–5, and 5–10 cm layers. While Nematoda (families Desmodoridae, Chromadoridae, Monhysteridae, Oxystominidae, Comesomatidae) dominated the community (>79% in all layers, both years), the total taxonomic richness did not differ substantially between study periods nor across the sediment column for 2006 or for 2007. Total density (0–10 cm) fluctuated between 3916 ± 2202 Ind 10 cm⁻² in 2006 and 4203 ± 2274 Ind 10 cm⁻² in 2007, with non-significant changes. Biomass (µgC 10 cm⁻²) in 2006 ranged from 80 ± 24 in the 5–10 cm section to 455 ± 134 in the 2–5 cm section. The uppermost 0–1 cm layer showed 238 ± 155, while the 1–2 cm section reached 302 ± 69. In 2007, biomass was consistently higher in the surface layers, with maximum values in the 1–2 cm section (500 ± 534), followed by the 0–1 cm section (376 ± 34). Hierarchical clustering produced depth-ordered groups with high within-depth similarity (>80–90%). SIMPER results identified Desmodora, Comesomatidae, and Chromadoridae among the top contributors to within-depth similarity and to the dissimilarity observed between surface and subsurface assemblages. A depth-related gradient of community composition was detected, suggesting vertical habitat heterogeneity modulated by several environmental factors; however, PERMANOVA analysis residuals (96.73%) indicate a high variation not explained by ENSO phase, sediment section, or their interaction, suggesting other unmeasured factors explaining meiofaunal community structure. Meiofauna’s production ranged from 2.836 ± 0.049 gC m⁻² y⁻¹ in 2006 to 3.106 ± 1.566 gC m⁻² y⁻¹ in 2007. These findings expand the limited knowledge on meiofaunal abundance and metabolic demands in this ocean region, fostering future efforts for comparative analyses across latitudes, depth gradients, and oceanographic regimes. Full article

Freshwater ecosystems face escalating degradation, demanding real-time, scalable, and biodiversity-aware monitoring solutions. This review proposes an integrated framework combining artificial intelligence (AI), geographic information systems (GISs), and environmental DNA (eDNA) to overcome these limitations and support next-generation river health assessment. The AI-GIS-eDNA system was applied to four representative river basins—the Mississippi, Amazon, Yangtze, and Danube—demonstrating enhanced predictive accuracy (up to 94%), spatial pollution mapping precision (85–95%), and species detection sensitivity (+18–30%) compared to conventional methods. Furthermore, the framework reduces operational costs by up to 40%, highlighting its potential for cost-effective deployment in low-resource regions. Despite its strengths, challenges persist in the areas of regulatory acceptance, data standardization, and digital infrastructure. We recommend legal recognition of AI and eDNA indicators, investment in explainable AI (XAI), and global data harmonization initiatives. The integrated AI-GIS-eDNA framework offers a scalable and policy-relevant tool for adaptive freshwater governance in the Anthropocene. Full article

The deterioration of European freshwater ecosystems, driven by habitat fragmentation and connectivity loss, seriously threatens biodiversity and ecosystem integrity. While restoration efforts often focus on reconnecting river networks, ecological assessments tend to overlook the broader concept of connectivity. This study highlights the need to incorporate ecological quality into connectivity assessments, ensuring more effective restoration that is aligned with European Union (EU) conservation policies. Using the dendritic connectivity index for potamodromous (DCIp) species, we analysed seven connectivity scenarios, integrating natural and artificial barriers to assess both structural connectivity and quality-weighted connectivity. These scenarios included: (1) structural connectivity considering only natural barriers (S_NB) and (2) all barriers (S_AB); (3) quality-weighted connectivity considering natural barriers (W_NB), and (4) all barriers (W_AB); three enhanced scenarios considering all barriers with (5) improved quality (W_AB_IQ), (6) improved probability of connectivity (W_AB_IC), and (7) improved quality and probability of connectivity (W_AB_IQC). Connectivity values varied across scenarios, with the natural baseline (S_NB) showing the highest connectivity values (mean = 0.98). When the natural baseline was weighted by the GES probability (W_NB), connectivity values dropped considerably (mean = 0.30). Incorporating all barriers (W_AB) further reduced the connectivity values (mean = 0.26). The improved scenario W_AB_IQC showed notable connectivity improvements (mean = 0.40). This study underscores the importance of integrating ecological quality into river connectivity assessments. It demonstrates that restoring habitat quality alongside connectivity restoration can substantially enhance river ecosystems. Prioritising restoration in high-quality areas maximises ecological and social benefits, supports sustainable river management, improves connectivity, and promotes biodiversity conservation. Full article

Intensive forestry, particularly the establishment of monospecific plantations with exotic species, can deeply impact the ecological functioning of forest streams, where riparian leaf litter is the primary source of energy. In this study, we investigated the effects of Eucalyptus globulus afforestation on macroinvertebrate communities in 20 streams in Galicia (NW Spain) with varying levels of accumulated eucalypt leaf litter. Sampling was done in autumn 2020 and spring 2021. In autumn, six streams had leaf litter composed of >50% of eucalypt leaves, a proportion that increased to 12 streams in spring. A total of 24,705 individuals were found in autumn and 12,529 in spring, belonging to 125 taxa. Although some taxa decreased their abundance with an increase in the proportion of eucalypt litter, variability in overall macroinvertebrate abundance was mainly explained by season, stream flow, and water temperature. However, species richness and diversity were significantly lower in streams mainly subsided by Eucalyptus litter compared to those dominated by native riparian vegetation. Macroinvertebrate abundance, richness, and diversity peaked in autumn, coinciding with the influx of deciduous litterfall and lower proportion of eucalypt litter. The lower quality, low-nutrient content, and presence of feeding deterrents in Eucalyptus leaf litter compared to native deciduous tree species likely drive these observed patterns, underscoring the importance of preserving native riparian forests to sustain stream biodiversity, even in managed landscapes dominated by Eucalyptus plantations. Full article

Understanding the factors influencing amphibian populations is essential for effective freshwater conservation, particularly for species with biphasic life histories. This study examined how pond- and landscape-level characteristics shape larval amphibian occupancy, abundance, and detection in a remnant Tupelo-Cypress wetland in southeastern Illinois. Given the small number of available ponds (n = 4), we standardized survey effort across sites and incorporated robust hierarchical Bayesian models to evaluate environmental effects at both community and species levels. Occupancy probabilities were generally high across species, with canopy cover significantly increasing both community and species occupancy, particularly for salamanders (up to 6.4-fold). Predatory backswimmers and fish substantially reduced occupancy (by 21.7-fold and 6.0-fold, respectively). Anurans, especially Pseudacris spp., were more abundant than salamanders, with abundance positively associated with canopy cover, leaf litter, and pond perimeter. Detection probabilities were generally low and varied by species, with predatory invertebrates reducing detection up to 83.3-fold. These findings underscore the importance of maintaining canopy cover while mitigating predation risks to support amphibian populations. The application of multi-species hierarchical models provides a nuanced understanding of species-specific responses, offering valuable insights for conservation strategies in regions affected by habitat loss and climate change. However, given the limited spatial replication, these findings should be interpreted cautiously and validated through additional studies across broader temporal and spatial scales. Full article

The present study aimed to describe the reproductive cycle of the black-footed limpet (Patella depressa Pennant, 1777) from an intertidal rocky shore on the Algarve coast (southern Portugal). Samples were collected monthly between January 2017 and December 2018, with the species’ gametogenic cycle being described based on gonad histology and the mean gonadal index. The presence of both transitional and mosaic hermaphrodites indicates that some individuals are able to change sex (sequential hermaphroditism). Despite the occurrence of hermaphroditism, sex proportions were approximately equal, suggesting the absence of protandric sex change in this species. The population exhibited an extensive occurrence of ripe and spawning gonads throughout almost the whole study period, probably related to consecutive processes of gonadal re-ripening and partial spawning events. The reproductive dynamics of P. depressa displayed clear inter-annual differences, with a short resting period recorded in 2017 (June–August) and the absence of resting gonads in 2018. The continued monitoring of this population and collection of environmental data are required to further improve knowledge of the reproductive dynamics of this species. Such information is crucial for proposing additional management measures for the sustainable harvesting of limpets in southern Portugal. Full article

Biologists commonly use standard sampling protocols to ensure that data are comparable spatiotemporally. Data also need to be precise to allow for statistically meaningful comparisons. However, the effort needed to precisely sample desert fishes is unclear. We used a resampling approach to evaluate the effort requirements needed to precisely sample fishes among six wadeable rivers in the Gila River basin, New Mexico. We evaluated the number of samples that are necessary to obtain relative density estimates that had 25% relative standard error 80% of the time. We also estimated the effort needed to precisely characterize species richness. Our results indicate that precisely sampling fish in the Gila River basin is difficult. Sonora Sucker Catostomus insignis, Desert Sucker C. clarkii, Longfin Dace Agosia chrysogaster, and Speckled Dace Rhinicthyes osculus were generally the only species that could be precisely sampled. Characterizing the native species assemblage in the Gila River basin required between two and seven reaches, whereas the entire species assemblage could only be characterized in 50% of the study systems. The challenge of precisely sampling fish in the Gila River basin suggests that alternative sampling methods may be required to characterize changes in density or species distribution in desert Southwest systems. Full article

An important top-down predator, the northern pike (Esox lucius), faces harsh environmental conditions in the northern boreal ecoregion. They are often managed for recreational fishing and, more recently, to create environmental offsets; strategies aimed at balancing ecological impacts by enhancing or restoring habitats. Our study examines northern pike populations in two remote boreal lakes in northern Alberta: Steepbank and Wappau. The lakes differ in size, vegetation cover, and trophic status, providing a natural experiment for investigating northern pike growth, condition, diet, and population density. Over three years (2018–2020), northern pike were sampled using gill nets. Population metrics, including growth, condition, and stomach contents, were compared between the lakes. Steepbank, a smaller, oligotrophic lake with low vegetation cover, showed lower prey fish densities compared to the larger, eutrophic Wappau, but it did not differ in northern pike catch per unit effort. Growth rates and body condition varied significantly between the lakes, with the northern pike in Wappau exhibiting faster growth and a better condition in the older age groups, while the younger northern pike in Steepbank had higher relative weights. A diet analysis revealed significant differences in prey consumption: Steepbank northern pike displayed higher rates of conspecific predation and invertebrate consumption, particularly in the younger age classes. These findings highlight how lake characteristics and prey availability shape northern pike population dynamics, offering valuable insights for lake management approaches in northern Alberta. Full article