Hydrobiology, Volume 4, Issue 3 (September 2025) – 5 articles

Reliable, timely and economical target organism detection in harbors and ballast water is urgently needed to prevent the spread of aquatic invasive species (AIS) by commercial ships in the North American Great Lakes (NAGL). Inter-Great Lake ships (Lakers) transport large volumes (ca. 52 million metric tons. annually) of untreated lake water between lakes, with over 50% transported against the natural flow from the lower lakes to Western Lake Superior ports. The transport of ballast water is the number one threat of AIS spread throughout the NAGL. A relatively new tool to fight the spread of AIS is the use of eDNA for rapid detection and identification of target organisms. This technology opens doors for advancing control of ballast-mediated AIS through rapid detection. To that end, we have developed species-specific, reliable eDNA primers to target specific detection of four AIS in water samples along with qPCR protocols. Target organisms were selected based on the following criteria: (1) they are known to be invasive in the lower NAGL, (2) they are established in the lower NAGL but not in Superior, (3) they are biodegradable, and (4) they are obtainable, morphologically distinct and have existing DNA sequence information. Working primers, qPCR protocols and detection limits are provided for three invertebrate species and one alga species. These species are Daphnia lumholtzi (a water flea), Cercopagis pengoi (the fishhook water flea), Echinogammarus ishnus (a scud) and Nitellopsis obtusa (Starry Stonewort). Full article

Myriophyllum heterophyllum is an aquatic macrophyte that is invasive to the northeastern United States and several western European countries. Spreading by vegetative clonal propagation, especially fragmentation, extensive resources are devoted to limiting its growth and spread; however, genetic assessments are not typically included in management strategies. Reduction in genetic (clonal) diversity should accompany biomass reduction, yet without genetic assessment, the efficacy of plant removal remains unclear. This paper is the first to describe a microsatellite marker library and its use in the characterization of Myriophyllum heterophyllum. Eighty-seven tissue samples were collected across the invasive distribution of Myriophyllum heterophyllum in Maine, USA. DNA was extracted, and PCR amplification was employed to screen 13 published microsatellites. Sequencing of the amplified loci was performed to characterize repeat motifs and confirm primer binding sites. Fragment sizing of PCR amplicons was employed to determine microsatellite lengths across the 87 samples. A total of 7 of the 13 tested markers were amplified, with six of those seven found to be variable. Polyploidy was evident from allelic diversity within individuals, although precise ploidy could not be determined. Observed heterozygosity ranged from 0.16 to 1.00 across variable markers. This seven-marker library was effective in characterizing the genetic diversity of both newly discovered (<5 years) and older (>50 years) infestations and is expected to be suitable for assessment of genetic diversity in populations within the native range of M. heterophyllum. The marker library also shows potential for use in several other Myriophyllum species. Full article

Fish coloration plays an important role in reproduction and camouflage, yet capturing color variation under field conditions remains challenging. We present a standardized, semi-automated protocol for measuring body coloration in the popular model fish threespine stickleback (Gasterosteus aculeatus). Individuals are photographed in a controlled light box within minutes of capture, and color is sampled from eight anatomically defined standard sites in human-perception-based CIELAB space. Analyses combine univariate color metrics, multivariate statistics, and the ΔE* perceptual difference index to detect subtle shifts in hue and brightness. Validation on pre-spawning fish shows the method reliably distinguishes males and females well before full breeding colors develop. Although it currently omits ultraviolet signals and fine-scale patterning, the approach scales efficiently to large sample sizes and varying lighting conditions, making it well suited for population-level surveys of camouflage dynamics, sexual dimorphism, and environmental influences on coloration in sticklebacks. 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