Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High-Throughput Nanofluidic Chip Technology: Species-Specific qPCR Assay Panel Development and Validation.

Stomach content DNA (scDNA) analyses have become the standard practice for measuring trophic interactions. scDNA metabarcoding has provided broadscale diet composition data but can potentially underestimate certain prey species, as many of the recovered sequence reads come from predator-derived DNA, potentially resulting in incomplete diet information. Targeted detection (quantitative real-time PCR-qPCR) strategies allow for single-species detection from complex multispecies scDNA mixtures.

Comprehensive evaluation of UV inactivation of using multiple gene targets and real-time quantitative PCR.

UV disinfection is extensively used for wastewater disinfection and disinfection efficiency is commonly monitored using culture-based enumeration of . While culture-independent real-time quantitative polymerase chain reaction (qPCR) based methods are attractive due to faster turnaround and easier application, previous attempts with qPCR to monitor disinfection have been unsuccessful. In this study, the effect of UV irradiation on a pure culture was examined in collimated beam (CB) experiments and monitored using both a culturing technique and DNA damage quantified using both short amplicon (SA; <∼200 bp) qPCR and longer amplicon (LA; ∼500-bp) qPCR.

Genetic architecture and correlations between the gut microbiome and gut gene transcription in Chinook salmon (Oncorhynchus tshawytscha).

Population divergence through selection can drive local adaptation in natural populations which has implications for the effective restoration of declining and extirpated populations. However, adaptation to local environmental conditions is complicated when both the host and its associated microbiomes must respond via co-evolutionary change. Nevertheless, for adaptation to occur through selection, variation in both host and microbiome traits should include additive genetic effects.

Behavioral transcriptomic effects of triploidy and probiotic therapy (Bifidobacterium, Lactobacillus, and Lactococcus mixture) on juvenile Chinook salmon (Oncorhynchus tshawytscha).

Aquaculturists use polyploid fish to maximize production albeit with some unintended consequences including compromised behaviors and physiological function. Given benefits of probiotic therapies (e.g.

Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.

Background: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario).

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha).

Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes.

The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha).

The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition.

Variation in the diversity of bacterial communities and potential sources of fecal contamination of beaches in the Huron to Erie corridor.

Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St.

Acute thermal stress elicits interactions between gene expression and alternative splicing in a fish of conservation concern.

Transcriptomic research provides a mechanistic understanding of an organism's response to environmental challenges such as increasing temperatures, which can provide key insights into the threats posed by thermal challenges associated with urbanization and climate change. Differential gene expression and alternative splicing are two elements of the transcriptomic stress response that may work in tandem, but relatively few studies have investigated these interactions in fishes of conservation concern. We studied the imperilled redside dace (Clinostomus elongatus) as thermal stress is hypothesized to be an important cause of population declines.

Conservation implications of revised genetic structure resulting from new population discovery: the threatened eastern sand darter (Ammocrypta pellucida) in Canada.

Human activity can put non-game fishes at higher risk of extinction because of inappropriate management action. Eastern sand darter (Ammocrypta pellucida), a small benthic fish classified as threatened across much of its northern range, inhabits increasingly fragmented sandy habitats and, as a non-game fish, may be easily overlooked in conservation efforts. In this study, the authors use genotype data from nine microsatellite loci and cytochrome oxidase I (COI) sequencing data across its northern native range to re-assess genetic structure and to characterize a newly discovered, geographically disjunct population.

Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance.

A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream.

Population differences in Chinook salmon () DNA methylation: Genetic drift and environmental factors.

Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species.

The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes.

Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications.

Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure.

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, , Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in 2 years (1996 and 2004) at nine microsatellite loci.

Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes.

The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes.

Spatial and environmental effects on Coho Salmon life history trait variation.

Adult size, egg size, fecundity, and mass of gonads are affected by trade-offs between reproductive investment and environmental conditions shaping the evolution of life history traits among populations for widely distributed species. Coho salmon have a large geographic distribution, and different environmental conditions are experienced by populations throughout their range. We examined the effect of environmental variables on female size, egg size, fecundity, and reproductive investment of populations of Coho Salmon from across British Columbia using an information theoretic approach.

Metabarcoding of native and invasive species in stomach contents of Great Lakes fishes.

As aquatic invasive species (AIS) proliferate worldwide, a better understanding of their roles in invaded habitats is needed to inform management and introduction prevention strategies and priorities. Metabarcoding of stomach content DNA (scDNA) shows considerable promise in such regard. We thus metabarcoded scDNA from two non-native fish species (alewife (Alosa pseudoharengus) and rainbow smelt (Osmerus mordax)), and three native ones (bloater (Coregonus hoyi), ninespine stickleback (Pungitius pungitius), and slimy sculpin (Cottus cognatus)).

Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon.

Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear.

Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario.

Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla.

Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene.

Background: Growth regulation is a complex process influenced by genetic and environmental factors. We examined differences between growth hormone (GH) transgenic (T) and non-transgenic (NT) coho salmon to elucidate whether the same loci were involved in controlling body size and gene expression phenotypes, and to assess whether physiological transformations occurring from GH transgenesis were under the influence of alternative pathways. The following genomic techniques were used to explore differences between size classes within and between transgenotypes (T vs.

DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects.

The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood.

Transcriptional Basis of Copper-Induced Olfactory Impairment in the Sea Lamprey, a Primitive Invasive Fish.

Olfaction mediates behaviors necessary for survival and reproduction in fishes. Anthropogenic inputs of contaminants into aquatic environments, specifically copper, are known to disrupt a broad range of olfactory-mediated behaviors and can cause long-lasting damage even at low concentrations that have profound impacts on the biology of aquatic organisms. The sea lamprey ( is a primitive fish species invasive to the North American Great Lakes that relies on olfaction to navigate during natal homing and in mate choice during reproduction.

Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription profiles among and within eight population crosses from British Columbia, Canada.

Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population-level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population- and family-level variation in gene transcription for 22 fitness-related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha).

Significant differences in maternal carotenoid provisioning and effects on offspring fitness in Chinook salmon colour morphs.

In oviparous species, maternal carotenoid provisioning can deliver diverse fitness benefits to offspring via increased survival, growth and immune function. Despite demonstrated advantages of carotenoids, large intra- and interspecific variation in carotenoid utilization exists, suggesting trade-offs associated with carotenoids. In Chinook salmon (Oncorhynchus tshawytscha), extreme variation in carotenoid utilization delineates two colour morphs (red and white) that differ genetically in their ability to deposit carotenoids into tissues.

Molecular Insights Into the Ctenophore Genus Beroe in Europe: New Species, Spreading Invaders.

The genus Beroe Browne, 1756 (Ctenophora, Beroidae) occurs worldwide, with 25 currently-described species. Because the genus is poorly studied, the definitive number of species is uncertain. Recently, a possible new Beroe species was suggested based on internal transcribed spacer 1 (ITS1) sequences from samples collected in Svalbard, Norway.