Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods.

Additional file 1. Summary RNA-seq statistics of all samples.

Additional file 3. Lists of genes within each principal component that are significantly correlated to a metadata variable, and lists of genes that are significantly differentially expressed due to temperature or pCO2 experiment treatments.

Additional file 1. Summary RNA-seq statistics of all samples.

Additional file 3. Lists of genes within each principal component that are significantly correlated to a metadata variable, and lists of genes that are significantly differentially expressed due to temperature or pCO2 experiment treatments.

The red sea urchin Mesocentrotus franciscanus supports a highly valuable wild fishery along the West Coast of North America, but despite its importance in the ecology of kelp forests and as a harvested species, little is known about how M. franciscanus responds to abiotic stressors associated with ocean warming and acidification during its early development. Here, embryos of M. franciscanus were raised under combinations of two temperatures (13 °C and 17 °C) and two pCO2 levels (475 μatm and 1050 μatm) that represent current and future coastal environments. Elevated pCO2 levels led to a decrease in body size of gastrula stage embryos while temperature had no effect. At the prism stage, both temperature and pCO2 affected body size. The warmer temperature increased the body size of prism stage embryos, offsetting the stunting effect of elevated pCO2 on growth. Thermal tolerance, which was estimated by exposing prism stage embryos to a range of temperatures and estimating the survivorship, was found to be slightly higher in those raised under warmer temperatures. The developmental temperature and pCO2 conditions under which embryos were raised did not have an effect on the metabolic rate as measured by oxygen consumption rate at the prism stage. This study provides important insights into a species of high ecological and economic value. Overall, early development under elevated pCO2 conditions may adversely impact M. franciscanus while moderate warming may improve growth and thermal tolerance. Understanding how fishery species respond to abiotic stressors will facilitate our predictive capacity of how climate change will impact future populations, which links to issues such as sustainability and food security.

Transgenerational plasticity occurs when the conditions experienced by the parental generation influence the phenotype of their progeny. This may in turn affect progeny performance and physiological tolerance, providing a means by which organisms cope with rapid environmental change. We conditioned adult purple sea urchins, Strongylocentrotus purpuratus, to combined pCO2 and temperature conditions reflective of in situ conditions of their natural habitat, the benthos in kelp forests of nearshore California, and then assessed the performance of their progeny raised under different pCO2 levels. Adults were conditioned during gametogenesis to treatments that reflected static non-upwelling (~650 μatm pCO2, ~17 °C) and upwelling (~1300 μatm pCO2, ~13 °C) conditions. Following approximately 4 months of conditioning, the adults were spawned and embryos were raised under low pCO2 (~450 μatm pCO2) or high pCO2 (~1050 μatm pCO2) treatments to determine if differential maternal conditioning impacted the progeny response to a single abiotic stressor: pCO2. We examined the size, protein content, and lipid content of eggs from both sets of conditioned female urchins. Offspring were sampled at four stages of early development: hatched blastula, gastrula, prism, and echinopluteus. This resulted in four sets of offspring: (1) progeny from non-upwelling-conditioned mothers raised under low pCO2, (2) progeny from non-upwelling-conditioned mothers raised under high pCO2, (3) progeny from upwelling-conditioned mothers raised under low pCO2, and (4) progeny from upwelling-conditioned mothers raised under high pCO2. We then assessed the effects of maternal conditioning along with the effects of developmental pCO2 levels on body size of the progeny. Our results showed that differential maternal conditioning had no impact on average egg size, although non-upwelling females produced eggs that were more variable in size. Maternal conditioning did not affect protein content but did have a modest impact on egg lipid content. Developing embryos whose mothers were conditioned to simulated upwelling conditions (~1300 μatm pCO2, ~13 °C) were greater in body size, although this effect was no longer evident at the echinopluteus larval stage. Although maternal conditioning affected offspring body size, the pCO2 levels under which the embryos were raised did not. Overall, this laboratory study provides insight into how transgenerational effects may function in nature. The impacts of parental environmental history on progeny phenotype during early development have important implications regarding recruitment success and population-level effects.

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