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IntroductionEnvironmental DNA (eDNA) metabarcoding of water is increasingly being used to monitor coastal biodiversity shifts. However, we have limited knowledge of whether samples collected during discreet temporal periods depict holistic ecosystem changes over longer time spans.MethodsHere, we show how eDNA community structure varies across repeated sampling events at different temporal scales ranging from years to months to days at an Arctic coastal site, Churchill (Canada), using metabarcoding analyses of water eDNA samples with four universal primer pairs (two primers in COI and two in the 18S rRNA).ResultsDaily variations were highly dynamic and less structured, likely due to the stochastic nature of estuarine ecosystems, but there was a clear annual consistency in eDNA communities with a high proportion of shared taxa between years. However, monthly sampling was the most efficient for capturing holistic biodiversity.DiscussionWe provide recommendations for optimal eDNA metabarcoding sampling design based on our observations. The study underscores the importance of understanding biological and physical factors altering eDNA detection to improve the efficiency of detecting and interpreting long-term eDNA changes.

Coastal embayments are dynamic ecosystems facing environmental and anthropogenic pressures, including bivalve aquaculture and climate change. Mesozooplankton, essential for transferring energy from primary producers to higher trophic levels, serve as indicators of habitat changes. Size structure is a critical trait that reflects local community dynamics, trophic interactions, and ecosystem conditions, offering insights into the functioning and resilience of aquatic environments. This study examines the spatio-temporal variation in mesozooplankton size structure across nine bivalve aquaculture embayments in Atlantic and Pacific Canada from 2020 to 2022. Using high-resolution imaging (FlowCam®) to measure individual zooplankton, we assessed the effects of location, tide, sampling day, season, and aquaculture pressure on the size distribution variation among and within bays. Results indicate that bays with similar size distributions tend to have larger mesozooplankton, while those with more variable distributions are dominated by medium-sized individuals. Significant associations between environmental factors and size variation were observed in four of eleven sampling events. Notably, St. Peters Bay, with the highest aquaculture pressure, showed significant variation associated with station location and sampling day. However, the tide effect was significant only in two sampling events. Seasonal analysis revealed that colder months generally exhibited larger median sizes, with some exceptions influenced by local conditions. Despite high levels of aquaculture pressure in some bays, no consistent association between aquaculture pressure and size variation was found, highlighting the influence of local environmental factors. This study underscores the importance of monitoring mesozooplankton size structure as a bioindicator for effective ecosystem management and targeted conservation strategies.

IntroductionBivalve aquaculture has direct and indirect effects on plankton communities, which are highly sensitive to short-term (seasonal, interannual) and long-term climate changes, although how these dynamics alter aquaculture ecosystem interactions is poorly understood. MethodsWe investigate seasonal patterns in plankton abundance and community structure spanning several size fractions from 0.2 µm up to 5 mm, in a deep aquaculture embayment in northeast Newfoundland, Canada.ResultsUsing flow cytometry and FlowCam imaging, we observed a clear seasonal relationship between fraction sizes driven by water column stratification (freshwater input, nutrient availability, light availability, water temperature). Plankton abundance decreased proportionally with increasing size fraction, aligning with size spectra theory. Within the bay, greater mesozooplankton abundance, and a greater relative abundance of copepods, was observed closest to the aquaculture lease. No significant spatial effect was observed for phytoplankton composition. DiscussionWhile the months of August to October showed statistically similar plankton composition and size distribution slopes (i.e., food chain efficiency) and could be used for interannual variability comparisons of plankton composition, sampling for longer periods could capture long-term phenological shifts in plankton abundance and composition. Conclusions provide guidance on optimal sampling to monitor and assess aquaculture pathways of effects.

IntroductionArctic marine ecosystems are changing rapidly, largely due to the observed accelerated warming that is associated with ongoing climate change. Environmental DNA (eDNA) combined with metabarcoding has great potential for large-scale biomonitoring of Arctic marine communities. However, important limitations remain, such as understanding the complexity and drivers of spatio-temporal variation in eDNA distribution.MethodsIn this study, we investigated the effect of tidal dynamics on aquatic metazoan (vertebrates and invertebrates) on eDNA metabarcoding results from nearshore estuarine and marine Arctic ports of Churchill (Manitoba) and Milne Inlet (Nunavut), respectively. We collected and sequenced 54 water samples per port at low, middle and high tide across three days, as well as two depths (surface, bottom), using four universal primer pairs (two primers in the COI gene and two in the 18S rRNA gene).ResultsWe observed a significant transition in the estuarine community structure from low to high tide, whereas the marine community structure was more stable across tides. The eDNA community structure differed between the surface and bottom waters in both the estuarine and marine ecosystems. However, the biodiversity pattern within the water column was significantly different between estuarine and marine ecosystems. Finally, we observed short-term temporal variation of the communities in both systems.DiscussionAltogether, our results highlight the short-term temporal dynamic nature of eDNA derived from coastal communities. This variability should be accounted for in eDNA sampling design to ensure robust characterization of coastal communities and long-term time series, particularly for estuarine environments where the effects of tide and depth are more important.

Abstract Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.

Bay-scale empirical evaluations of how bivalve aquaculture alters plankton composition, and subsequently ecological functioning and higher trophic levels, are lacking. Temporal, inter- and within-bay variation in hydrodynamic, environmental, and aquaculture pressure complicate plankton monitoring design to detect bay-scale changes and inform aquaculture ecosystem interactions. Here, we used flow cytometry to investigate spatio-temporal variations in bacteria and phytoplankton (< 20 μm) composition in four bivalve aquaculture embayments. We observed higher abundances of bacteria and phytoplankton in shallow embayments that experienced greater freshwater and nutrient inputs. Depleted nutrient conditions may have led to the dominance of picophytoplankton cells, which showed strong within-bay variation as a function of riverine vs marine influence and nutrient availability. Although environmental forcings appeared to be a strong driver of spatio-temporal trends, results showed that bivalve aquaculture may reduce near-lease phytoplankton abundance and favor bacterial growth. We discuss confounding environmental factors that must be accounted for when interpreting aquaculture effects such as grazing, benthic-pelagic coupling processes, and microbial biogeochemical cycling. Conclusions provide guidance on sampling considerations using flow cytometry in aquaculture sites based on embayment geomorphology and hydrodynamics.

Bay-scale empirical evaluations of how bivalve aquaculture alters plankton composition, and subsequently ecological functioning and higher trophic levels, are lacking. Temporal, inter- and within-bay variation in hydrodynamic, environmental, and aquaculture pressure complicate plankton monitoring design to detect bay-scale changes and inform aquaculture ecosystem interactions. Here, we used flow cytometry to investigate spatio-temporal variations in bacteria and phytoplankton (< 20 μm) composition in four bivalve aquaculture embayments. We observed higher abundances of bacteria and phytoplankton in shallow embayments that experienced greater freshwater and nutrient inputs. Depleted nutrient conditions may have led to the dominance of picophytoplankton cells, which showed strong within-bay variation as a function of riverine vs marine influence and nutrient availability. Although environmental forcings appeared to be a strong driver of spatio-temporal trends, results showed that bivalve aquaculture may reduce near-lease phytoplankton abundance and favor bacterial growth. We discuss confounding environmental factors that must be accounted for when interpreting aquaculture effects such as grazing, benthic-pelagic coupling processes, and microbial biogeochemical cycling. Conclusions provide guidance on sampling considerations using flow cytometry in aquaculture sites based on embayment geomorphology and hydrodynamics. [ABSTRACT FROM AUTHOR]

Introduction: Bivalve aquaculture has direct and indirect effects on plankton communities, which are highly sensitive to short-term (seasonal, interannual) and long-term climate changes, although how these dynamics alter aquaculture ecosystem interactions is poorly understood. Methods: We investigate seasonal patterns in plankton abundance and community structure spanning several size fractions from 0.2 µm up to 5 mm, in a deep aquaculture embayment in northeast Newfoundland, Canada. Results: Using flow cytometry and FlowCam imaging, we observed a clear seasonal relationship between fraction sizes driven by water column stratification (freshwater input, nutrient availability, light availability, water temperature). Plankton abundance decreased proportionally with increasing size fraction, aligning with size spectra theory. Within the bay, greater mesozooplankton abundance, and a greater relative abundance of copepods, was observed closest to the aquaculture lease. No significant spatial effect was observed for phytoplankton composition. Discussion: While the months of August to October showed statistically similar plankton composition and size distribution slopes (i.e., food chain efficiency) and could be used for interannual variability comparisons of plankton composition, sampling for longer periods could capture long-term phenological shifts in plankton abundance and composition. Conclusions provide guidance on optimal sampling to monitor and assess aquaculture pathways of effects. [ABSTRACT FROM AUTHOR]

The invasive colonial tunicate, Didemnum vexillum Kott, 2022 was initially observed in Atlantic Canada in Nova Scotia in 2013 and has since been expected to spread to the western side of the Canadian Bay of Fundy due to colonies known to be present in nearby Eastport, Maine. Since 2018, we collected water environmental DNA (eDNA) samples at eight sites in the Quoddy Region in the western side of the Canadian Bay of Fundy. In 2021 and 2022 we used diver-based visual surveys and sample collection, as well as a surface-deployed near-seafloor optical imaging system to document the presence and extent of D. vexillum in the Head Harbour/West Isles/Passages Ecologically and Biologically Significant Area (EBSA) within the Quoddy Region. Forty-one dive sites were surveyed via SCUBA, and seven near-seafloor camera transects were conducted at depths deeper than dive limits (~ 30 m), collecting continuous highdefinition video and periodic high-resolution still images. Didemnum vexillum was detected at two sites from eDNA metabarcoding and quantitative PCR in 2018, 2020 and 2021, and observed by divers at 11 sites, two of which exhibited extensive tunicate coverage. Of the 1945 m² area surveyed by the near-seafloor drift camera system, D. vexillum occurred at depths to 118 m and across a spatial extent of 858 m², of which 170 m2 contained numerous tunicate patches and/or a homogenous mat. Didemnum vexillum was observed extensively overgrowing benthic substrates and fauna, possibly threatening the diversity of natural benthic habitats in the EBSA and adjacent areas supporting numerous commercial fisheries. This study is the first to report D. vexillum presence in the Canadian western Bay of Fundy, and the first to observe colonies at depths exceeding previous records of 81 m. We conclude by providing advice on how to improve coastal invasive species surveys from the combination of biodiversity metrics. [ABSTRACT FROM AUTHOR]

Abstract Large‐scale biomonitoring of Arctic coastal marine communities is essential to track temporal changes in ecosystems. Despite the potential of environmental DNA (eDNA) as an innovative coastal biomonitoring tool, important questions remain pertaining to its temporal and spatial variation and how this may affect the evaluation of ecosystem changes over time in hydrodynamic ecosystems. In this study, we used eDNA metabarcoding of coastal water samples in two Canadian Arctic ports to evaluate the potential of eDNA to detect temporal transition in marine coastal communities. We sequenced eDNA from approximately 20 surface water samples collected each month (N ≈ 150 samples) covering the transition period between summer and late fall using four different universal primer pairs (two pairs of COI mitochondrial genes and two pairs of 18S rRNA genes). Our results from both primer pairs highlighted a significant transition from the summer to the fall marine community. We also observed a putative link between eDNA peaks of read abundance and timing for different life stages (e.g., spawning and larvae) of several species with the most abundant sequence reads. As such, our results show that temporal variation must be considered in ensuring comprehensive coastal biomonitoring with eDNA. Although much remains to be investigated about the ecology of eDNA, our results contribute to fundamental knowledge on the origin of eDNA and highlight the importance of considering temporal variation in developing guidance for coastal biomonitoring with this approach.

Introduction: Arctic marine ecosystems are changing rapidly, largely due to the observed accelerated warming that is associated with ongoing climate change. Environmental DNA (eDNA) combined with metabarcoding has great potential for large-scale biomonitoring of Arctic marine communities. However, important limitations remain, such as understanding the complexity and drivers of spatiotemporal variation in eDNA distribution. Methods: In this study, we investigated the effect of tidal dynamics on aquatic metazoan (vertebrates and invertebrates) on eDNA metabarcoding results from nearshore estuarine and marine Arctic ports of Churchill (Manitoba) and Milne Inlet (Nunavut), respectively. We collected and sequenced 54 water samples per port at low, middle and high tide across three days, as well as two depths (surface, bottom), using four universal primer pairs (two primers in the COI gene and two in the 18S rRNA gene). Results: We observed a significant transition in the estuarine community structure from low to high tide, whereas the marine community structure was more stable across tides. The eDNA community structure differed between the surface and bottom waters in both the estuarine and marine ecosystems. However, the biodiversity pattern within the water column was significantly different between estuarine and marine ecosystems. Finally, we observed short-term temporal variation of the communities in both systems. Discussion: Altogether, our results highlight the short-term temporal dynamic nature of eDNA derived from coastal communities. This variability should be accounted for in eDNA sampling design to ensure robust characterization of coastal communities and long-term time series, particularly for estuarine environments where the effects of tide and depth are more important. [ABSTRACT FROM AUTHOR]

Aquaculture contributes a significant portion of the global aquatic biomass destined for human consumption. Bivalve and marine finfish aquaculture operations require sea‐based farm sites that result in considerable interactions with the natural environment. The addition of feed waste and physical structures (e.g., net pens and longline mussel culture) can provide an attractive artificial reef for many species and studies have shown both positive and negative effects on the surrounding ecosystem due to wild species interactions with aquaculture sites. Assessing these interactions can be complex, depending on the local ecosystem, and several monitoring techniques have been used to accurately determine associations of wild finfish and decapods to marine farms. In this review, we assessed the main methods used to monitor aquaculture‐ecosystem interactions. The advantages and disadvantages of each technique are discussed and suggestions to mitigate shortfalls for future studies are outlined. It was evident that combining methodologies should be prioritised to lessen the impact of identified weaknesses of any given approach. Designing studies with complementary approaches may help attain robust data that can be used to further understand aquaculture‐ecosystem interactions and the underlying proximate mechanisms. [ABSTRACT FROM AUTHOR]

The integration of environmental DNA (eDNA) within management strategies for lotic organisms requires translating eDNA detection and quantification data into inferences of the locations and abundances of target species. Understanding how eDNA is distributed in space and time within the complex environments of rivers and streams is a major factor in achieving this translation. Here we study bidimensional eDNA signals in streams to predict the position and abundance of Atlantic salmon (Salmo salar) juveniles. We use data from sentinel cages with a range of abundances (3–63 juveniles) that were deployed in three coastal streams in New Brunswick, Canada. We evaluate the spatial patterns of eDNA dispersal and determine the effect of discharge on the dilution rate of eDNA. Our results show that eDNA exhibits predictable plume dynamics downstream from sources, with eDNA being initially concentrated and transported in the midstream, but eventually accumulating in stream margins with time and distance. From these findings we developed a fish detection and distribution prediction model based on the eDNA ratio in midstream versus bankside sites for a variety of fish distribution scenarios. Finally, we advise that sampling midstream at every 400 m is sufficient to detect a single fish at low velocity, but sampling efforts need to be increased at higher water velocity (every 100 m in the systems surveyed in this study). Studying salmon eDNA spatio-temporal patterns in lotic environments is essential to developing strong quantitative population assessment models that successfully leverage eDNA as a tool to protect salmon populations.

Abstract Because significant global changes are currently underway in the Arctic, creating a large‐scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio‐temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large‐scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern‐based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well‐mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI‐based eDNA metabarcoding may quickly improve large‐scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.