The disaggregated inorganic grain size (DIGS) of bottom sediment analyzed with a Coulter Counter (CC) has been used to show that the fraction of sediment deposited in flocs (floc fraction) increased ...in both the near and far field after the introduction of open cage salmon aquaculture, altering benthic habitat and species composition. As a result, DIGS was identified as a potential indicator of regional environmental changes due to aquaculture. Laser diffraction is an attractive alternative to the CC because of its greater efficiency and larger size range. To determine if a laser diffraction instrument, Beckman-Coulter LS 13 320 (LS), could replace the CC within a Canadian national aquaculture monitoring program, the DIGS of 581 samples from five different regions in eastern Canada were analyzed with an LS and a CC. Results show that the LS could not be used to calculate floc fraction. Instead, % sortable silt and the volume % of inorganic particles < 16 µm were evaluated as alternative proxies for fine sediment properties. LS and CC values for these parameters were correlated, but they were significantly different and the relationship between the instruments was dependent on the area sampled. The LS did not capture variations between areas seen in the CC DIGS data. Where the DIGS from the CC found no sorting in the finest size classes, all the LS samples had similar size distributions characterized by smooth modal peaks. The LS and CC both return values that can be used to monitor changes in the deposition of fine-grained sediment, but the LS cannot determine changes in floc deposition and caution is required if comparing different sedimentary environments.
The presence of in-feed anti-sea lice drugs and their relationship with organic enrichment is poorly understood in sediment surrounding salmon farms. Using data from an aquaculture monitoring program ...(2018–2020), we describe this relationship at ten sites in four Canadian provinces. Three anti-sea lice pesticides (lufenuron, teflubenzuron, emamectin benzoate and metabolite desmethyl emamectin benzoate), and one antibiotic (oxytetracycline) were detected. Concentrations were often below limits of quantification. Values are also lower than those reported in other aquaculture salmon-producing countries. Highest concentrations, along with organic enrichment, were observed ~200 m of cages with lower concentrations detected up to 1.5 km away. Most samples had at least two drugs present: 75.2 % (British Columbia), 91.4 % (Newfoundland), and 54.8 % (New Brunswick/Nova Scotia) highlighting the potential for cumulative effects. Emamectin benzoate and oxytetracycline were detected four and three years respectively after last known treatments, demonstrating the need for research on overall persistence of compounds.
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•Sediment data collected through an aquaculture monitoring program were used.•Three anti-sea lice drugs and one antibiotic were detected at ten salmon sites.•The highest concentrations and organic enrichment were observed within 200 m of cages.•Most sediment samples had at least two drugs present.•There is a significant patchiness in drug presence and organic matter enrichment.
Several trace-elements have been identified as indicators of finfish aquaculture organic enrichment. In this study, sediment sampling at finfish farms was completed as part of an Aquaculture ...Monitoring Program in three distinct Canadian regions. Despite diverse datasets, multivariate analyses show a consistent clustering of known direct (Cu and Zn) and indirect (Cd, Mo and U) tracers of aquaculture activities with sediment organic matter (OM) and/or total dissolved sulfides concentrations. OM content was also a predictor of Cu, Zn, Mo and U concentrations according to decision tree analyses. Distance from cages did not emerge as a strong driver of differences among sampling points; however, a tendency towards negative associations is clear especially for Zn. Enriched stations as determined after geochemical normalization were mostly localized within 150 m of net-pens. Selected trace-elements (in particular Zn) can be useful indicators of aquaculture organic enrichment in different ecosystems and valuable tools for monitoring programs.
•Sediment sampling at finfish farms was completed in three distinct Canadian regions.•Multivariate analyses show a clustering of Cu, Zn, Cd, Mo and U with sediment organic matter and/or total dissolved sulfides.•Organic matter content is a predictor of Cu, Zn, Mo and U concentrations as per decision tree analyses.•Enriched stations in selected trace-metals were localized within 150 m of net-pens.•Selected trace-elements (in particular Zn) are useful indicators of aquaculture organic enrichment.
We developed a new predictive approach to evaluate the relative invasion hazard posed by recreational boats as vectors for non-indigenous species (NIS) in marine ecoregions on the Atlantic coast of ...Canada. It combines data from behavioral boater questionnaires, surveys of boat macrofouling, and an extensive NIS monitoring program in marinas. The relative invasion hazard posed by boats in nine marine ecoregions was estimated by combining information on NIS infestation levels in source ecoregions, the probability that boats will be fouled, boat movements and environmental similarity between source and receiving marinas, and estimates of annual recreational traffic within and between ecoregions. A total of 52.1% of surveyed boats had macrofouling on hull or niche areas, suggesting a high potential for NIS transport. High-risk boats were those that had spent extended periods in water, traveled extensively from invaded locations, and received little maintenance. Further, the high degree of connectivity between and within ecoregions, and high survival probabilities of NIS, highlight the threat of NIS introduction and spread via recreational boating in Atlantic Canadian waters. Of all Atlantic Canadian ecoregions, the Scotian Shelf ecoregion was classified as having the “Highest” Final Hazard score. However, boats with Intermediate to Highest scores travel to most ecoregions, underlining the importance of this vector to the introduction and spread of NIS in Atlantic Canadian coast. A simulated out-of-water cleaning after 3 months reduced the hazard in ecoregions with greater scores.
Environmental DNA (eDNA) promises to ease noninvasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of ...understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the unknown effect of water temperature on eDNA concentrations poses practical limitations on quantifying fish populations using eDNA from water samples. This study aimed to clarify how water temperature and the eDNA capture method alter the relationships between eDNA concentration and fish abundance/biomass. Water samples (1 L) were collected from 30 aquaria including triplicate of 0, 5, 10, 15 and 20 Brook Charr specimens at two different temperatures (7 °C and 14 °C). Water samples were filtered with five different types of filters. The eDNA concentration obtained by quantitative PCR (qPCR) varied significantly with fish abundance and biomass and types of filters (mixed‐design ANOVA, P < 0.001). Results also show that fish released more eDNA in warm water than in cold water and that eDNA concentration better reflects fish abundance/biomass at high temperature. From a technical standpoint, higher levels of eDNA were captured with glass fibre (GF) filters than with mixed cellulose ester (MCE) filters and support the importance of adequate filters to quantify fish abundance based on the eDNA method. This study supports the importance of including water temperature in fish abundance/biomass prediction models based on eDNA.
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA from diverse kinds of ...environmental samples (termed “environmental DNA” or “eDNA”). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called “eDNA metabarcoding” and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.
Environmental DNA is not the tool by itself Lacoursière‐Roussel, Anaïs; Deiner, Kristy
Journal of fish biology,
February 2021, 2021-Feb, 2021-02-00, 20210201, Volume:
98, Issue:
2
Journal Article
1. Assessment and monitoring of exploited fish populations are challenged by costs, logistics and negative impacts on target populations. These factors therefore limit large-scale effective ...management strategies. 2. Evidence is growing that the quantity of eDNA may be related not only to species presence/absence, but also to species abundance. In this study, the concentrations of environmental DNA (eDNA) from a highly prized sport fish species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in water samples from 12 natural lakes and compared to abundance and biomass data obtained from standardized gillnet catches as performed routinely for fisheries management purposes. To reduce environmental variability among lakes, all lakes were sampled in spring, between ice melt and water stratification. 3. The eDNA concentration did not vary significantly with water temperature, dissolved oxygen, pH and turbidity, but was significantly positively correlated with relative fish abundance estimated as catch per unit effort (CPUE), whereas the relationship with biomass per unit effort (BPUE) was less pronounced. 4. The value of eDNA to inform about local aquatic species distribution was further supported by the similarity between the spatial heterogeneity of eDNA distribution and spatial variation in CPUE measured by the gillnet method. 5. Synthesis and applications. Large-scale empirical evidence of the relationship between the eDNA concentration and species abundance allows for the assessment of the potential to integrate eDNA within fisheries management plans. As such, the eDNA quantitative method represents a promising population abundance assessment tool that could significantly reduce the costs associated with sampling and increase the power of detection, the spatial coverage and the frequency of sampling, without any negative impacts on fish populations.
In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be ...used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this view. However, we are concerned that their proposed two‐level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra‐organismal) from which ecological interpretations are derived.
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