Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Marine ecosystems worldwide are under threat with many fish species and populations suffering from human over-exploitation. This is greatly impacting global biodiversity, economy and human health. Intriguingly, marine fish are largely surveyed using selective and invasive methods, which are mostly limited to commercial species, and restricted to particular areas with favourable conditions. Furthermore, misidentification of species represents a major problem. Here, we investigate the potential of using metabarcoding of environmental DNA (eDNA) obtained directly from seawater samples to account for marine fish biodiversity. This eDNA approach has recently been used successfully in freshwater environments, but never in marine settings. We isolate eDNA from ½-litre seawater samples collected in a temperate marine ecosystem in Denmark. Using next-generation DNA sequencing of PCR amplicons, we obtain eDNA from 15 different fish species, including both important consumption species, as well as species rarely or never recorded by conventional monitoring. We also detect eDNA from a rare vagrant species in the area; European pilchard (Sardina pilchardus). Additionally, we detect four bird species. Records in national databases confirmed the occurrence of all detected species. To investigate the efficiency of the eDNA approach, we compared its performance with 9 methods conventionally used in marine fish surveys. Promisingly, eDNA covered the fish diversity better than or equal to any of the applied conventional methods. Our study demonstrates that even small samples of seawater contain eDNA from a wide range of local fish species. Finally, in order to examine the potential dispersal of eDNA in oceans, we performed an experiment addressing eDNA degradation in seawater, which shows that even small (100-bp) eDNA fragments degrades beyond detectability within days.Although further studies are needed to validate the eDNA approach in varying environmental conditions, our findings provide a strong proof-of-concept with great perspectives for future monitoring of marine biodiversity and resources.

Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188–918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus) showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic habitats. This relates directly to applied fisheries as well as to monitoring effects of ongoing climate change on marine biodiversity—especially in polar ecosystems.

Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.

a b s t r a c tThe European weather loach (Misgurnus fossilis) represents one of many European freshwater fishes in decline. Efficient monitoring is essential if conservation efforts are to be successful, but due to the species' cryptic biology, traditional monitoring methods currently in use are inefficient, time consuming and likely prone to non-detection error. Here, we investigate the usefulness of environmental DNA (eDNA) monitoring as an alternative or supplementary method for surveying the Danish weather loach population, which is presumed to consist primarily of a single group of no more than 50 individuals. In 2008, the majority of historical Danish localities were surveyed, using traditional fishing techniques. We then applied eDNA methods to a number of these, as well as other potential localities. We successfully detected the weather loach at multiple sites in the single known remaining locality; a result that was later confirmed when local managers caught eight live specimens. Furthermore, the eDNA method indicated presence of the weather loach in another historical locality, where the species has not been observed since 1995. At the remaining localities, weather loach eDNA was not detected, providing further evidence for its absence. Importantly, the eDNA survey required less effort in person-hours and lower costs than the traditional fishing survey. This study confirms that eDNA monitoring is a valid supplement to traditional monitoring methods currently applied to monitor rare freshwater fishes. We propose that by providing reliable distribution data at lower cost and limited effort, the eDNA method can allow for increased management efficiency of endangered freshwater species such as the European weather loach.

Background:A rich body of literature exists that has demonstrated adverse human health effects following exposure to ambient air particulate matter (PM), and there is strong support for an important role of ultrafine (nanosized) particles. At present, relatively few human health or epidemiology data exist for engineered nanomaterials (NMs) despite clear parallels in their physicochemical properties and biological actions in in vitro models.Objectives:NMs are available with a range of physicochemical characteristics, which allows a more systematic toxicological analysis. Therefore, the study of ultrafine particles (UFP, <100 nm in diameter) provides an opportunity to identify plausible health effects for NMs, and the study of NMs provides an opportunity to facilitate the understanding of the mechanism of toxicity of UFP.Methods:A workshop of experts systematically analyzed the available information and identified 19 key lessons that can facilitate knowledge exchange between these discipline areas.Discussion:Key lessons range from the availability of specific techniques and standard protocols for physicochemical characterization and toxicology assessment to understanding and defining dose and the molecular mechanisms of toxicity. This review identifies a number of key areas in which additional research prioritization would facilitate both research fields simultaneously.Conclusion:There is now an opportunity to apply knowledge from NM toxicology and use it to better inform PM health risk research and vice versa. https://doi.org/10.1289/EHP424

Background: The toxic and inflammatory potential of 5 different types of nanoparticles were studied in a sensitive model for pulmonary effects in apolipoprotein E knockout mice (ApoE -/-). We studied the effects instillation or inhalation Printex 90 of carbon black (CB) and compared CB instillation in ApoE-/-and C57 mice. Three and 24 h after pulmonary exposure, inflammation was assessed by mRNA levels of cytokines in lung tissue, cell composition, genotoxicity, protein and lactate dehydrogenase activity in broncho-alveolar lavage (BAL) fluid.

Taxonomic and distributional information on each fish species found in arctic marine waters is reviewed, and a list of families and species with commentary on distributional records is presented. The list incorporates results from examination of museum collections of arctic marine fishes dating back to the 1830s. It also incorporates results from DNA barcoding, used to complement morphological characters in evaluating problematic taxa and to assist in identification of specimens collected in recent expeditions. Barcoding results are depicted in a neighbor-joining tree of 880 CO1 (cytochrome c oxidase 1 gene) sequences distributed among 165 species from the arctic region and adjacent waters, and discussed in the family reviews. Using our definition of the arctic region, we count 242 species with documented presence, if 12 species that likely are synonyms are excluded. The 242 species are distributed among 45 families.Six families in Cottoidei with 72 species and five in Zoarcoidei with 55 species account for more than half (52.5%) the species. This study produced CO1 sequences for 106 of the 242 species. Sequence variability in the barcode region permits discrimination of all species. The average sequence variation within species was 0.3% (range 0-3.5%), while the average genetic distance between congeners was 4.7% (range 3.7-13.3%). The CO1 sequences support taxonomic separation of some species, such as Osmerus dentex and O. mordax and Liparis bathyarcticus and L. gibbus; and synonymy of others, like Myoxocephalus verrucosus in M. scorpius and Gymnelus knipowitschi in G. hemifasciatus. They sometimes revealed the presence of additional species that were not entirely expected, such as an unidentified species of Ammodytes in the western Gulf of Alaska, most likely A. personatus; and an unidentified Icelus species of the I. spatula complex with populations in the western Gulf of Alaska and the northern Bering and Chukchi Seas which could be a new species or a species in synonymy. Reviewing distribution, we found that for 24 species the patterns assigned by authors understated historical presence in the arctic region, and for 12 species they overstated presence. For instance, Hippoglossoides robustus is counted as an arctic-boreal species rather than predominantly boreal, and Artediellus uncinatus as predominantly arctic rather than predominantly boreal. Species with arctic, predominantly arctic, or arctic-boreal distributions composed 41% of the 242 species in the region, and predominantly boreal, boreal, and widely distributed species composed 59%. For some continental shelf species, such as the primarily amphiboreal Eumesogrammus praecisus and Leptoclinus maculatus, distributions appear to reflect changes, including reentry into Arctic seas and reestablishment of continuous ranges, that zoogeographers believe have been going on since the end of land bridge and glacial times. This article belongs to the special issue "Arctic Ocean Diversity Synthesis"Electronic supplementary material The online version of this arti...