Search

Background: Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods: We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results: Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs. [ABSTRACT FROM AUTHOR]

Risk assessment methods are used worldwide to evaluate threats posed by fisheries and other impacts on living marine resources, and to prioritize management of these threats. We derive a simplified risk analysis for aggregate fish communities as a preliminary tool to identify priorities for further detailed assessment. Because some of the largest observed rates of sea surface temperature increase are on the northeast US continental shelf, we focused on climate change-driven risks to marine communities in this region. We evaluated climate vulnerability for six communities across two ecosystems: both commercial and non-commercial demersal fish, pelagic fish, and benthic invertebrates in the Gulf of Maine (GOM) and Mid-Atlantic bight (MAB). We first evaluated the probability that anticipated climate changes (e.g. warming water, decreased salinity, increased acidity, altered boundary currents) would occur in these regions, and rated the potential severity of change over the next 10 years. Then, we evaluated the sensitivity of each biological community in each region using 12 attributes (e.g. habitat and prey specificity, temperature and acidity sensitivity, larval dispersal, adult mobility, population productivity, etc.). Exposure to the key climate risks was related to community sensitivity in each region for an overall assessment of climate vulnerability. Climate risks from increased surface water temperature, sea level rise, and earlier spring were rated moderate to high in both regions, with additional moderate to high risks in the GOM from increased bottom temperature, stratification, and river inputs. Benthic invertebrates were rated most sensitive, with demersals intermediate and pelagics lowest. Two MAB communities were rated more sensitive than corresponding GOM communities, but greater short-term climate risks in the GOM indicated increased exposure for GOM communities. Overall, this simple analysis may help prioritize short-term regional climate risk management action, thus addressing key conditions related to fishery fluctuations beyond fishing itself. [ABSTRACT FROM AUTHOR]

1. We tested how strongly aquatic macroinvertebrate taxa richness and composition were associated with natural variation in both flow regime and stream temperatures across streams of the western United States. 2. We used long-term flow records from 543 minimally impacted gauged streams to quantify 12 streamflow variables thought to be ecologically important. A principal component analysis reduced the dimensionality of the data from 12 variables to seven principal component (PC) factors that characterised statistically independent aspects of streamflow: (1) zero flow days, (2) flow magnitude, (3) predictability, (4) flood duration, (5) seasonality, (6) flashiness and (7) base flow. K-means clustering was used to group streams into 4-8 hydrologically different classes based on these seven factors. 3. We also used empirical models to estimate mean annual, mean summer and mean winter stream temperatures at each stream site. We then used invertebrate data from 63 sites to develop Random Forest models to predict taxa richness and taxon-specific probabilities of capture at a site from flow and temperature. We used the predicted taxon-specific probabilities of capture to estimate how well predicted assemblages matched observed assemblages as measured by RIVPACS-type observed/expected (O/E) indices and Bray-Curtis dissimilarities. 4. Macroinvertebrate taxon richness was only weakly associated with streamflow and temperature variables, implying that other factors more strongly influenced taxa richness. 5. In contrast to taxa richness, taxa composition was strongly associated with streamflow and temperature. Predictions of taxa composition (O/E and Bray-Curtis) were most precise when both temperature and streamflow PC factors were used, although predictions based on either streamflow PC factors or temperature alone were also better than null model predictions. Of the seven aspects of the streamflow regime we examined, variation in baseflow conditions appeared to be most directly associated with invertebrate biotic composition. We were also able to predict assemblage composition from the conditional probabilities of hydrological class membership nearly as well as Random Forests models that were based directly on continuous PC factors. 6. Our results have direct implication for understanding the relative importance of streamflow and temperature in regulating the structure and composition of stream assemblages and for improving the accuracy and precision of biological assessments. [ABSTRACT FROM AUTHOR]

In August 2007, as part of the NOAA National Marine Fisheries Service (NMFS) West Coast Groundfish Bottom Trawl Survey, we examined the biomass of demersal organisms in a known hypoxic area off the Oregon coast. Although observed each summer, the intensity of hypoxia has varied annually (2002–2007) with the greatest temporal and spatial extent noted in 2006. In 2007 we identified the geographic extent of the hypoxic zone and sampled 17 stations along two depth contours (50 and 70 m) within the area. A Sea-Bird SBE 19 plus equipped with a dissolved oxygen (DO) sensor was attached to the bottom trawl to monitor oxygen concentration during each tow. Bottom DO concentrations at all stations were hypoxic with means along the tow tracts ranging from 0.43 to 1.27 mL L−1. Total catch per unit effort (ln CPUE, kg hectare−1) and species diversity (number of species, N) were significantly and positively related to oxygen concentration along the hypoxic gradient. In addition, CPUE (natural log-transformed) for eight fish species and five benthic invertebrate species were significantly and positively related to bottom oxygen concentration within the hypoxic region. Condition factors for five fish species, as well as Dungeness crab ( Cancer magister) increased with increased bottom oxygen levels along the hypoxic gradient. Historical catch (2003–2006) within the hypoxic zone indicates that biomass was significantly lower in 2006, the year with the lowest bottom DO levels, relative to other years. [ABSTRACT FROM AUTHOR]

Although floodplains are known to be tightly controlled by the flood cycle, we know comparatively little about how flooding influences predators and their consumption of secondary production, particularly in highly seasonal floodplains typical of Mediterranean climates. In this study, we investigate how the seasonal dynamics of a central California floodplain influence the timing and magnitude of fish predation and the abundance and composition of invertebrates. For 3 years (2000–2002), we compared changes in abundances and size distributions of invertebrates through the flood season (January–June) with seasonal changes in the abundance of larval and juvenile fishes. Using diet analysis of fishes and manipulative feeding experiments with fishes in field enclosures, we link specific changes in invertebrate populations directly to feeding preferences of seasonally abundant fish. Early in the flood season prior to March, we found little influence of fish predation, consistent with the near absence of larval and juvenile fishes during this period. Coinciding with the midseason increase in the abundance of larval and juvenile fishes in April, we found significant declines in zooplankton abundance as well as declines in the size of zooplankton consistent with fish feeding preferences. Our results were consistent with results from feeding enclosure experiments that showed that fish rapidly depressed populations of larger cladocerans with much less effect on smaller cladocerans and calanoid copepods. At the end of the flood season, zooplankton abundances rapidly increased, consistent with a switch in the feeding of juvenile fish to aquatic insects and subsequent fish mortality. We also found that zooplankton biomass on the floodplain reached a maximum 2–3 weeks after disconnection with the river. We suggest that floodplain restoration in this region should consider management strategies that would ensure repeated flooding every 2–3 weeks during periods that would best match the peaks in abundance of native fishes. [ABSTRACT FROM AUTHOR]

Understanding and mapping the spatial variation in stream biological condition could provide an important tool for conservation, assessment, and restoration of stream ecosystems. The USEPA's 2008-2009 National Rivers and Streams Assessment (NRSA) summarizes the percentage of stream lengths within the conterminous United States that are in good, fair, or poor biological condition based on a multimetric index of benthic invertebrate assemblages. However, condition is usually summarized at regional or national scales, and these assessments do not provide substantial insight into the spatial distribution of conditions at unsampled locations. We used random forests to model and predict the probable condition of several million kilometers of streams across the conterminous United States based on nearby and upstream landscape features, including human-related alterations to watersheds. To do so, we linked NRSA sample sites to the USEPA's StreamCat Dataset; a database of several hundred landscape metrics for all 1:100,000-scale streams and their associated watersheds within the conterminous United States. The StreamCat data provided geospatial indicators of nearby and upstream land use, land cover, climate, and other landscape features for modeling. Nationally, the model correctly predicted the biological condition class of 75% of NRSA sites. Although model evaluations suggested good discrimination among condition classes, we present maps as predicted probabilities of good condition, given upstream and nearby landscape settings. Inversely, the maps can be interpreted as the probability of a stream being in poor condition, given human-related watershed alterations. These predictions are available for download from the USEPA's StreamCat website. Finally, we illustrate how these predictions could be used to prioritize streams for conservation or restoration., (© 2017 by the Ecological Society of America.)