Influence of sediment and stream transport on detecting a source of environmental DNA.

Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors-settling, resuspension, dispersion, eDNA stability/decay-influence eDNA estimations and potentially population abundance. In a series of field and controlled mesocosm experiments, we examined the detection and accumulation of eDNA in sediment and water and the transport of eDNA in a small stream in the Lake Michigan watershed, using the invasive round goby fish (Neogobius melanostomus) as a DNA source. Experiment 1: caged fish (average n = 44) were placed in a stream devoid of round goby; water was collected over 24 hours along 120-m of stream, including a simultaneous sampling event at 7 distances from DNA source; stream monitoring continued for 24 hours after fish were removed. Experiment 2: round goby were placed in laboratory tanks; water and sediment were collected over 14 days and for another 150 days post-fish removal to calculate eDNA shedding and decay rates for water and sediment. For samples from both experiments, DNA was extracted, and qPCR targeted a cytochrome oxidase I gene (COI) fragment specific to round goby. Results indicated that eDNA accumulated and decayed more slowly in sediment than water. In the stream, DNA shedding was markedly lower than calculated in the laboratory, but models indicate eDNA could potentially travel long distances (up to 50 km) under certain circumstances. Collectively, these findings show that the interactive effects of ambient conditions (e.g., eDNA stability and decay, hydrology, settling-resuspension) are important to consider when developing comprehensive models. Results of this study can help resource managers target representative sites downstream of potential invasion sites, thereby maximizing resource use.

Environmental DNA (eDNA): A tool for quantifying the abundant but elusive round goby (Neogobius melanostomus).

Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, occupancy estimates, and real-time detections of invasive species. In the Great Lakes, the round goby (Neogobius melanostomus), an invasive benthic fish from the Black Sea, has spread to encompass all five lakes and many tributaries, outcompeting or consuming native species; however, estimates of round goby abundance are confounded by behavior and habitat preference, which impact reliable methods for estimating their population. By integrating eDNA into round goby monitoring, improved estimates of biomass may be obtainable. We conducted mesocosm experiments to estimate rates of goby DNA shedding and decay. Further, we compared eDNA with several methods of traditional field sampling to compare its use as an alternative/complementary monitoring method. Environmental DNA decay was comparable to other fish species, and first-order decay was lower at 12°C (k = 0.043) than at 19°C (k = 0.058). Round goby eDNA was routinely detected in known invaded sites of Lake Michigan and its tributaries (range log10 4.8-6.2 CN/L), but not upstream of an artificial fish barrier. Traditional techniques (mark-recapture, seining, trapping) in Lakes Michigan and Huron resulted in fewer, more variable detections than eDNA, but trapping and eDNA were correlated (Pearson R = 0.87). Additional field testing will help correlate round goby abundance with eDNA, providing insight on its role as a prey fish and its impact on food webs.

Characterization of Coastal Drift-Cell Sediment Processes Effecting the Restoration of the Southern Lake Michigan Shoreline.

Hard structures along the southern shore of Lake Michigan restrict natural longshore sediment transport, destabilizing the shoreline, and dissecting the coast into localized shoreline reaches. A geometric design was used to sample (n = 590 nodes) at nine shoreline reaches near the Indiana Dunes National Lakeshore to characterize existing sediment in the offshore and onshore zones. Cluster Analysis grouped shoreline sites into two clusters. Factor Analysis showed that 35 % of the sand fractionation's cumulative variance across all sites was explained by an increased loading on medium sand (0.250 mm) with a corresponding decrease loading on small pebbles (4.750 mm), and an additional 30 % of the cumulative variance was explained by a negative loading on very fine sand (0.075 mm). Individual clusters showed that 43 % of the cumulative variance within cluster one could be explained by increased loadings on fine and medium sand (0.149-0.250 mm) with a corresponding negative loading on small pebbles (4.75 mm). An additional 22 % of the cumulative variance was explained by the positive loading on coarse sand (0.850 mm). Cluster two was explained by a single factor (62 % cumulative variance) highlighting an increased loading on small pebbles and coarse sand, and decreased loadings on medium to very fine sand. Principal component analysis showed that sediment characterization of the swash zone provided the best explanation of between site variance.

Biological diversity, ecological health and condition of aquatic assemblages at national wildlife refuges in southern indiana, USA.

The National Wildlife Refuge system is a vital resource for the protection and conservation of biodiversity and biological integrity in the United States. Surveys were conducted to determine the spatial and temporal patterns of fish, macroinvertebrate, and crayfish populations in two watersheds that encompass three refuges in southern Indiana. The Patoka River National Wildlife Refuge had the highest number of aquatic species with 355 macroinvertebrate taxa, six crayfish species, and 82 fish species, while the Big Oaks National Wildlife Refuge had 163 macroinvertebrate taxa, seven crayfish species, and 37 fish species. The Muscatatuck National Wildlife Refuge had the lowest diversity of macroinvertebrates with 96 taxa and six crayfish species, while possessing the second highest fish species richness with 51 species. Habitat quality was highest in the Muscatatuck River drainage with increased amounts of forested habitats compared to the Patoka River drainage. Biological integrity of the three refuges ranked the Patoka NWR as the lowest biological integrity (mean IBI reach scores = 35 IBI points), while Big Oaks had the highest biological integrity (mean IBI reach score = 41 IBI points). The Muscatatuck NWR had a mean IBI reach score of 31 during June, which seasonally increased to a mean of 40 IBI points during summer. Watershed IBI scores and habitat condition were highest in the Big Oaks NWR.

Relationships among varying sampling distance and the IBI in warmwater, headwater streams of the Eastern Corn Belt Plain.

Single-pass electrofishing was used to define the most efficient sampling distance to assess stream condition using the index of biotic integrity (IBI) methodology in headwater (<36 km(2) drainage area), warmwater streams in the Eastern Corn Belt Plain ecoregion. Based on wetted widths (1-3.3 m) of sampled reaches, we defined effort based on increased area (range 50-555 m(2)). Sampled area necessary to capture a representative fish assemblage increased until 167-m(2) distance, which is equivalent to a minimum sampling distance of one habitat cycle. No significant difference in metric actual observed value response was found with increasing habitat cycle. Increased effort is required in smaller streams widths (≤1 m) to achieve the recommended sample area. The effect of rare fish on the IBI was tested using a modified Walford method. A significant decrease in IBI score was observed when 10% of the rare data were removed. The presence of rare fish did not influence individual IBI metrics or scores for either the increased effort or reduced effort calibrations until greater than 3% of the data was removed for number of species, 15% removal of data for number of minnow species, and 5% removal of data for catch per unit effort (CPUE). Increased effort did not affect any metric or IBI score, while reduced effort influenced the number of darter, madtom, and sculpin species and catch per unit effort metric scores but did not affect IBI score.

Patterns in stream fish assemblage structure and function associated with a PCB gradient.

Stream fish assemblage structure and function were examined for significant response along a polychlorinated biphenyl (PCB) gradient from two PCB-contaminated streams (Clear Creek and Richland Creek watershed) at three locations and a control stream (Little Indian Creek), Indiana, USA. Fish were sampled in the summer months of 1995 and from 1999 to 2002. 51 fish assemblage attributes-including structure (i.e., fish composition) and function (i.e., trophic, reproductive, condition guilds), biomass, and index of biotic integrity (IBI) metric scores-were evaluated for significance according to an increasing PCB gradient. Eight biomass attributes of fish assemblages decreased with increasing PCB concentration: number of species biomass, number of sunfish biomass, percent sunfish biomass, number of sucker biomass, percent sucker biomass, biomass of sensitive species, percent sensitive species biomass, and percent carnivore biomass. Three biomass attributes increased with PCB concentration: percent minnow biomass, percent pioneer species biomass, and percent tolerant species biomass. Seven species composition and relative abundance characters decreased with increasing PCB concentration: number of species; number of darter, madtom, and sculpin; number of darter; number of sunfish; number of sucker; number of sensitive species; and percent individuals as carnivores. Percent individuals as pioneer species increased with increasing PCB concentration. Two IBI metrics, percent individuals as headwater species and number of minnow species, increased as PCB concentrations increased, whereas number of sucker species and percent individuals as pioneer species decreased with increasing PCB concentration class. We observed a direct response between decreased relative abundance and biomass of carnivores and increased relative abundance minnows as the PCB gradient increased. Total IBI score did not detect subtle changes to the fish community that were observed along a PCB gradient, whereas diagnostic analysis of the individual metrics did.

Biological response signature of oil brine threats, sediment contaminants, and crayfish assemblages in an Indiana watershed, USA.

The Patoka River watershed contains a divergent landscape of oil and gas exploration, intensive agriculture, and surface mining mixed with National Forest, Wildlife Refuges, and a large recreational reservoir. We evaluated species diversity among different land uses, including, commercial, forested, residential, and agriculture, and determined relationships among disturbance scale, habitat requirements, contaminants, and patterns in species distributions. Primary burrowing species, Cambarus polychromatus, Cambarus cf diogenes (Lacunicambarus A), and Fallicambarus fodiens, were tolerant of higher concentrations of contaminants than aquatic tertiary burrowing species. Cambarus polychromatus was among the last species of crayfish at the most disturbed sites, while it was absent from pasture and agricultural landscapes that allowed cattle access along banks. Four species of Orconectes were found in the reference and agricultural landscapes within the watershed, including O. immunis, O. indianensis, O. inermis inermis, and O. propinquus. Orconectes indianensis distribution was determined by the presence of rock habitat and absence of contaminants. No Orconectes species were found in acid mine leachate-affected streams with high levels of molybdenum. Cambarus laevis was found in the highest-quality reference areas, which were associated with karst habitats and no contaminants. Burrowing crayfish species were associated with the oil derricks in the lower and middle watershed, which contained increased concentrations of strontium, phosphorus, and various organic parameters associated with oil brine PAHs.