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USGS2007

Distribution and accumulation of mercury in tissues of captive-reared common loon (Gavia immer) chicks

We determined the distribution and accumulation of Hg in tissues of common loon (Gavia immer) chicks maintained for up to 15 weeks on either a control diet with no added methylmercury chloride (MeHgCl) or one containing either 0.4 or 1.2 ??g Hg (as MeHgCl)/g wet-weight food. Total Hg and MeHg tissue concentrations were strongly positively correlated (r2 > 0.95) with the amount of Hg delivered to individual chicks throughout the course of the experiment. The pattern of differential Hg concentration in internal tissues was consistent within each treatment: Liver > kidney > muscle > carcass > brain. Feather Hg concentrations were consistently higher than those of internal tissues and represented an important route of Hg elimination. Feather mass accounted for 4.3% ?? 0.1% (average ?? standard error) of body mass, yet 27.3% ?? 2.6% of total Hg intake was excreted into feathers. Our calculations indicate that 26.7% ?? 4.9% of ingested Hg was not accounted for and, thus, either was never absorbed or was absorbed and subsequently eliminated in feces. With the additional excretion into feathers, 54% of ingested Hg was excreted. Demethylation was evident in the liver at all treatment levels and in the kidneys of chicks dosed at 1.2 ??g Hg/g. Mercury concentrations were strongly positively correlated (r2 ??? 0.95) among internal tissues and with blood Hg concentration. Mercury concentrations of secondary feathers were moderately correlated (r2 = 0.82-0.93) with internal tissues. We supply regression models that may be used to provide perspective and a useful means of interpreting the variety of measures of Hg exposure reported in the literature. ?? 2007 SETAC.

Environmental Toxicology and Chemistry↗

USGS2006

Effects of lead-contaminated sediment on Rana sphenocephala tadpoles

We exposed larval southern leopard frogs (Rana sphenocephala) to lead-contaminated sediments to determine the lethal and sublethal effects of this metal. Tadpoles were laboratory-raised from early free-swimming stage through metamorphosis at lead concentrations of 45, 75, 180, 540, 2360, 3940, 5520, and 7580 mg/kg dry weight in sediment. Corresponding pore water lead concentrations were 123, 227, 589, 1833, 8121, 13,579, 19,038, and 24,427 ug/L. Tadpoles exposed to lead concentrations in sediment of 3940 mg/kg or higher died within 2 to 5 days of exposure. At lower concentrations, mortality through metamorphosis ranged from 3.5% at 45 mg/kg lead to 37% at 2360 mg/kg lead in sediment. The LC50 value for lead in sediment was 3728 mg/kg (95% CI=1315 to 72,847 mg/kg), which corresponded to 12,539 ug/L lead in pore water (95% CI= 4000 to 35,200 ug/L). Early growth and development were depressed at 2,360 mg/kg lead in sediment (8100 ug/L in pore water) but differences were not evident by the time of metamorphosis. The most obvious effect of lead was its pronounced influence on skeletal development. Whereas tadpoles at 45 mg/kg lead in sediment did not display permanent abnormalities, skeletal malformations increased in frequency and severity at all higher lead concentrations. By 2360 mg/kg, 100% of surviving metamorphs displayed severe spinal problems, reduced femur and humerus lengths, deformed digits, and other bone malformations. Lead concentrations in tissues correlated positively with sediment and pore water concentrations.

Archives of Environmental Contamination and Toxico↗

USGS2005

Phosphate reactivity in long-term poultry litter-amended southern Delaware sandy soils

Eutrophication caused by dissolved P from poultry litter (PL)-amended agricultural soils has been a serious environmental concern in the Delaware-Maryland-Virginia Peninsula (Delmarva), USA. To evaluate state and federal nutrient management strategies for reducing the environmental impact of soluble P from long-term PL-amended Delaware (DE) soils, we investigated (i) inorganic P speciation; (ii) P adsorption capacity; and (iii) the extent of P desorption. Although the electron microprobe (EMP) analyses showed a strong correlation between P and Al/Fe, crystalline Al/Fe-P precipitates were not detected by x-ray diffraction (XRD). Instead, the inorganic P fractionation analyses showed high levels of oxalate extractable P, Al, and Fe fractions (615-858, 1215-1478, and 337-752 mg kg-1, respectively), which were susceptible to slow release during the long-term (30-d) P desorption experiments at a moderately acidic soil pHwater. The labile P in the short-term (24-h) desorption studies was significantly associated with oxalate and F extractable Fe and Al, respectively. This was evident in an 80% reduction maximum in total desorbable P from NH4 oxalate/F pretreated soils. In the adsorption experiments, P was strongly retained in soils at near targeted pH of lime (???6.0), but P adsorption gradually decreased with decreasing pH near the soil pHwater (???5.0). The overall findings suggest that P losses from the can be suppressed by an increase in the P retention capacity of soils via (i) an increase in the number of lime applications to maintain soil pHwater at near targeted pH values, and/or (ii) alum/iron sulfate amendments to provide additional Al- and Fe-based adsorbents. ?? Soil Science Society of America.

Soil Science Society of America Journal↗

USGS2015

Hydrogeologic and geochemical characterization of groundwater resources in Deep Creek Valley and adjacent areas, Juab and Tooele Counties, Utah, and Elko and White Pine Counties, Nevada

The water resources of Deep Creek Valley were assessed during 2012–13 with an emphasis on better understanding the groundwater flow system and groundwater budget. Surface-water resources are limited in Deep Creek Valley and are generally used for agriculture. Groundwater is the predominant water source for most other uses and to supplement irrigation. Most groundwater withdrawal in Deep Creek Valley occurs from the unconsolidated basin-fill deposits, in which conditions are generally unconfined near the mountain front and confined in the lower-altitude parts of the valley. Productive aquifers are also present in fractured bedrock that occurs along the valley margins and beneath the basin-fill deposits. The consolidated-rock and basin-fill aquifers are hydraulically connected in many areas with much of the recharge occurring in the consolidated-rock mountain blocks and most of the discharge occurring from the lower-altitude basin-fill deposits. Average annual recharge to the Deep Creek Valley hydrographic area was estimated to be between 19,000 and 29,000 acre-feet. Groundwater recharge occurs mostly from the infiltration of precipitation and snowmelt at high altitudes. Additional, but limited recharge occurs from the infiltration of runoff from precipitation near the mountain front, infiltration along stream channels, and possible subsurface inflow from adjacent hydrographic areas. Groundwater moves from areas of recharge to springs and streams in the mountains, and to evapotranspiration areas, springs, streams, and wells in the basins. Discharge may also occur as subsurface groundwater outflow to adjacent hydrographic areas. Average annual discharge from the Deep Creek Valley hydrographic area was estimated to be between 21,000 and 22,000 acre-feet, with the largest portion of discharge occurring as evapotranspiration. Groundwater samples were collected from 10 sites for geochemical analysis. Dissolved-solids concentrations ranged from 126 to 475 milligrams per liter, and none of the sites sampled during this study had dissolved-solids concentrations that exceeded the Environmental Protection Agency secondary standard for drinking water of 500 milligrams per liter. Tritium concentrations from 1.6 to 10.1 tritium units at 3 of the 10 sample sites indicate the presence of modern (less than 60 years old) groundwater, and apparent tritium/helium-3 ages calculated for these sites ranged from 7 to 29 years. The other seven sample sites had tritium concentrations less than or equal to 0.4 tritium units and are assumed to be pre-modern. Adjusted minimum radiocarbon ages of these seven pre-modern water samples ranged from 1,000 to 8,000 years with the ages of at least four of the samples being more than 3,000 years. Noble-gas recharge temperatures indicate that groundwater sampled along the valley axis recharged at both mountain and valley altitudes, providing evidence for both mountain-block and mountain-front recharge. Water-level altitude contours and groundwater ages indicate the potential for a long flow path from southwest to northeast between northern Spring and Deep Creek Valleys through Tippett Valley. Although information gathered during this study is insufficient to conclude whether or not groundwater travels along this interbasin flow path, dissolved sulfate and chloride data indicate that a small fraction of the lower altitude, northern Deep Creek Valley discharge may be sourced from these areas. Despite the uncertainty due to limited data collection points, a hydraulic connection between northern Spring Valley, Tippett Valley, and Deep Creek Valley appears likely, and potential regional effects resulting from future groundwater withdrawals in northern Spring Valley warrant ongoing monitoring of groundwater levels across this area.

Nevada, Utah↗

USGS2006

Comparison of trace element concentrations in livers of diseased, emaciated and non-diseased southern sea otters from the California coast

Infectious diseases have been implicated as a cause of high rates of adult mortality in southern sea otters. Exposure to environmental contaminants can compromise the immuno-competence of animals, predisposing them to infectious diseases. In addition to organic pollutants, certain trace elements can modulate the immune system in marine mammals. Nevertheless, reports of occurrence of trace elements, including toxic heavy metals, in sea otters are not available. In this study, concentrations of 20 trace elements (V, Cr, Mn, Co, Cu, Zn, Rb, Sr, Mo, Ag, Cd, In, Sn, Sb, Cs, Ba, Hg, Tl, Pb, and Bi) were measured in livers of southern sea otters found dead along the central California coast (n = 80) from 1992 to 2002. Hepatic concentrations of trace elements were compared among sea otters that died from infectious diseases (n = 27), those that died from non-infectious causes (n = 26), and otters that died in emaciated condition with no evidence of another cause of death (n = 27). Concentrations of essential elements in sea otters varied within an order of magnitude, whereas concentrations of non-essential elements varied by two to five orders of magnitude. Hepatic concentrations of Cu and Cd were 10- to 100-fold higher in the sea otters in this study than concentrations reported for any other marine mammal species. Concentrations of Mn, Co, Zn, and Cd were elevated in the diseased and emaciated sea otters relative to the non-diseased sea otters. Elevated concentrations of essential elements such as Mn, Zn, and Co in the diseased/emaciated sea otters suggest that induction of synthesis of metallothionein and superoxide dismutase (SOD) enzyme is occurring in these animals, as a means of protecting the cells from oxidative stress-related injuries. Trace element profiles in diseased and emaciated sea otters suggest that oxidative stress mediates the perturbation of essential-element concentrations. Elevated concentrations of toxic metals such as Cd, in addition to several other organic pollutants, may contribute to oxidative stress-meditated effects in sea otters.

California↗

USGS2022

Life and death in a dynamic environment: Invasive trout, floods, and intraspecific drivers of translocated populations

Understanding the relative strengths of intrinsic and extrinsic factors regulating populations is a long-standing focus of ecology and critical to advancing conservation programs for imperiled species. Conservation could benefit from an increased understanding of factors influencing vital rates (somatic growth, recruitment, survival) in small, translocated populations, which is lacking owing to difficulties in long-term monitoring of rare species. Translocations, here defined as the transfer of wild-captured individuals from source populations to new habitats, are widely used for species conservation, but outcomes are often minimally monitored, and translocations that are monitored often fail. To improve our understanding of how translocated populations respond to environmental variation, we developed and tested hypotheses related to intrinsic (density dependent) and extrinsic (introduced rainbow trout Oncorhynchus mykiss , stream flow and temperature regime) causes of vital rate variation in endangered humpback chub ( Gila cypha ) populations translocated to Colorado River tributaries in the Grand Canyon (GC), USA. Using biannual recapture data from translocated populations over 10 years, we tested hypotheses related to seasonal somatic growth, and recruitment and population growth rates with linear mixed-effects models and temporal symmetry mark–recapture models. We combined data from recaptures and resights of dispersed fish (both physical captures and continuously recorded antenna detections) from throughout GC to test survival hypotheses, while accounting for site fidelity, using joint live-recapture/live-resight models. While recruitment only occurred in one site, which also drove population growth (relative to survival), evidence supported hypotheses related to density dependence in growth, survival, and recruitment, and somatic growth and recruitment were further limited by introduced trout. Mixed-effects models explained between 67% and 86% of the variation in somatic growth, which showed increased growth rates with greater flood-pulse frequency during monsoon season. Monthly survival was 0.56–0.99 and 0.80–0.99 in the two populations, with lower survival during periods of higher intraspecific abundance and low flood frequency. Our results suggest translocations can contribute toward the recovery of large-river fishes, but continued suppression of invasive fishes to enhance recruitment may be required to ensure population resilience. Furthermore, we demonstrate the importance of flooding to population demographics in food-depauperate, dynamic, invaded systems.

Arizona↗

USGS2022

Invasion of annual grasses following wildfire corresponds to maladaptive habitat selection by a sagebrush ecosystem indicator species

Numerous wildlife species within semi-arid shrubland ecosystems across western North America are experiencing substantial habitat loss and fragmentation. These changes in habitat are often attributed to a diverse suite of factors including prolonged and increasingly severe droughts, conifer expansion, anthropogenic development, domestic and feral livestock grazing, and invasion of exotic annual grasses, which promotes increased wildfire frequency and severity. Greater sage-grouse ( Centrocercus urophasianus ; hereafter, sage-grouse) are considered an indicator of sagebrush ecosystem health and have experienced widespread population decline associated with habitat loss and degradation, as well as changes in predator communities. Our objectives were to model and map sage-grouse habitat selection and survival during the important brood-rearing life stage in relation to landscape-scale environmental predictors. Furthermore, we sought to understand impacts of wildfire and annual grass invasion on brood habitat, as these accelerated disturbance regimes are a primary cause of habitat loss within the Great Basin region of the USA. We used a hierarchical Bayesian modeling framework to estimate resource selection functions and survival for early and late brood-rearing stages of sage-grouse in relation to a broad suite of habitat characteristics evaluated at multiple spatial scales within the Great Basin from 2009 to 2019. Sage-grouse selected for greater perennial grass cover, higher relative elevations, and areas closer to springs and wet meadows during both early and late brood-rearing. Terrain characteristics, including heat load and aspect, were important in survival models, as was variation in shrub height. We also found strong evidence for higher survival for both early and late broods within previously burned areas, but survival within burned areas decreased as annual grass cover (i.e. cheatgrass , Bromus tectorum ) increased. This interaction effect demonstrates how invasion of annual grasses into burned areas, which has become prevalent in Great Basin sagebrush ecosystems, can lead to maladaptive habitat selection by brood-rearing greater sage-grouse. Understanding these complex relationships aids wildlife conservation and habitat management as wildfire and annual grass cycles continue to accelerate across western ecosystems.

California, Nevada↗

USGS2023

Movement ecology of diploid and triploid grass carp in a large reservoir and upstream tributaries

Grass carp Ctenopharyngodon idella , is an herbivorous fish originally brought to North America from Asia in 1963 to control nuisance aquatic vegetation. Since their arrival, detrimental alterations to aquatic ecosystems have sometimes occurred in waterways where they were initially stocked and into which they have escaped. The movements of grass carp from lentic systems into tributaries required for spawning is poorly understood, and understanding environmental conditions associated with upstream migrations may aid in management of the species. We stocked 43 fertile diploid and 43 sterile triploid grass carp implanted with acoustic transmitters into Truman Reservoir, Missouri, USA between January 2017 and October 2018 to characterize movements during spring and summer when spawning conditions occur. Twenty fish (11 diploid/9 triploid) exhibited upstream migration behavior in the Osage River, a major tributary, in 2018 and 2019. Migration primarily occurred in April and May, during high discharge events associated with increasing river stage when water temperatures were between 15 and 28°C. Observed migrations ranged from 3.0–108 river km in length, and six individuals were observed making multiple upstream migrations in one season. Eleven fish initiated upstream migrations while in the lentic main body of the reservoir. These findings provide some evidence for upstream migrations by diploid and triploid grass carp as well both lake and river residents. Evidence of similar upstream migration behavior by both diploid and triploid grass carp suggests that triploids may be suitable surrogates for diploids for study of movement ecology. Removal efforts in tributaries targeting periods of increasing river stage during spring may provide the best opportunity of encountering large concentrations of grass carp.

Missouri↗

USGS2019

In ovo exposure to brominated flame retardants Part I: Assessment of effects of TBBPA-BDBPE on survival, morphometric and physiological endpoints in zebra finches

Tetrabromobisphenol A bis(2,3-dibromopropyl) ether (TBBPA-BDBPE) is an additive flame retardant used in polyolefins and polymers. It has been detected in biota, including in avian eggs, yet little is known of its effects. We assessed the pattern of TBBPA-BDBPE concentrations in songbird eggs over the incubation period, and the effects of embryonic exposure to TBBPA-BDBPE in a model songbird species, the zebra finch (Taeniopygia guttata). To assess concentrations during embryo development, eggs were injected on the day they were laid with the vehicle control (safflower oil) or 100 ng TBBPA-BDBPE/g egg, and whole egg contents were collected throughout embryonic development on day 0 (unincubated), 5, 10 and 13. To evaluate effects of embryonic exposure to TBBPA-BDBPE, eggs were injected at Hamburger-Hamilton stage 18 (~80 hours after initiation of incubation) with safflower oil only, 10, 50 or 100 ng TBBPA-BDBPE/g egg (albumin injection volume 1 µl/g). Eggs were monitored for hatching success, and nestlings were monitored for growth and survival. At 15 days post-hatch, tissues were collected to assess physiological effects. TBBPA-BDBPE was incorporated into the egg as the embryo developed, and concentrations started declining in late incubation, suggesting biotransformation by the embryo. There were no effects on hatching success, nestling survival, growth, organ somatic indices, or thyroid hormone homeostasis; however, there was evidence that body condition declined in a dose-dependent manner towards the end of the rapid nestling growth phase. This decreased body condition could be a delayed effect of early developmental exposure, or it may be the result of increased exposure to biotransformation products of TBBPA-BDBPE produced over the nestling period, which are predicted to be more bioaccumulative and toxic than the parent compound.

Ecotoxicology and Environmental Safety↗

USGS2008

DDE in sediments of the Palos Verdes shelf, California: In situ transformation rates and geochemical fate

From 1947 to 1971 the world's largest manufacturer of DDT discharged process wastes into the sewers of Los Angeles County. Roughly 870-1450 t of DDT were released to the ocean off Palos Verdes, CA, a portion of which (???100 t) resides in sediments on the continental shelf and slope. The most abundant DDT compound in the sediments, p,p???-DDE, is degrading by reductive dechlorination, butthe rate of transformation and factors controlling it are not well understood. In order to estimate in situ transformation rates and predict the long-term fate of p,p???-DDE, box cores were collected in 1992 and 2003 from a single location on the Palos Verdes Shelf and analyzed for 8 DDT compounds and 84 polychlorinated biphenyl (PCB) congeners. The PCBs show no evidence of dechlorination, and inventories did not change between 1992 and 2003. By contrast, the inventory of p,p???-DDE decreased by 43%, whereas that of p,p???-DDMU, the putative reductive dechlorination product increased by 34%. The first-order transformation rate for p,p???-DDE at the study site is 0.051 ?? 0.006 yr-1. A multistep reaction model suggests that inventories of p,p???-DDE and p,p???-DDMU will continue to decline, whereas that of p,p???-DDNU will reach a maximum around 2014.

Environmental Science & Technology↗

USGS2021

Mussel mass mortality and the microbiome: Evidence for shifts in the bacterial microbiome of a declining freshwater bivalve

Freshwater mussels (Unionida) are suffering mass mortality events worldwide, but the causes remain enigmatic. Here, we describe an analysis of bacterial loads, community structure, and inferred metabolic pathways in the hemolymph of pheasantshells ( Actinonaias pectorosa ) from the Clinch River, USA, during a multi-year mass mortality event. Bacterial loads were approximately 2 logs higher in moribund mussels (cases) than in apparently healthy mussels (controls). Bacterial communities also differed between cases and controls, with fewer sequence variants (SVs) and higher relative abundances of the proteobacteria Yokenella regensburgei and Aeromonas salmonicida in cases than in controls. Inferred bacterial metabolic pathways demonstrated a predominance of degradation, utilization, and assimilation pathways in cases and a predominance of biosynthesis pathways in controls. Only two SVs correlated with Clinch densovirus 1, a virus previously shown to be strongly associated with mortality in this system: Deinococcota and Actinobacteriota, which were associated with densovirus-positive and densovirus-negative mussels, respectively. Overall, our results suggest that bacterial invasion and shifts in the bacterial microbiome during unionid mass mortality events may result from primary insults such as viral infection or environmental stressors. If so, bacterial communities in mussel hemolymph may be sensitive, if generalized, indicators of declining mussel health.

Tennessee, Virginia↗

USGS2013

Transport of nitrate in the Mississippi river in July-August 1999

Lagrangian sampling was conducted on the Mississippi River in late July through early August 1999 to test the hypothesis that nitrate (NO 3 - ) is transported conservatively in the Mississippi River. Three different approaches were pursued to test the hypothesis: (1) a mass balance for NO 3 - was evaluated for evidence of net gains and losses, (2) stable isotopes of NO 3 - were measured (δ 15 N and δ 18 O) to determine if fractionation occurred, and (3) the concentrations of dissolved gases (N 2 O, N 2 and Ar) in river water were measured and compared to theoretical equilibrium concentrations. Integrated water samples and flow measurements were obtained at 10 sites on the Mississippi River and 7 sites near the mouths of major tributaries from northern Iowa to southern Louisiana, a distance of about 2,250 river kilometers. Mass balance calculations indicate that more than 80 percent of the NO 3 - mass discharged from the Mississippi River (1,930 metric tons/day) during the study period originated in the first 500 river kilometers of the study reach. The mass balance calculations also indicate that NO 3 - was not lost from the water column upstream of Vicksburg, MS, but that there might have been some loss of NO 3 - in the lower 700 kilometers of the study reach. The stable isotope ratios of N and O (δ 15 N and δ 18 O) of NO 3 - were consistent with mixing and transport in the absence of fractionating gains or losses. The concentrations of nitrogen (N 2 ) and argon (Ar) dissolved in river water decreased in the downstream direction, approximately in equilibrium with air at increasing temperatures, giving no evidence of gains or losses of N 2 by nitrogen fixation or denitrification. Nitrous oxide (N 2 O) concentrations in the Mississippi River were approximately 26 to 200 percent of air saturation, indicating relatively low net production by combination of nitrification and denitrification. Results from this study indicate that most (>90%) of the NO 3 - that entered the Mississippi River during July-August 1999 was transported to the Gulf of Mexico.

Mississippi River↗

USGS2024

Asymmetric mate preference and reproductive interference mediate climate-induced changes in mate availability in a small mammal hybrid zone

Range expansion and contraction are among the most common biotic responses to changing environmental conditions, yet much is to be learned about the mechanisms that underlie range-edge population dynamics, especially when those areas are points of secondary contact between closely related species. Here, we present field-measured parentage data that document the reproductive outcomes of changes in mate availability at a secondary contact zone between two species of woodrat in the genus Neotoma . Changes in mate availability resulted from drought-driven differential survival between the species and their hybrids. As the availability of conspecifc mates declined, rates of hybridization increased, leading to the accumulation of admixed individuals in the zone of contact. Patterns of reproductive success in the wild appear to be the result of a combination of both pre-mating isolation and post-zygotic selection resulting from genomic incompatibilities between the parental lineages. Evidence of asymmetric mate preference between the parental lineages came from both skewed reproductive output in the field and laboratory preference trials. Moreover, partial genomic incompatibility was evident from the near-zero reproductive success of F1 males and because nearly all surviving hybrids had one pure parent. Nonetheless, the high reproductive success of F1 females and backcrossing in both parental directions allow for introgression between the parental species. These findings reveal how climate change may alter evolutionary outcomes for species at the edge of their ranges through an interplay of behavioral, demographic, and genetic mechanisms.

California↗

USGS1998

Assessment of the potential for biodegradation of petroleum hydrocarbons in the Railroad Industrial Area, Fairbanks, Alaska

Many technologies for the clean-up of petroleum-hydrocarbon contaminated sites depend on microbial degradation of the pollutant. In these technologies the site may be modified to enhance microbial activity, or may simply be monitored for naturally occurring microbial activity. In either case, an important aspect of site assessment for these technologies is to determine if the microorganisms present at the site have the potential to break down contaminants under the prevailing environmental conditions. We examined the numbers and activity of hydrocarbon-degrading microorganisms in ground water collected from petroleum-hydrocarbon contaminated and uncontaminated wells at the Railroad Industrial Area near Fairbanks, Alaska. We found that the population of gasoline-degrading microorganisms in ground water was correlated to the degree of contamination by benzene, toluene, ethylbenzene and xylenes (BTEX). We also found that these organisms could actively mineralize these types of compounds in laboratory mineralization assays. Increasing temperature and adding nutrients both enhanced the rate of mineralization in the laboratory, but measurable degradation still occurred under conditions similar to those found in the field. Dissolved oxygen in ground water at this site ranged from 0 to 3.6 milligrams per liter. Therefore, oxygen may not always be available to microorganisms as a terminal electron acceptor. Preliminary geochemical evidence from the field indicates that alternative electron acceptors such as Fe(III), sulfate, or nitrate may be used, contributing to degradation of contaminants at this site.

Open-File Report↗

USGS2025

Environmental DNA metabarcoding for monitoring fish biodiversity in remote lakes

Objective Environmental DNA (eDNA) metabarcoding provides an attractive option for monitoring biodiversity in remote freshwater ecosystems, where the deployment of conventional gears encounters major logistical constraints. We evaluated eDNA metabarcoding for monitoring fish communities and early detection of nonnative species in three remote lakes on Isle Royale, Michigan, USA. Methods At each of the three lakes, we collected surface, midwater, and lake bottom samples from 10 sites during spring and fall sampling events. We performed metabarcoding on all the water samples, targeting the 12S region of all fish species. Results Despite a relatively small sample size ( N = 60 samples per lake across two visits; 10 locations with three depths per location), we recovered 70% of all the species that were previously observed using conventional methods. We recovered several detections of putative Cisco Coregonus artedi , a vulnerable coldwater species, providing evidence that Cisco have persisted in these lakes. However, we found disentangling likely false positives from rare species challenging, which we overcame by employing multiple types of detection thresholds and a species-specific quantitative PCR assay. Conclusions Although we were able to successfully characterize the fish communities using eDNA metabarcoding, more attention needs to be given to the detection thresholds and communication protocols that provide guidance in interpretating new eDNA detections and using eDNA detections to inform management decisions. Although eDNA metabarcoding has limitations that should be accounted for at the outset of the project, the ease of sample collection makes eDNA metabarcoding an option for monitoring freshwater biodiversity in remote systems.

Michigan↗

USGS2004

Population structure and inbreeding vary with successional stage in created Spartina alterniflora marshes

Recruitment patterns in clonal plant populations are predicted to vary with seed dispersal capability and disturbance regime, such that species with small, widely dispersed seeds will become increasingly dominated by vegetative recruitment on disturbed areas following early colonization. Subsequent mortality due to competitive or stochastic effects is then predicted to cause a gradual decline in both clonal diversity and the ability of surviving clones to avoid geitonogamous mating and possible inbreeding depression. We tested predictions of these hypotheses by comparing four adjacent populations of the salt marsh plant, Spartina alterniflora, ranging in age from 2 to ∼50 yr, by measuring fine‐scale genetic structure at the level of both ramets and genets, and the rate of inbreeding. For this purpose, we sampled maternal tissue and seeds from discrete patches in the field and then genotyped both maternal and seedling tissue (germinated in a growth chamber) using standard molecular protocols. As predicted, we observed an increase in clonal diversity (measured as the complement of the Simpson Index corrected for finite sample sizes, 1 − D ) up to a maximum of 0.71 within 3‐m 2 patches at 16 yr, declining to 0.55 by ∼50 yr. Local recruitment of seedlings was evident as genetic structure occurring at the level of patches, as measured by the fixation index, θ, which was inversely correlated with diversity ( R 2 > 0.90 at all patch scales). Outcrossing rates were positively associated with clonal diversity, with the highest level (89%) at an intermediate level of 1 − D. The greatest selfing (32%) occurred in young (2‐yr‐old) patches with low diversity. Biparental inbreeding was minimal in all populations, never exceeding 1%. Inbreeding depression was inferred to be severe, as evidenced by near‐zero adult inbreeding coefficients. These results suggest a possible fitness trade‐off between clonal growth and the opportunity for outcrossing. We recommend that restoration plantings of clonal species with limited sexual recruitment capabilities should be designed to ensure adequate clonal diversity for the avoidance of inbreeding and the ability to adapt to subsequent environmental disturbances.

Louisiana↗

USGS2008

Anthropogenic influences on the input and biogeochemical cycling of nutrients and mercury in Great Salt Lake, Utah, USA

Despite the ecological and economic importance of Great Salt Lake (GSL), little is known about the input and biogeochemical cycling of nutrients and trace elements in the lake. In response to increasing public concern regarding anthropogenic inputs to the GSL ecosystem, the US Geological Survey (USGS) and US Fish and Wildlife Service (USFWS) initiated coordinated studies to quantify and evaluate the significance of nutrient and Hg inputs into GSL. A 6??? decrease in ??15N observed in brine shrimp (Artemia franciscana) samples collected from GSL during summer time periods is likely due to the consumption of cyanobacteria produced in freshwater bays entering the lake. Supporting data collected from the outflow of Farmington Bay indicates decreasing trends in ??15N in particulate organic matter (POM) during the mid-summer time period, reflective of increasing proportions of cyanobacteria in algae exported to GSL on a seasonal basis. The C:N molar ratio of POM in outflow from Farmington Bay decreases during the summer period, supportive of the increased activity of N fixation indicated by decreasing ??15N in brine shrimp and POM. Although N fixation is only taking place in the relatively freshwater inflows to GSL, data indicate that influx of fresh water influences large areas of the lake. Separation of GSL into two distinct hydrologic and geochemical systems from the construction of a railroad causeway in the late 1950s has created a persistent and widespread anoxic layer in the southern part of GSL. This anoxic layer, referred to as the deep brine layer (DBL), has high rates of SO42 - reduction, likely increasing the Hg methylation capacity. High concentrations of methyl mercury (CH3Hg) (median concentration = 24 ng/L) were observed in the DBL with a significant proportion (31-60%) of total Hg in the CH3Hg form. Hydroacoustic and sediment-trap evidence indicate that turbulence introduced by internal waves generated during sustained wind events can temporarily mix the elevated CH3Hg concentrations in the DBL with the more biologically active upper brine layer (UBL). Brine shrimp collected during the summer/fall time periods contained elevated Hg concentrations (median concentration = 0.34 mg/kg, dry weight (dw)) relative to samples collected during the spring (median concentration < 0.2 mg/kg, dw). Higher Hg in brine shrimp during the summer and fall may reflect the higher proportion of adult brine shrimp during this time period, resulting in an increased time for bioaccumulation of Hg. Eared grebes (Podiceps nigricollis) consume brine shrimp from GSL during the fall molting period. Median Hg concentrations in eared grebe livers increased by almost three times during the 3-5 month fall molting period. Selected duck species utilizing GSL have consistently exceeded the US Environmental Protection Agency (USEPA) screening level for Hg (0.3 mg/kg Hg wet weight), resulting in the issuance of warnings against unlimited human consumption of breast muscle tissue.

Applied Geochemistry↗

USGS2015

Spatial and temporal variability in growth of southern flounder ( Paralichthys lethostigma )

Delineation of stock structure is important for understanding the ecology and management of many fish populations, particularly those with wide-ranging distributions and high levels of harvest. Southern flounder ( Paralichthys lethostigma ) is a popular commercial and recreational species along the southeast Atlantic coast and Gulf of Mexico, USA. Recent studies have provided genetic and otolith morphology evidence that the Gulf of Mexico and Atlantic Ocean stocks differ. Using age and growth data from four states (Texas, Alabama, South Carolina, and North Carolina) we expanded upon the traditional von Bertalanffy model in order to compare growth rates of putative geographic stocks of southern flounder. We improved the model fitting process by adding a hierarchical Bayesian framework to allow each parameter to vary spatially or temporally as a random effect, as well as log transforming the three model parameters ( L ∞ , K , and t 0 ). Multiple comparisons of parameters showed that growth rates varied (even within states) for females, but less for males. Growth rates were also consistent through time, when long-term data were available. Since within-basin populations are thought to be genetically well-mixed, our results suggest that consistent small-scale environmental conditions (i.e., within estuaries) likely drive growth rates and should be considered when developing broader scale management plans.

Fisheries Research↗