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USGS2020

Water quality and ecological risk assessment of intermittent streamflow through mining and urban areas of San Marcos River sub-basin, Mexico

Intermittent rivers are becoming more ecologically stressed worldwide. Flow cessation occurs naturally and spatiotemporally in these systems and anthropogenic activities such as wastewater discharges can have considerable impacts. Public entities mostly monitor water quality in permanent streams, leading to insufficient monitoring of intermittent streams and consequently to their potentially inadequate management.. This study analyzed spatiotemporal patterns of water quality and associated ecological risk through the quantification of physicochemical and microbiological pollutants in the intermittent river system of El Novillo and San Marcos in Northeast Mexico. Results showed that water quality varied geographically and seasonally. Based on national and international criteria, annual averages of water quality parameters analyzed suggested that streamflow in these river systems is of poor quality and poses high ecological risk to aquatic life. In the urban area, annual mean concentrations of Cd and Pb (0.14 and 0.4 mg/L) were 77- and 10-fold higher than their respective water quality criteria (<0.0018 and 0.04 mg/L). Statistically significant (q < 0.05) correlations were identified in concentrations of cyanide, Cd, Cu and Pb between wastewater seeping into the river and streamflow within the urban area. These observations highlight the unique sensitivity of intermittent urban streams to anthropogenic activities and may provide useful information to enhance current water management plans for the El Novillo-San Marcos River system for the protection of ecosystem integrity and human health.

El Novillo Canyon↗

USGS2015

Large-scale dam removal on the Elwha River, Washington, USA: river channel and floodplain geomorphic change

A substantial increase in fluvial sediment supply relative to transport capacity causes complex, large-magnitude changes in river and floodplain morphology downstream. Although sedimentary and geomorphic responses to sediment pulses are a fundamental part of landscape evolution, few opportunities exist to quantify those processes over field scales. We investigated the downstream effects of sediment released during the largest dam removal in history, on the Elwha River, Washington, USA, by measuring changes in riverbed elevation and topography, bed sediment grain size, and channel planform as two dams were removed in stages over two years. As 10.5 million t (7.1 million m 3 ) of sediment was released from two former reservoirs, downstream dispersion of a sediment wave caused widespread bed aggradation of ~ 1 m (greater where pools filled), changed the river from pool–riffle to braided morphology, and decreased the slope of the lowermost river. The newly deposited sediment, which was finer than most of the pre-dam-removal bed, formed new bars (largely pebble, granule, and sand material), prompting aggradational channel avulsion that increased the channel braiding index by almost 50%. As a result of mainstem bed aggradation, floodplain channels received flow and accumulated new sediment even during low to moderate flow conditions. The river system showed a two- to tenfold greater geomorphic response to dam removal (in terms of bed elevation change magnitude) than it had to a 40-year flood event four years before dam removal. Two years after dam removal began, as the river had started to incise through deposits of the initial sediment wave, ~ 1.2 million t of new sediment (~ 10% of the amount released from the two reservoirs) was stored along 18 river km of the mainstem channel and 25 km of floodplain channels. The Elwha River thus was able to transport most of the released sediment to the river mouth. The geomorphic alterations and changing bed sediment grain size along the Elwha River have important ecological implications, affecting aquatic habitat structure, benthic fauna, salmonid fish spawning and rearing potential, and riparian vegetation. The response of the river to dam removal represents a unique opportunity to observe and quantify fundamental geomorphic processes associated with a massive sediment influx, and also provides important lessons for future river-restoration endeavors.

Washington↗

USGS2015

Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae)

Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or ‘species group’ level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor-joining analysis reported here describes the application and confirmation of a useful tool that can accelerate identification and bioassesment of chironomid communities.

Bulletin of Entomological Research↗

USGS2016

Climate-induced glacier and snow loss imperils alpine stream insects

Climate warming is causing rapid loss of glaciers and snowpack in mountainous regions worldwide. These changes are predicted to negatively impact the habitats of many range-restricted species, particularly endemic, mountaintop species dependent on the unique thermal and hydrologic conditions found only in glacier-fed and snowmelt-driven alpine streams. Though progress has been made, existing understanding of the status, distribution, and ecology of alpine aquatic species, particularly in North America, is lacking, thereby hindering conservation and management programs. Two aquatic insects – the meltwater stonefly Lednia tumana and the glacier stonefly Zapada glacier – were recently proposed for listing under the U.S. Endangered Species Act due to climate-change-induced habitat loss. Using a large dataset (272 streams, 482 total sites) with high-resolution climate and habitat information, we describe the distribution, status, and key environmental features that limit L. tumana and Z. glacier across the northern Rocky Mountains. Lednia tumana was detected in 113 streams (175 sites) within Glacier National Park (GNP) and surrounding areas. The probability of L. tumana occurrence increased with cold stream temperatures and close proximity to glaciers and permanent snowfields. Similarly, densities of L. tumana declined with increasing distance from stream source. Zapada glacier was only detected in 10 streams (20 sites), six in GNP and four in mountain ranges up to ~600 km southwest. Our results show that both L. tumana and Z. glacier inhabit an extremely narrow distribution, restricted to short sections of cold, alpine streams often below glaciers predicted to disappear over the next two decades. Climate warming-induced glacier and snow loss clearly imperils the persistence of L. tumana and Z. glacier throughout their ranges, highlighting the role of mountaintop aquatic invertebrates as sentinels of climate change in mid-latitude regions.

Global Change Biology↗

USGS2013

Tracking animals in freshwater with electronic tags: past, present and future

Considerable technical developments over the past half century have enabled widespread application of electronic tags to the study of animals in the wild, including in freshwater environments. We review the constraints associated with freshwater telemetry and biologging and the technical developments relevant to their use. Technical constraints for tracking animals are often influenced by the characteristics of the animals being studied and the environment they inhabit. Collectively, they influence which and how technologies can be used and their relative effectiveness. Although radio telemetry has historically been the most commonly used technology in freshwater, passive integrated transponder (PIT) technology, acoustic telemetry and biologgers are becoming more popular. Most telemetry studies have focused on fish, although an increasing number have focused on other taxa, such as turtles, crustaceans and molluscs. Key technical developments for freshwater systems include: miniaturization of tags for tracking small-size life stages and species, fixed stations and coded tags for tracking large samples of animals over long distances and large temporal scales, inexpensive PIT systems that enable mass tagging to yield population- and community-level relevant sample sizes, incorporation of sensors into electronic tags, validation of tag attachment procedures with a focus on maintaining animal welfare, incorporation of different techniques (for example, genetics, stable isotopes) and peripheral technologies (for example, geographic information systems, hydroacoustics), development of novel analytical techniques, and extensive international collaboration. Innovations are still needed in tag miniaturization, data analysis and visualization, and in tracking animals over larger spatial scales (for example, pelagic areas of lakes) and in challenging environments (for example, large dynamic floodplain systems, under ice). There seems to be a particular need for adapting various global positioning system and satellite tagging approaches to freshwater. Electronic tagging provides a mechanism to collect detailed information from imperilled animals and species that have no direct economic value. Current and future advances will continue to improve our knowledge of the natural history of aquatic animals and ecological processes in freshwater ecosystems while facilitating evidence-based resource management and conservation.

Animal Biotelemetry↗

USGS2014

Wetland management and rice farming strategies to decrease methylmercury bioaccumulation and loads from the Cosumnes River Preserve, California

We evaluated mercury (Hg) concentrations in caged fish (deployed for 30 days) and water from agricultural wetland (rice fields), managed wetland, slough, and river habitats in the Cosumnes River Preserve, California. We also implemented experimental hydrological regimes on managed wetlands and post-harvest rice straw management techniques on rice fields in order to evaluate potential Best Management Practices to decrease methylmercury bioaccumulation within wetlands and loads to the Sacramento-San Joaquin River Delta. Total Hg concentrations in caged fish were twice as high in rice fields as in managed wetland, slough, or riverine habitats, including seasonal managed wetlands subjected to identical hydrological regimes. Caged fish Hg concentrations also differed among managed wetland treatments and post-harvest rice straw treatments. Specifically, Hg concentrations in caged fish decreased from inlets to outlets in seasonal managed wetlands with either a single (fall-only) or dual (fall and spring) drawdown and flood-up events, whereas Hg concentrations increased slightly from inlets to outlets in permanent managed wetlands. In rice fields, experimental post-harvest straw management did not decrease Hg concentrations in caged fish. In fact, in fields in which rice straw was chopped and either disked into the soil or baled and removed from the fields, fish Hg concentrations increased from inlets to outlets and were higher than Hg concentrations in fish from rice fields subjected to the more standard post-harvest practice of simply chopping rice straw prior to fall flood-up. Finally, aqueous methylmercury (MeHg) concentrations and export were highly variable, and seasonal trends in particular were often opposite to those of caged fish. Aqueous MeHg concentrations and loads were substantially higher in winter than in summer, whereas caged fish Hg concentrations were relatively low in winter and substantially higher in summer. Together, our results highlight the importance of habitat, seasonal processes, and wetland management practices on Hg cycling and ecological risk in aquatic ecosystems.

California↗

USGS2009

Continuous Turbidity Monitoring in the Indian Creek Watershed, Tazewell County, Virginia, 2006-08

Thousands of miles of natural gas pipelines are installed annually in the United States. These pipelines commonly cross streams, rivers, and other water bodies during pipeline construction. A major concern associated with pipelines crossing water bodies is increased sediment loading and the subsequent impact to the ecology of the aquatic system. Several studies have investigated the techniques used to install pipelines across surface-water bodies and their effect on downstream suspended-sediment concentrations. These studies frequently employ the evaluation of suspended-sediment or turbidity data that were collected using discrete sample-collection methods. No studies, however, have evaluated the utility of continuous turbidity monitoring for identifying real-time sediment input and providing a robust dataset for the evaluation of long-term changes in suspended-sediment concentration as it relates to a pipeline crossing. In 2006, the U.S. Geological Survey, in cooperation with East Tennessee Natural Gas and the U.S. Fish and Wildlife Service, began a study to monitor the effects of construction of the Jewell Ridge Lateral natural gas pipeline on turbidity conditions below pipeline crossings of Indian Creek and an unnamed tributary to Indian Creek, in Tazewell County, Virginia. The potential for increased sediment loading to Indian Creek is of major concern for watershed managers because Indian Creek is listed as one of Virginia's Threatened and Endangered Species Waters and contains critical habitat for two freshwater mussel species, purple bean (Villosa perpurpurea) and rough rabbitsfoot (Quadrula cylindrical strigillata). Additionally, Indian Creek contains the last known reproducing population of the tan riffleshell (Epioblasma florentina walkeri). Therefore, the objectives of the U.S. Geological Survey monitoring effort were to (1) develop a continuous turbidity monitoring network that attempted to measure real-time changes in suspended sediment (using turbidity as a surrogate) downstream from the pipeline crossings, and (2) provide continuous turbidity data that enable the development of a real-time turbidity-input warning system and assessment of long-term changes in turbidity conditions. Water-quality conditions were assessed using continuous water-quality monitors deployed upstream and downstream from the pipeline crossings in Indian Creek and the unnamed tributary. These paired upstream and downstream monitors were outfitted with turbidity, pH (for Indian Creek only), specific-conductance, and water-temperature sensors. Water-quality data were collected continuously (every 15 minutes) during three phases of the pipeline construction: pre-construction, during construction, and post-construction. Continuous turbidity data were evaluated at various time steps to determine whether the construction of the pipeline crossings had an effect on downstream suspended-sediment conditions in Indian Creek and the unnamed tributary. These continuous turbidity data were analyzed in real time with the aid of a turbidity-input warning system. A warning occurred when turbidity values downstream from the pipeline were 6 Formazin Nephelometric Units or 15 percent (depending on the observed range) greater than turbidity upstream from the pipeline crossing. Statistical analyses also were performed on monthly and phase-of-construction turbidity data to determine if the pipeline crossing served as a long-term source of sediment. Results of this intensive water-quality monitoring effort indicate that values of turbidity in Indian Creek increased significantly between the upstream and downstream water-quality monitors during the construction of the Jewell Ridge pipeline. The magnitude of the significant turbidity increase, however, was small (less than 2 Formazin Nephelometric Units). Patterns in the continuous turbidity data indicate that the actual pipeline crossing of Indian Creek had little influence of downstream water quality; co

Scientific Investigations Report↗

USGS2010

Use of Continuous Monitors and Autosamplers to Predict Unmeasured Water-Quality Constituents in Tributaries of the Tualatin River, Oregon

Management of water quality in streams of the United States is becoming increasingly complex as regulators seek to control aquatic pollution and ecological problems through Total Maximum Daily Load programs that target reductions in the concentrations of certain constituents. Sediment, nutrients, and bacteria, for example, are constituents that regulators target for reduction nationally and in the Tualatin River basin, Oregon. These constituents require laboratory analysis of discrete samples for definitive determinations of concentrations in streams. Recent technological advances in the nearly continuous, in situ monitoring of related water-quality parameters has fostered the use of these parameters as surrogates for the labor intensive, laboratory-analyzed constituents. Although these correlative techniques have been successful in large rivers, it was unclear whether they could be applied successfully in tributaries of the Tualatin River, primarily because these streams tend to be small, have rapid hydrologic response to rainfall and high streamflow variability, and may contain unique sources of sediment, nutrients, and bacteria. This report evaluates the feasibility of developing correlative regression models for predicting dependent variables (concentrations of total suspended solids, total phosphorus, and Escherichia coli bacteria) in two Tualatin River basin streams: one draining highly urbanized land (Fanno Creek near Durham, Oregon) and one draining rural agricultural land (Dairy Creek at Highway 8 near Hillsboro, Oregon), during 2002-04. An important difference between these two streams is their response to storm runoff; Fanno Creek has a relatively rapid response due to extensive upstream impervious areas and Dairy Creek has a relatively slow response because of the large amount of undeveloped upstream land. Four other stream sites also were evaluated, but in less detail. Potential explanatory variables included continuously monitored streamflow (discharge), stream stage, specific conductance, turbidity, and time (to account for seasonal processes). Preliminary multiple-regression models were identified using stepwise regression and Mallow's Cp, which maximizes regression correlation coefficients and accounts for the loss of additional degrees of freedom when extra explanatory variables are used. Several data scenarios were created and evaluated for each site to assess the representativeness of existing monitoring data and autosampler-derived data, and to assess the utility of the available data to develop robust predictive models. The goodness-of-fit of candidate predictive models was assessed with diagnostic statistics from validation exercises that compared predictions against a subset of the available data. The regression modeling met with mixed success. Functional model forms that have a high likelihood of success were identified for most (but not all) dependent variables at each site, but there were limitations in the available datasets, notably the lack of samples from high-flows. These limitations increase the uncertainty in the predictions of the models and suggest that the models are not yet ready for use in assessing these streams, particularly under high-flow conditions, without additional data collection and recalibration of model coefficients. Nonetheless, the results reveal opportunities to use existing resources more efficiently. Baseline conditions are well represented in the available data, and, for the most part, the models reproduced these conditions well. Future sampling might therefore focus on high flow conditions, without much loss of ability to characterize the baseline. Seasonal cycles, as represented by trigonometric functions of time, were not significant in the evaluated models, perhaps because the baseline conditions are well characterized in the datasets or because the other explanatory variables indirectly incorporate seasonal aspects. Multicollinearity among independent variabl

Scientific Investigations Report↗

USGS2016

Critical considerations for the application of environmental DNA methods to detect aquatic species

Species detection using environmental DNA (eDNA) has tremendous potential for contributing to the understanding of the ecology and conservation of aquatic species. Detecting species using eDNA methods, rather than directly sampling the organisms, can reduce impacts on sensitive species and increase the power of field surveys for rare and elusive species. The sensitivity of eDNA methods, however, requires a heightened awareness and attention to quality assurance and quality control protocols. Additionally, the interpretation of eDNA data demands careful consideration of multiple factors. As eDNA methods have grown in application, diverse approaches have been implemented to address these issues. With interest in eDNA continuing to expand, supportive guidelines for undertaking eDNA studies are greatly needed. Environmental DNA researchers from around the world have collaborated to produce this set of guidelines and considerations for implementing eDNA methods to detect aquatic macroorganisms. Critical considerations for study design include preventing contamination in the field and the laboratory, choosing appropriate sample analysis methods, validating assays, testing for sample inhibition and following minimum reporting guidelines. Critical considerations for inference include temporal and spatial processes, limits of correlation of eDNA with abundance, uncertainty of positive and negative results, and potential sources of allochthonous DNA. We present a synthesis of knowledge at this stage for application of this new and powerful detection method.

Methods in Ecology and Evolution↗

USGS2018

Use of remote sensing to detect and predict aquatic nuisance vegetation growth in coastal Louisiana: Summary of findings

On an annual basis, federal and state agencies are responsible for mapping and removing large expanses of aquatic nuisance vegetation from navigable waterways. This study set out to achieve four primary objectives: (1) utilize recent advancements in remote sensing techniques to classify the extent and distribution of aquatic vegetation in coastal ecosystems using satellite imagery, (2) assess primary aquatic vegetation growth and management efforts in coastal Louisiana, (3) statistically identify the ecological drivers that promote growth and infestation of aquatic nuisance vegetation, and (4) develop numerical models and a spatial tool to predict the probability of occurrence and growth of aquatic vegetation given ecological drivers. Moderate spatial resolution multispectral satellite imagery were used in conjunction with environmental variables from available data streams to generate regression models that predict aquatic vegetation occurrence in the eastern coastal region of south Louisiana. Geospatial tools were developed to execute the model logic using recent environmental conditions, thereby predicting aquatic vegetation occurrence and producing classified maps for end users. These products provide more efficient and enhanced capabilities for management of aquatic nuisance vegetation.

Louisiana↗

USGS2018

Modeling water quality in the Anthropocene: Directions for the next-generation aquatic ecosystem models

“Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.

Current Opinion in Environmental Sustainability↗

USGS2017

2010-2015 Juvenile fish ecology in the Nisqually River Delta and Nisqually Reach Aquatic Reserve

The return of tidal inundation to over 750 acres of the U. S. Fish and Wildlife Service Billy Frank Jr. Nisqually National Wildlife Refuge (NNWR) in fall of 2009 was the crowning moment in the effort to protect and restore the Nisqually Delta. The Nisqually NWR project complemented three earlier restoration projects completed by the Nisqually Indian Tribe (Tribe) on tribal property to restore over 900 acres of the estuary, representing the largest estuary restoration project in the Pacific Northwest and one of the most significant advances to date towards the recovery of Puget Sound (USFWS 2005). In 2011 the Washington Department of Natural Resources (WADNR established the over 14000 acre Nisqually Reach Aquatic Reserve (Reserve), complementing the protection and restoration successes in the Nisqually Delta. The Reserve includes all state-owned aquatic lands around Anderson, Ketron and Eagle islands and part of McNeil Island (Figure 1, WDNR 2011). The Reserve also includes a diverse assemblage of nearshore and offshore habitats important to resident and migratory fish including federal endangered species act listed fish like Chinook salmon (Oncorynchus tshawytscha) and steelhead (O. mykiss). Studies in the Nisqually Estuary (Ellings and Hodgson 2007, David et al. 2014, Ellings et al. 2016) and South Puget Sound (Duffy 2003) have summarized fish use of the area. However, the fish ecology of the reserve had not been systematically surveyed. The Tribe, U.S. Geological Survey (USGS), NNWR, Nisqually River Foundation (NRF), and others are currently conducting a multi-year, interdisciplinary, hypothesis-based research and monitoring study investigating the impact of delta restoration on estuarine processes, habitat structures, and functions. Our interdisciplinary monitoring framework enables us to link key estuarine processes with habitat development and biological response at multiple scales across the restored footprint, reference marshes, and throughout the Nisqually Reach. Key research components include hydrology and sediment regime, channel and marsh topography and development, vegetation colonization, and invertebrate, bird, and fish abundance, habitat use, and foraging ecology. After the Reserve was established, the WDNR and the research partnership led by the Tribe expanded the existing delta fish ecology assessment to include sampling stations throughout the Reserve. The results of the Reserve fish ecology assessment provide a unique regional analysis of fish ecology from the Nisqually River to McNeil Island.

Salmon Recovery Program Technical Report↗

USGS2003

Covariance of bacterioplankton composition and environmental variables in a temperate delta system

We examined seasonal and spatial variation in bacterioplankton composition in the Sacramento-San Joaquin River Delta (CA) using terminal restriction fragment length polymorphism (T-RFLP) analysis. Cloned 16S rRNA genes from this system were used for putative identification of taxa dominating the T-RFLP profiles. Both cloning and T-RFLP analysis indicated that Actinobacteria , Verrucomicrobia , Cytophaga-Flavobacterium and Proteobacteria were the most abundant bacterioplankton groups in the Delta. Despite the broad variety of sampled habitats (deep water channels, lakes, marshes, agricultural drains, freshwater and brackish areas), and the spatial and temporal differences in hydrology, temperature and water chemistry among the sampling campaigns, T-RFLP electropherograms from all samples were similar, indicating that the same bacterioplankton phylotypes dominated in the various habitats of the Delta throughout the year. However, principal component analysis (PCA) and partial least-squares regression (PLS) of T-RFLP profiles revealed consistent grouping of samples on a seasonal, but not a spatial, basis. b- Proteobacteria related to Ralstonia , Actinobacteria related to Microthrix , and b- Proteobacteria identical to the environmental Clone LD12 had the highest relative abundance in summer/fall T-RFLP profiles and were associated with low river flow, high pH, and a number of optical and chemical characteristics of dissolved organic carbon (DOC) indicative of an increased proportion of phytoplankton-produced organic material as opposed to allochthonous, terrestrially derived organic material. On the other hand, Geobacter -related b- Proteobacteria showed a relative increase in abundance in T-RFLP analysis during winter/spring, and probably were washed out from watershed soils or sediment. Various phylotypes associated with the same phylogenetic division, based on tentative identification of T-RFLP fragments, exhibited diverse seasonal patterns, suggesting that ecological roles of Delta bacterioplankton were partitioned at the genus or species level.

Aquatic Microbial Ecology↗

USGS2021

Testing a generalizable machine learning workflow for aquatic invasive species on Rainbow Trout (Oncorhynchus mykiss) in northwest Montana

Biological invasions are accelerating worldwide, causing major ecological and economic impacts in aquatic ecosystems. The urgent decision-making needs of invasive species managers can be better met by the integration of biodiversity big data with large-domain models and data-driven products. Remotely sensed data products can be combined with existing invasive species occurrence data via machine learning models to provide the proactive spatial risk analysis necessary for implementing coordinated and agile management paradigms across large scales. We present a workflow that generates rapid spatial risk assessments on aquatic invasive species using occurrence data, spatially explicit environmental data, and an ensemble approach to species distribution modeling using five machine learning algorithms. For proof of concept and validation, we tested this workflow using extensive spatial and temporal hybridization and occurrence data from a well-studied, ongoing, and climate-driven species invasion in the upper Flathead River system in northwestern Montana, USA. Rainbow Trout (RBT; Oncorhynchus mykiss), an introduced species in the Flathead River basin, compete and readily hybridize with native Westslope Cutthroat Trout (WCT; O. clarkii lewisii), and the spread of RBT individuals and their alleles has been tracked for decades. We used remotely sensed and other geospatial data as key environmental predictors for projecting resultant habitat suitability to geographic space. The ensemble modeling technique yielded high accuracy predictions relative to 30-fold cross-validated datasets (87% 30-fold cross-validated accuracy score). Both top predictors and model performance relative to these predictors matched current understanding of the drivers of RBT invasion and habitat suitability, indicating that temperature is a major factor influencing the spread of invasive RBT and hybridization with native WCT. The congruence between more time-consuming modeling approaches and our rapid machine-learning approach suggest that this workflow could be applied more broadly to provide data-driven management information for early detection of potential invaders.

Alberta, British Columbia, Montana↗

USGS2021

Microbial ecology of coral-dominated reefs in the Federated States of Micronesia

Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km 2 . On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features.

Aquatic Microbial Ecology↗

USGS2014

Ecological risks of shale oil and gas development to wildlife, aquatic resources and their habitats

Technological advances in hydraulic fracturing and horizontal drilling have led to the exploration and exploitation of shale oil and gas both nationally and internationally. Extensive development of shale resources has occurred within the United States over the past decade, yet full build out is not expected to occur for years. Moreover, countries across the globe have large shale resources and are beginning to explore extraction of these resources. Extraction of shale resources is a multistep process that includes site identification, well pad and infrastructure development, well drilling, high-volume hydraulic fracturing and production; each with its own propensity to affect associated ecosystems. Some potential effects, for example from well pad, road and pipeline development, will likely be similar to other anthropogenic activities like conventional gas drilling, land clearing, exurban and agricultural development and surface mining (e.g., habitat fragmentation and sedimentation). Therefore, we can use the large body of literature available on the ecological effects of these activities to estimate potential effects from shale development on nearby ecosystems. However, other effects, such as accidental release of wastewaters, are novel to the shale gas extraction process making it harder to predict potential outcomes. Here, we review current knowledge of the effects of high-volume hydraulic fracturing coupled with horizontal drilling on terrestrial and aquatic ecosystems in the contiguous United States, an area that includes 20 shale plays many of which have experienced extensive development over the past decade. We conclude that species and habitats most at risk are ones where there is an extensive overlap between a species range or habitat type and one of the shale plays (leading to high vulnerability) coupled with intrinsic characteristics such as limited range, small population size, specialized habitat requirements, and high sensitivity to disturbance. Examples include core forest habitat and forest specialists, sagebrush habitat and specialists, vernal pond inhabitants and stream biota. We suggest five general areas of research and monitoring that could aid in development of effective guidelines and policies to minimize negative impacts and protect vulnerable species and ecosystems: (1) spatial analyses, (2) species-based modeling, (3) vulnerability assessments, (4) ecoregional assessments, and (5) threshold and toxicity evaluations.

Environmental Science & Technology↗

USGS2016

Hydrologic exchange flows and their ecological consequences in river corridors

The actively flowing waters of streams and rivers remain in close contact with surrounding off-channel and subsurface environments. These hydrologic linkages between relatively fast flowing channel waters, with more slowly flowing waters off-channel and in the subsurface, are collectively referred to as hydrologic exchange flows (HEFs). HEFs include surface exchange with a channel’s marginal areas and subsurface flow through the streambed (hyporheic flow), as well as storm-driven bank storage and overbank flows onto floodplains. HEFs are important, not only for storing water and attenuating flood peaks, but also for their role in influencing water conservation, water quality improvement, and related outcomes for ecological values and services of aquatic ecosystems. Biogeochemical opportunities for chemical transformations are increased by HEFs as a result of the prolonged contact between flowing waters and geochemically and microbially active surfaces of sediments and vegetation. Chemical processing is intensified and water quality is often improved by removal of excess nutrients, metals, and organic contaminants from flowing waters. HEFs also are important regulators of organic matter decomposition, nutrient recycling, and stream metabolism that helps establish a balanced and resilient aquatic food web. The shallow and protected storage zones associated with HEFs support nursery and feeding areas for aquatic organisms that sustain aquatic biological diversity. Understanding of these varied roles for HEFs has been driven by the related disciplines of stream ecology, fluvial geomorphology, surface-water hydraulics, and groundwater hydrology. A current research emphasis is on the role that HEFs play in altered flow regimes, including restoration to achieve diverse goals, such as expanding aquatic habitats and managing dissolved and suspended river loads to reduce over-fertilization of coastal waters and offset wetland loss. New integrative concepts and models are emerging (eg, hydrologic connectivity) that emphasize HEF functions in river corridors over a wide range of spatial and temporal scales.

Book chapter↗

USGS1998

Successful water quality monitoring: The right combination of intent, measurement, interpretation, and a cooperating ecosystem

Water quality monitoring is invaluable to ensure compliance with regulations, detect trends or patterns, and advance ecological understanding. However, monitoring typically measures only a few characteristics in a small fraction of a large and complex system, and thus the information contained in monitoring data depends upon which features of the ecosystem are actually captured by the measurements. Difficulties arise when these data contain something other than intended, but this can be minimized if the purpose of the sampling is clear, and the sampling design, measurements, and data interpretations are all compatible with this purpose. The monitoring program and data interpretation must also be properly matched to the structure and functioning of the system. Obtaining this match is sometimes an iterative process that demands a close link between research and monitoring. This paper focuses on water quality monitoring that is intended to track trends in aquatic resources and advance ecological understanding. It includes examples from three monitoring programs and a simulation exercise that illustrate problems that arise when the information content of monitoring data differs from expectation. The examples show (1) how inconsistencies among, or lack of information about, the basic elements of a monitoring program (intent, design, measurement, interpretation, and the monitored system) can produce a systematic difference (bias) between monitoring measurements and sampling intent or interpretation, and (2) that bias is not just a statistical consideration, but an insidious problem that can undermine the scientific integrity of a monitoring program. Some general suggestions are provided and hopefully these examples will help those engaged in water quality monitoring to enhance and protect the value of their monitoring investment.

Lake and Reservoir Management↗