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USGS2014

Population trends of smallmouth bass in the upper Colorado River basin with an evaluation of removal effects

Smallmouth bass Micropterus dolomieu were rare in the upper Colorado River basin until the early 1990’s when their abundance dramatically increased in the Yampa River sub-basin. Increased abundance was due primarily to colonization from Elkhead Reservoir, which was rapidly drawn down twice, first to make improvements to the dam (1992) and a second time for reservoir expansion (2005), and allowed escapement of resident bass to the river through an unscreened outlet. Elkhead Reservoir is located on Elkhead Creek, a tributary of the Yampa River. The rapid Elkhead Reservoir drawdown in 1992 was followed by a period of drought years with low, early runoff in the Yampa River sub-basin that benefitted smallmouth bass reproduction. This combination of factors allowed smallmouth bass to establish a self-sustaining population in the Yampa River. Subsequently, successful recruitment allowed smallmouth bass to disperse upstream and downstream in the Yampa River and eventually move into the downstream Green River. Smallmouth bass were also likely introduced, by unknown means, into the upper Colorado River and have since dispersed in this sub-basin. The rapid increase of smallmouth bass in the upper Colorado River basin overlapped with significant reductions in native fish populations in some locations. The threat to these native fishes initiated intensive mechanical removal of smallmouth bass by the Upper Colorado River Endangered Fish Recovery Program. In general, three factors explain fluctuating patterns in smallmouth bass density in the upper Colorado River basin in the last decade: reductions due to electrofishing removal, bass recovery after exploitation due to recruitment and immigration, and changes due to environmental factors not related to electrofishing and other management actions. Our analyses indicated that smallmouth bass densities were substantially reduced in most years by 7 electrofishing removal efforts. Less often, but dramatically in some cases, environmental effects were also responsible for significant declines in smallmouth bass densities in some reaches. Abundant year classes of young smallmouth bass produced in low flow and warm years such as 2007 have potential to overwhelm removal efforts, and the year class persists for one or more years. Nonetheless, it appears that increased electrofishing removal efforts from 2007 to 2011 resulted in sustained reductions in density of smallmouth bass sub-adults and adults throughout the upper basin despite environmental conditions that favored smallmouth bass reproduction in some years (e.g. 2007 and 2009), subsequent recruitment into sub-adult and adult age classes, and movement of smallmouth bass which previously (prior to increases in electrofishing removal efforts) allowed densities to recover in some reaches. We recommend that removal efforts continue in most areas of the upper basin but that the Recovery Program consider allocating effort based on population trends and suspected areas of highest smallmouth bass reproduction. For instance, reproduction, recruitment, and movement of smallmouth bass allowed densities to recover in some reaches, particularly Little Yampa Canyon. Smallmouth bass population recovery implies that areas such as Little Yampa Canyon itself or adjacent reaches (especially upstream), may provide important habitat for age-0 production. We recommend continued assessment of smallmouth bass populations in reaches where reproduction or age-1 nurseries are suspected, such as Little Yampa Canyon and the adjacent upstream reach. It may also be necessary to expand monitoring to areas surrounding suspected sources of smallmouth bass reproduction and increase electrofishing removal effort in these reaches.

Colorado, Utah↗

USGS2006

Comprehensive water quality of the Boulder Creek Watershed, Colorado, during high-flow and low-flow conditions, 2000

Executive Summary The Boulder Creek Watershed, Colorado, is 1160 square kilometers in area and ranges in elevation from 1480 to 4120 meters above sea level. Streamflow originates primarily as snowmelt near the Continental Divide, and thus discharge varies seasonally and annually (Chapter 1). Most of the water in Boulder Creek is diverted for domestic, agricultural, and industrial use. Some diverted water is returned to the creek as wastewater effluent and by ditch returns, and additional water enters as groundwater and by transbasin diversions. These diversions and returns lead to complex temporal and spatial variations in discharge. The variations in discharge, along with natural factors such as geology and climate, and anthropogenic factors such as wastewater treatment, agriculture, mining, and urbanization, can affect water chemistry. As with many watersheds in the American West, dependable water quality and sufficient water supply are issues facing local water managers and users. Detailed water-quality and sediment sampling allows the identification of sources and sinks of chemical constituents and an understanding of the processes at work in a river system. This study, the most comprehensive water-quality analysis performed for Boulder Creek to date, was a cooperative effort of the U.S. Geological Survey (USGS) and the city of Boulder. Geographic information systems and modeling programs were used to delineate watershed boundaries, land cover, and geology (Chapter 2). During high-flow (June 2000) and low-flow (October 2000) conditions, researchers evaluated 226 water-quality variables, including basic water-quality indicators (Chapter 3), major ions and trace elements (Chapter 4), wastewater-derived organic compounds (Chapter 5), and pesticides (Chapter 6). Discharge (Chapter 1) and bed-sediment particle size and mineralogy (Chapter 7) were also evaluated. This cooperative study was facilitated by the Boulder Area Sustainability Information Network (BASIN), which provides public access to environmental information about the Boulder Creek Watershed on a website, www.basin.org. In addition to the USGS and city of Boulder data, researchers at the Institute of Arctic and Alpine Research at the University of Colorado provided water chemistry data for the headwaters of North Boulder Creek, upstream of the reach of the USGS/city of Boulder sampling sites (Chapter 8). Snowmelt produces high flows in Boulder Creek in late spring to early summer (Chapter 1). Because precipitation falling in the headwaters is very dilute (specific conductance about 5 microsiemens per centimeter), most chemical constituents are present in lower concentrations during high flows (Chapters 3, 4, 5, 6, and 8). However, concentrations of some constituents, such as total suspended solids (Chapter 3) and organic carbon (Chapter 5), increase during the spring snowmelt flush. The upper basin, which consists of alpine, subalpine, montane, and foothills regions west of the mouth of Boulder Canyon, is underlain by Precambrian igneous and metamorphic rocks (Chapter 1). Major dissolved inorganic constituents in headwater sites were found to be enriched by factors of 10 to 20 relative to precipitation; this is consistent with minor weathering of the local crystalline bedrock (Chapter 4). Some anthropogenic input is observed in the headwaters; precipitation introduces nitrogen derived from fossil fuel combustion and agricultural activities (Chapter 8). The lower basin, which consists of the plains region east of the mouth of Boulder Canyon, is underlain by Mesozoic sedimentary rock and Quaternary alluvium, and has substantially more anthropogenic sources. Concentrations of most dissolved inorganic constituents increased in the lower basin. Differentiation between natural and anthropogenic sources of some dissolved constituents is difficult because both sources contribute to the water composition in this region. The increase of most major constituents (bicarbonate, calcium, chloride, magnesium, sodium, and sulfate) is consistent with weathering of the underlying sedimentary bedrock (Chapter 4). It is likely that anthropogenic loading of constituents in this reach occurs during storm events. Fecal coliform concentrations were variable and in some cases exceeded state standards, primarily during low-flow conditions (Chapter 3). Effluent from Boulder’s 75th Street Wastewater Treatment Plant (WWTP) has a substantial impact on the water chemistry of lower Boulder Creek. The WWTP increases the concentrations of nutrients such as nitrogen and phosphorus (Chapter 3), major ions and trace metals (Chapter 4), and organic carbon (Chapter 5) in Boulder Creek. The effluent contained a spike in gadolinium, a rare earth element that is ingested for magnetic resonance imaging as a contrasting agent and then excreted to the urban wastewater system. The effluent also contained trace organic compounds such as surfactants, pharmaceuticals, hormones (Chapter 5), and pesticides (Chapter 6), which also were detected at downstream Boulder Creek sites. Water chemistry of Boulder Creek downstream of the WWTP is largely controlled by the degree of dilution of the wastewater effluent, which varies depending on the baseflow of Boulder Creek, the volume of wastewater effluent, and depletion by agricultural diversions. Coal Creek, a tributary of Boulder Creek, contains wastewater effluent from four additional WWTPs, and increases the load of many constituents in Boulder Creek. In addition to the impact from wastewater effluent, lower Boulder Creek is affected by agricultural land use. Eleven of 84 analyzed pesticides were detected in Boulder Creek or its inflows, primarily in the eastern section of the watershed (Chapter 6). This collaborative study provides an in-depth evaluation of the hydrology, water chemistry, and sediment mineralogy of North Boulder Creek, Middle Boulder Creek, Boulder Creek, and major inflows. The detailed sampling and analysis in this report provide a baseline for future reference, as well as information on the effect of land use and geology on water chemistry.

Colorado↗

USGS2022

Local environment and individuals’ beliefs: The dynamics shaping public support for sustainability policy in an agricultural landscape

Agricultural landscapes are the bleeding-edge in the advancement of sustainability and climate change adaptation. Our study focuses on how individual support for sustainability policy is shaped in coupled natural and human systems. We present an agent-based model in which a cultural decision-rule quantifies the probability that a stakeholder decides to support an easement policy for a region in the Central Great Plains, USA. Our model defines a cultural threshold used to assess how culturally meaningful the policy is for each stakeholder. The individual cultural threshold is estimated using the value-belief-norm framework and is modified by perceived changes in the environment. Results demonstrated that few stakeholders support the policy in the average cultural setting (8.9%). However, enough stakeholders would support the policy under a lower cultural threshold (40.7%). Our results indicate that sustainability policies do not need to be cheap if they are culturally meaningful.

Kansas↗

USGS2018

Urban growth and landscape connectivity threats assessment at Saguaro National Park, Arizona, USA

Urban and exurban expansion results in habitat and biodiversity loss globally. We hypothesize that a coupled-model approach could connect urban planning for future cities with landscape ecology to consider wildland habitat connectivity. Our work combines urban growth simulations with models of wildlife corridors to examine how species will be impacted by development to test this hypothesis. We leverage a land use change model (SLEUTH) with structural and functional landscape-connectivity modeling techniques to ascertain the spatial extent and locations of connectivity related threats to a national park in southern Arizona, USA, and describe how protected areas might be impacted by urban expansion. Results of projected growth significantly altered structural connectivity (80%) when compared to current (baseline) corridor conditions. Moreover, projected growth impacted functional connectivity differently amongst species, indicating resilience of some species and near-complete displacement of others. We propose that implementing a geospatial-design-based model will allow for a better understanding of the impacts management decisions have on wildlife populations. The application provides the potential to understand both human and environmental impacts of land-system dynamics, critical for long-term sustainability.

Arizona↗

USGS2008

Availability, sustainability, and suitability of ground water, Rogers Mesa, Delta County, Colorado: Types of analyses and data for use in subdivision water-supply reports

The population of Delta County, Colorado, like that in much of the Western United States, is forecast to increase substantially in the next few decades. A substantial portion of the increased population likely will reside in rural subdivisions and use residential wells for domestic water supplies. In Colorado, a subdivision developer is required to submit a water-supply plan through the county for approval by the Colorado Division of Water Resources. If the water supply is to be provided by wells, the water-supply plan must include a water-supply report. The water-supply report demonstrates the availability, sustainability, and suitability of the water supply for the proposed subdivision. During 2006, the U.S. Geological Survey, in cooperation with Delta County, Colorado, began a study to develop criteria that the Delta County Land Use Department can use to evaluate water-supply reports for proposed subdivisions. A table was prepared that lists the types of analyses and data that may be needed in a water-supply report for a water-supply plan that proposes the use of ground water. A preliminary analysis of the availability, sustainability, and suitability of the ground-water resources of Rogers Mesa, Delta County, Colorado, was prepared for a hypothetical subdivision to demonstrate hydrologic analyses and data that may be needed for water-supply reports for proposed subdivisions. Rogers Mesa is a 12-square-mile upland mesa located along the north side of the North Fork Gunnison River about 15 miles east of Delta, Colorado. The principal land use on Rogers Mesa is irrigated agriculture, with about 5,651 acres of irrigated cropland, grass pasture, and orchards. The principal source of irrigation water is surface water diverted from the North Fork Gunnison River and Leroux Creek. The estimated area of platted subdivisions on or partially on Rogers Mesa in 2007 was about 4,792 acres of which about 2,756 acres was irrigated land in 2000. The principal aquifer on Rogers Mesa consists of alluvial-fan deposits that overlie shale and, locally, sandstone. Maps of the base of the aquifer, the water table, and the saturated thickness of the aquifer were prepared from data from the well files of the Colorado Division of Water Resources. The base of the aquifer generally is topographically higher than the valleys of the North Fork Gunnison River and Leroux Creek, and direct hydraulic connection of the aquifer to North Fork Gunnison River and Leroux Creek is limited. The aquifer is recharged primarily by infiltration of surface water diverted for irrigation. Ground water discharges to seeps and springs and through slope deposits at the boundaries of the aquifer. Data from the well files also were used to estimate the specific capacity of wells and to estimate the transmissivity and hydraulic conductivity of the aquifer. A water budget was used to estimate recharge to and discharge from the aquifer. Although storage within the aquifer likely varies seasonally and from year to year, it was assumed that there were no long-term changes in ground-water storage. Estimated average annual recharge to and discharge from the aquifer during November 1998 through October 2006 were about 30,767 acre-feet per year. Although sufficient ground water is available on Rogers Mesa for additional domestic water supplies, conversion of irrigated land to residential land use likely would reduce recharge to the aquifer, affecting the sustainability of ground-water supplies on Rogers Mesa. Stream-depletion analyses indicate that the ground water in the aquifer likely would be considered tributary ground water and additional uses of ground water to supply new subdivisions likely would require implementation of augmentation plans. Although sufficient ground water is available on Rogers Mesa for additional domestic water supplies, conversion of irrigated land to residential land use likely would reduce recharge to the aquifer, affecting the sustainability of ground-water supplies on Rogers Mesa. Stream-depletion analyses indicate that the ground water in the aquifer likely would be considered tributary ground water and additional uses of ground water to supply new subdivisions likely would require implementation of augmentation plans. Although the dissolved solids and dissolved sulfate concentrations in ground water from Rogers Mesa aquifer commonly exceeded the U.S. Environmental Protection Agency Secondary Maximum Contaminant Levels for drinking-water supplies, the quality of ground water from the aquifer generally is suitable for residential use. Concentrations of total nitrogen (nitrite plus nitrate, as nitrogen) in ground water ranged from 0.38 to 3.2 milligrams per liter and were less than the State of Colorado maximum contaminant level of 10 milligrams per liter. Concentrations of selenium from seeps and springs at the boundaries of the aquifer commonly exceeded 50 micrograms per liter, the State of Colorado maximum contaminant level for drinking-water supplies. This preliminary evaluation of ground-water supplies on Rogers Mesa could be improved with the collection of additional data including: additional mapping of hydrogeologic features; more accurate locations and altitudes of wells; accurate estimates of water-budget components; measurements of ground-water levels; and collection and analyses of ground-water samples. The use of numerical models of ground-water flow could improve evaluations of the potential effects of changes in land and water use on the water budget, aquifer storage, stream depletion, and well interference.

Colorado↗

USGS2018

Determinants of Pseudogymnoascus destructans within bat hibernacula: Implications for surveillance and management of white-nose syndrome

Fungal diseases are an emerging global problem affecting human health, food security and biodiversity. Ability of many fungal pathogens to persist within environmental reservoirs can increase extinction risks for host species and presents challenges for disease control. Understanding factors that regulate pathogen spread and persistence in these reservoirs is critical for effective disease management. White-nose syndrome (WNS) is a disease of hibernating bats caused by Pseudogymnoascus destructans ( Pd ), a fungus that establishes persistent environmental reservoirs within bat hibernacula, which contribute to seasonal disease transmission dynamics in bats. However, host and environmental factors influencing distribution of Pd within these reservoirs are unknown. We used model selection on longitudinally collected field data to test multiple hypotheses describing presence–absence and abundance of Pd in environmental substrates and on bats within hibernacula at different stages of WNS. First detection of Pd in the environment lagged up to 1 year after first detection on bats within that hibernaculum. Once detected, the probability of detecting Pd within environmental samples from a hibernaculum increased over time and was higher in sediment compared to wall surfaces. Temperature had marginal effects on the distribution of Pd . For bats, prevalence and abundance of Pd were highest on Myotis lucifugus and on bats with visible signs of WNS. Synthesis and applications . Our results indicate that distribution of Pseudogymnoascus destructans ( Pd ) within a hibernaculum is driven primarily by bats with delayed establishment of environmental reservoirs. Thus, collection of samples from Myotis lucifugus , or from sediment if bats cannot be sampled, should be prioritized to improve detection probabilities for Pd surveillance. Long-term persistence of Pd in sediment suggests that disease management for white-nose syndrome should address risks of sustained transmission from environmental reservoirs.

Journal of Applied Ecology↗

USGS2006

Modeling wetland plant community response to assess water-level regulation scenarios in the Lake Ontario-St. Lawrence River basin

The International Joint Commission has recently completed a five-year study (2000-2005) to review the operation of structures controlling the flows and levels of the Lake Ontario - St. Lawrence River system. In addition to addressing the multitude of stakeholder interests, the regulation plan review also considers environmental sustainability and integrity of wetlands and various ecosystem components. The present paper outlines the general approach, scientific methodology and applied management considerations of studies quantifying the relationships between hydrology and wetland plant assemblages (% occurrence, surface area) in Lake Ontario and the Upper and Lower St. Lawrence River. Although similar study designs were used across the study region, different methodologies were required that were specifically adapted to suit the important regional differences between the lake and river systems, range in water-level variations, and confounding factors (geomorphic types, exposure, sediment characteristics, downstream gradient of water quality, origin of water masses in the Lower River). Performance indicators (metrics), such as total area of wetland in meadow marsh vegetation type, that link wetland response to water levels will be used to assess the effects of different regulation plans under current and future (climate change) water-supply scenarios.

Environmental Monitoring and Assessment↗

USGS2025

Non-native prey availability and over-compensatory density dependence drive population dynamics of a native fish predator

Understanding the factors that regulate population dynamics is crucial for conserving imperiled species. Bull trout ( Salvelinus confluentus ), a piscivorous salmonid and one of North America's most threatened cold-water species, has declined significantly due to habitat loss, overfishing, invasive species, and climate change. While recovery efforts have primarily targeted these threats, the role of prey availability in influencing bull trout population dynamics under multiple stressors remains poorly understood. Using a stage-based integrated population model, we quantified the effects of non-native prey availability (kokanee; Oncorhynchus nerka ), angling pressure, climatic variation, and density-dependent processes on bull trout population dynamics in Lake Koocanusa, a transboundary reservoir and river system (United States and Canada), over a 40-year period (1980–2023). Our results show that bull trout populations are regulated by density-dependent processes, including over-compensation in sub-adult recruitment and reduced adult survival at high densities. Increased kokanee biomass and restricted harvest significantly enhanced bull trout survival and abundance, whereas reduced water availability had a limited negative effect on sub-adult production. Model simulations indicate that as kokanee biomass availability increases, the number of bull trout that can be sustainably harvested also increases. In fact, a modest annual fishery (300 individuals) can be sustained, especially under moderate to high kokanee biomass conditions. These results underscore the importance of prey availability, including non-native species, in supporting bull trout populations. Effective management of threatened apex fish predators like bull trout requires addressing the complex interplay between environmental threats, prey dynamics, and density-dependent mechanisms across all life stages.

British Columbia, Montana↗

USGS2020

Vulnerability of resource-users in Louisiana’s oyster fishery to environmental hazards

Knowledge of vulnerability provides the foundation for developing actions that minimize impacts on people while maximizing the sustainability of ecosystem goods and services. As a result, it is becoming increasingly important to determine how resource-dependent people are vulnerable to environmental hazards. This is particularly true in coastal Louisiana where the current era of rapid land loss has the potential to undermine oyster fisheries. Yet, little is known about how such environmental change might differentially impact resource-users and stakeholders. We examined social components of vulnerability to environmental hazards using indicators of susceptibility and adaptive capacity within the oyster fishery of Terrebonne Parish, Louisiana. Specifically, we used structured interviews to compare three resource-user roles: oyster fishers, oyster fishers/lease owners, and oyster lease owners only. Results indicated that oyster fishers/lease owners were highly dependent and thus susceptible to changes in the fishery due to high levels of occupational identity. The same people, however, were the most adaptable to change, which was reflected in their willingness to learn about new practices and evolve over time; higher susceptibility in this group was offset by an increased ability to adapt, cope, and respond to changes in the environment. In contrast to these findings, oyster fishers that did not own any portion of a lease or business in which they operated were bad at coping with change and frequently held negative or fatalistic views on financial planning. These attributes made them the most vulnerable to environmental hazards. Overall, the most vulnerable participants in the Terrebonne Parish oyster fishery were those with low to moderate levels of personal and financial buffers and trust, coupled with high occupational identity and a low motivation to change. Local policy actions that target these attributes are likely to be the best entry points to reducing vulnerability of stakeholders to hazards.

Louisianna↗

USGS2009

Application of the Hydroecological Integrity Assessment Process for Missouri Streams

Natural flow regime concepts and theories have established the justification for maintaining or restoring the range of natural hydrologic variability so that physiochemical processes, native biodiversity, and the evolutionary potential of aquatic and riparian assemblages can be sustained. A synthesis of recent research advances in hydroecology, coupled with stream classification using hydroecologically relevant indices, has produced the Hydroecological Integrity Assessment Process (HIP). HIP consists of (1) a regional classification of streams into hydrologic stream types based on flow data from long-term gaging-station records for relatively unmodified streams, (2) an identification of stream-type specific indices that address 11 subcomponents of the flow regime, (3) an ability to establish environmental flow standards, (4) an evaluation of hydrologic alteration, and (5) a capacity to conduct alternative analyses. The process starts with the identification of a hydrologic baseline (reference condition) for selected locations, uses flow data from a stream-gage network, and proceeds to classify streams into hydrologic stream types. Concurrently, the analysis identifies a set of non-redundant and ecologically relevant hydrologic indices for 11 subcomponents of flow for each stream type. Furthermore, regional hydrologic models for synthesizing flow conditions across a region and the development of flow-ecology response relations for each stream type can be added to further enhance the process. The application of HIP to Missouri streams identified five stream types ((1) intermittent, (2) perennial runoff-flashy, (3) perennial runoff-moderate baseflow, (4) perennial groundwater-stable, and (5) perennial groundwater-super stable). Two Missouri-specific computer software programs were developed: (1) a Missouri Hydrologic Assessment Tool (MOHAT) which is used to establish a hydrologic baseline, provide options for setting environmental flow standards, and compare past and proposed hydrologic alterations; and (2) a Missouri Stream Classification Tool (MOSCT) designed for placing previously unclassified streams into one of the five pre-defined stream types.

Open-File Report↗

USGS2009

Sustaining visitor use in protected areas: Future opportunities in recreation ecology research based on the USA experience

Recreation ecology, the study of environmental consequences of outdoor recreation activities and their effective management, is a relatively new field of scientific study having emerged over the last 50 years. During this time, numerous studies have improved our understanding of how use-related, environmental and managerial factors affect ecological conditions and processes. Most studies have focused on vegetation and soil responses to recreation-related trampling on trails and recreation sites using indicators such as percent vegetation cover and exposed mineral soil. This applied approach has and will continue to yield important information for land managers. However, for the field to advance, more attention needs to be given to other ecosystem attributes and to the larger aspects of environmental conservation occurring at landscape scales. This article is an effort at initiating a dialog on needed advances in the field. We begin by reviewing broadly generalizable knowledge of recreation ecology, to separate what is known from research gaps. Then, based on the authors’ perspective of research in the USA and North America, several research directions are suggested as essential for continued progress in this field including theoretical development, broadening scale, integration with other disciplines, and examination of synergistic effects.

Environmental Management↗

USGS2025

Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix

Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis -dominated blooms, despite the increasing prevalence of filamentous genera ( Aphanizomenon and Planktothrix ). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis , Snowella , and Aphanizomenon had the broadest range of cyanotoxin synthetase genes ( mcy E, cyr J, ana F and sxt A). Microcystis blooms correlated with increased Roseomonas , while Planktothrix co-occurred with Flavobacterium – both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen – ( ure B, gln A, nar B, and nar HZ) and phosphorus-cycling genes ( pho BHPR and ppk 1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon . These findings suggest that Aphanizomenon -dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.

Frontiers in Microbiology↗

USGS2022

Ecological and socioeconomic factors associated with the human burden of environmentally mediated pathogens: A global analysis

Background Billions of people living in poverty are at risk of environmentally mediated infectious diseases—that is, pathogens with environmental reservoirs that affect disease persistence and control and where environmental control of pathogens can reduce human risk. The complex ecology of these diseases creates a global health problem not easily solved with medical treatment alone. Methods We quantified the current global disease burden caused by environmentally mediated infectious diseases and used a structural equation model to explore environmental and socioeconomic factors associated with the human burden of environmentally mediated pathogens across all countries. Findings We found that around 80% (455 of 560) of WHO-tracked pathogen species known to infect humans are environmentally mediated, causing about 40% (129 488 of 359 341 disability-adjusted life years) of contemporary infectious disease burden (global loss of 130 million years of healthy life annually). The majority of this environmentally mediated disease burden occurs in tropical countries, and the poorest countries carry the highest burdens across all latitudes. We found weak associations between disease burden and biodiversity or agricultural land use at the global scale. In contrast, the proportion of people with rural poor livelihoods in a country was a strong proximate indicator of environmentally mediated infectious disease burden. Political stability and wealth were associated with improved sanitation, better health care, and lower proportions of rural poverty, indirectly resulting in lower burdens of environmentally mediated infections. Rarely, environmentally mediated pathogens can evolve into global pandemics (eg, HIV, COVID-19) affecting even the wealthiest communities. Interpretation The high and uneven burden of environmentally mediated infections highlights the need for innovative social and ecological interventions to complement biomedical advances in the pursuit of global health and sustainability goals. Funding Bill & Melinda Gates Foundation, National Institutes of Health, National Science Foundation, Alfred P. Sloan Foundation, National Institute for Mathematical and Biological Synthesis, Stanford University, and the US Defense Advanced Research Projects Agency.

The Lancet Planetary Health↗

USGS2017

Submersed aquatic vegetation in Chesapeake Bay: Sentinel species in a changing world

Chesapeake Bay has undergone profound changes since European settlement. Increases in human and livestock populations, associated changes in land use, increases in nutrient loadings, shoreline armoring, and depletion of fish stocks have altered the important habitats within the Bay. Submersed aquatic vegetation (SAV) is a critical foundational habitat and provides numerous benefits and services to society. In Chesapeake Bay, SAV species are also indicators of environmental change because of their sensitivity to water quality and shoreline development. As such, SAV has been deeply integrated into regional regulations and annual assessments of management outcomes, restoration efforts, the scientific literature, and popular media coverage. Even so, SAV in Chesapeake Bay faces many historical and emerging challenges. The future of Chesapeake Bay is indicated by and contingent on the success of SAV. Its persistence will require continued action, coupled with new practices, to promote a healthy and sustainable ecosystem.

Chesapeake Bay↗

USGS2021

Microbial and viral indicators of pathogens and human health risks from recreational exposure to waters impaired by fecal contamination

Fecal indicator bacteria (FIB) (e.g., fecal coliforms, Escherichia coli , and enterococci) have been used for decades to monitor for and protect the public from waterborne pathogens from fecal contamination. However, FIB may not perform well at predicting the presence of waterborne pathogens or human health outcomes from recreational exposure to fecal-contaminated surface waters. Numerous factors can influence the relationship between FIB and pathogens or human health outcomes, including the source(s) of contamination, the type of pathogen(s) present, differences in the survival and behavior of FIB and pathogens in the wastewater conveyance and treatment process, and varying environmental conditions. As a result, different indicators, such as source-specific microbial source tracking (MST) markers and viral fecal indicators, have been used as possible surrogates to better approximate pathogen abundance and human health risks in recreational waters. The performance of these alternative indicators has been mixed, with some promise of viral indicators better approximating viral pathogens than bacterial fecal indicators, and FIB generally more closely associated with bacterial and protozoal pathogen presence than human MST markers. Many of the assays to detect and quantify fecal indicators and pathogens are polymerase chain reaction-based assays, which detect and quantify nucleic acid [deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)] sequences specific to a target of interest. Recent advances in DNA and RNA sequencing technologies may push the field toward metabarcoding approaches, where multiple targets can be detected and quantified simultaneously. Metabarcoding is currently more applicable to bacterial and protozoal assessments than viral assessments based on a lack of universal metabarcoding markers for viruses. Innovative technologies, such as biosensors and nanotechnologies, may provide more sensitive and accurate tools to detect and quantify pathogens. When a specific pathogen is of concern for a recreational water body, a practical approach in estimating the likelihood of human health outcomes is the application of quantitative microbial risk assessments (QMRAs). Quantitative microbial risk assessments can be used to model the likelihood of pathogen-specific human health outcomes from recreational exposure as a function of a surrogate indicator. Inputs for QMRAs include the ratio between the indicator to be monitored and the pathogen of interest, the concentration of the indicator, the amount of water ingested, and the likelihood of the health outcome based on the estimated amount of pathogen consumed. There are numerous unknowns about the behavior and survival of fecal indicators and pathogens in environmental waters. Developing accurate models to predict pathogen concentrations from fecal indicators in recreational waters will require a better understanding of these unknowns. Current methods and technologies for detecting and quantifying fecal indicators and pathogens are limited due to the rare and patchy nature of pathogens. Technological advances may help improve sensitivity for detecting and quantifying pathogens.

Journal of Sustainable Water in the Built Environm↗

USGS2000

An evaluation of restoration efforts in fishless lakes stocked with exotic trout

Detrimental effects of introduced fishes on native amphibian populations have prompted removal of introduced cutthroat (Oncorhynchus clarki), rainbow (Oncorhynchus mykiss), and brook trout (Salvelinus fontinalis) from naturally fishless lakes at Mt. Rainier National Park, Washington (U.S.A.). Using paleolimnological indicators (diatoms, invertebrates, and sediment characteristics) in eight 480-year-old sediment cores from eight lakes, we (1) derived estimates of baseline environmental conditions and natural variation, (2) assessed the effects of stocking naturally fishless lakes, and (3) determined whether lakes returned to predisturbance conditions after fish removal (restoration). Diatom floras were relatively stable between 315 and 90 years before present in all lakes; we used this time period to define lake-specific "baseline" conditions. Dissimilarity analyses of diatoms revealed sustained, dramatic changes in diatom floras that occurred approximately 80 years ago (when fish were introduced) in four of five stocked lakes, whereas the diatom floras in two unstocked lakes had not changed significantly in the last 315 years. Diatoms were not preserved in an eighth lake. State changes also occurred in two lakes over 200 years before European settlement of the Pacific Northwest. Preserved invertebrate densities fluctuated dramatically over time in all cores, providing a poor reference for assessing the effects of fishes. Nevertheless, fish-invertebrate interactions have been demonstrated in other paleolimnological studies and may be useful for lower-elevation or more productive lakes. Because diatom communities have not returned to predisturbance assemblages in restored lakes, even 20-30 years after fish removal, we conclude that Mt. Rainier lakes were not successfully restored by the removal of fishes.

Conservation Biology↗

USGS2016

Chesapeake Bay fish–osprey ( Pandion haliaetus ) food chain: Evaluation of contaminant exposure and genetic damage

From 2011 to 2013, a large-scale ecotoxicological study was conducted in several Chesapeake Bay (USA) tributaries (Susquehanna River and flats, the Back, Baltimore Harbor/Patapsco Rivers, Anacostia/ middle Potomac, Elizabeth and James Rivers) and Poplar Island as a mid-Bay reference site. Osprey ( Pandion haliaetus ) diet and the transfer of contaminants from fish to osprey eggs were evaluated. The most bioaccumulative compounds (biomagnification factor > 5) included p,p′ -dichlorodiphenyldichloroethylene (DDE), total polychlorinated biphenyls (PCBs), total polybrominated diphenyl ethers (PBDEs), and bromodiphenyl ether (BDE) congeners 47, 99, 100, and 154. This analysis suggested that alternative brominated flame retardants and other compounds (methoxytriclosan) are not appreciably biomagnifying. A multivariate analysis of similarity indicated that major differences in patterns among study sites were driven by PCB congeners 105, 128, 156, 170/190, and 189, and PBDE congeners 99 and 209. An integrative redundancy analysis showed that osprey eggs from Baltimore Harbor/Patapsco River and the Elizabeth River had high residues of PCBs and p,p ′-DDE, with PBDEs making a substantial contribution to overall halogenated contamination on the Susquehanna and Anacostia/middle Potomac Rivers. The redundancy analysis also suggested a potential relation between PBDE residues in osprey eggs and oxidative DNA damage in nestling blood samples. The results also indicate that there is no longer a discernible relation between halogenated contaminants in osprey eggs and their reproductive success in Chesapeake Bay. Osprey populations are thriving in much of the Chesapeake, with productivity rates exceeding those required to sustain a stable population.

Chesapeake Bay↗

USGS2025

Multi-species telemetry quantifies current and future efficacy of a remote marine protected area

Large-scale marine protected areas (LSMPAs; > 1000 km 2 ) provide important refuge for large mobile species, but most do not encompass species' ranges. To better understand current and future LSMPA value, we concurrently tracked nine species (seabirds, cetaceans, pelagic fishes, manta rays, reef sharks) at Palmyra Atoll and Kingman Reef (PKMPA) in the U.S. Pacific Islands Heritage Marine National Monument. PKMPA and the U.S. Exclusive Economic Zone encompassed 39% and 54% of species movements ( n = 83; tracking duration range: 0.5–350 days), respectively. Species distribution models indicated 73% of PKMPA contained highly suitable habitat. Under two projected future scenarios (SSP 1–2.6, “Sustainability”; SSP 3–7.0, “Rocky Road”), strong sea surface temperature gradients initially could cause abrupt oceanic change resulting in predicted habitat loss in 2040–2050, followed by an equilibrium response and regained habitat by 2090–2100. Current and future suitable habitats were available adjacent to PKMPA, suggesting that increased MPA size could enhance protection. Our three-tiered approach combining animal tracking with publicly available remote sensing data and future projected environmental scenarios could be used to design, study, and monitor protected areas throughout the world. Holistic approaches that encompass diverse species and habitat use can enhance assessments of protected area designs. Animal telemetry and remote sensing may be helpful for ascertaining the extent to which other MPAs protect large mobile species in the future.

Kingman Reef, Palmyra Atoll, U.S. Pacific Islands ↗