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USGS2019

Southern sea otter (Enhydra lutris nereis) population biology at Big Sur and Monterey, California --Investigating the consequences of resource abundance and anthropogenic stressors for sea otter recovery

The range of the southern sea otter ( Enhydra lutris nereis ) spans most of the central California coast from Half Moon Bay to Gaviota. Some coastal areas within this range are heavily developed and highly impacted by humans, while other areas are wild and largely pristine. Determining the relative importance of food resource abundance, environmental conditions, and anthropogenic increases in pathogens and pollutants to population change in sea otters is critical to understanding limitations to population growth. To investigate the causal links between the sluggish population growth of sea otters in central California and factors that could be driving variation in survival and reproduction, we designed a study to compare two distinct subpopulations—one in an area of low human impact (Big Sur) and one in an area of high human impact (Monterey). Between 2008 and 2011, the U.S. Geological Survey and collaborators conducted a telemetry-based study of sea otters at these two locations. The results of this study were not consistent with the hypothesis that sea otters adjacent to human population centers (Monterey) experience higher exposure to pollutants and pathogens than those in lower impacted areas (Big Sur). In fact, based on serological analysis, female sea otters from Big Sur showed higher exposure rates to Toxoplasma gondii than did female otters from Monterey, while domoic acid exposure appeared to be similar at both sites. Gene expression (specifically transcription) analysis did not indicate any consistent differences between the two populations that would have suggested a response to pathogen or toxin exposure, although there were temporal changes in gene transcription for sea otters at Big Sur following potential exposure to run-off from wildfires that occurred during the study. Together, these metrics suggest that variation in exposure to environmental stressors occurred, but patterns were not clearly attributable to differences in human population densities or land-use patterns. When compared to Monterey, sea otters in Big Sur spent more time feeding, had a higher degree of dietary specialization, were in poorer body condition, and had lower survival rates (both pups and adults). Together, these metrics suggest that otters at Big Sur had greater nutritional stress, consistent with lower per-capita resource abundance. Overall, study results indicate that density-dependent population regulation, mediated by per-capita resource abundance, is the most significant factor currently limiting population growth in the center part of the range. Additionally, spatial and temporal variation in environmental and anthropogenic stressors also can affect sea otter health, although patterns of variation are complex and are not simply a function of proximity to human populations. We also found that exposure to environmental stressors (either natural or anthropogenic in origin) often is associated with resource limitation. Finally, our results indicate that sea otter populations are structured at relatively small spatial scales, and the processes that regulate population abundance (including density-dependent resource abundance) also occur at these smaller, more local scales.

California↗

USGS1962

Biogeochemistry of vanadium

Vanadium is known to occur in soils as vanadates of copper, zinc, lead, uranium, ferric iron, manganese, calcium, and potassium. Vanadium replaces aluminum in clays and occurs in porphyrin complexes in bituminous sediments. Small amounts of vanadium are stimulating to plants; large amounts are toxic. Ten to 20 ppm vanadium in nutrient solution is commonly harmful to plants, but larger amounts can be tolerated by specific legumes, which use vanadium in the nitrogen-fixation process. Old wood in vegetation contains more vanadium than young wood, and roots contain the greatest accumulations. Herbs are more efficient accumulators of vanadium than trees and shrubs. Allium and some species of Astragalus, Castilleja, and Chrysothamnus are shown to be accumulators of vanadium. The vanadium content of plants rooted in highly calcic soils is very low, and that of plants rooted in seleniferous soils is high. Outdoor plot experiments verify a decrease in the presence of selenium. The absorption and translocation of vanadium by several plant species was found to be in direct ratio to that of selenium. Plant species that absorb large amounts of calcium are most tolerant of high-vanadium soils as the vanadium is precipitated in the root. Vanadium occurs in all animals and is accumulated in large amounts by Ascidians and by Holothuroidians. Vanadium is probably essential to vertebrates. Vanadium has been shown to decrease dental caries in animals and children. Vanadium inhibits the biosynthesis of cholesterol in both animals and man. Seleniferous areas in the western conterminous United States may support vegetation that contains large amounts of vanadium. Many areas of this country on the other hand may be nutritionally deficient in vanadium.

Open-File Report↗

USGS1975

Relation of water level and fish availability to wood stork reproduction in the southern Everglades, Florida

The wood stork is a species of colonial wading bird in the Everglades that is most sensitive to changes in the availability of food. Previous studies have shown that the initiation and success of wood stork nesting depends on high densities of fish concentrated in ponds and other catchment basins during the dry season. The extreme dependence of the wood stork on the cyclic hydrologic regime of the southern Florida wetlands makes it an indicator of the well-being and ecological stability of the Everglades. The wood stork has declined in numbers over the last 25 years. One reason for the decline in wood stork population was the change in the hydrologic regimen of the Everglades which affected the feeding habitat and the food production. The fish on which the wood stork feeds increase in density during the dry season as water levels fall. In the Everglades marsh, densities were highest in front of the drying edge of surface water at a depth of about 0.3 m. Dry-season densities were greatest when a drought occurred the previous year. Historically wood stork nesting success was associated with high summer water levels, high rates of surface-water discharge and high rates of drying. Before the closure of the south side of Conservation Area 3 in 1962, years of successful and unsuccessful nesting were characterized by different patterns of drying. These patterns changed after 1962 and generally the predictability of successful nesting breaks down thereafter. Only two nesting years after 1962 were successful and in only one of these was the drying rate similar to years of successful nesting before 1962. Two other potentially successful years failed after 1962. This suggests that further changes in the hydrobiological relations occurred within the Everglades after 1962. Lack of successful nesting after 1962 can be attributed in large part to late colony formation and the interruption of nesting by winter rainfall. In this period (1962-72), colonies formed earlier in years of high early drying rates than in years of low early drying rates. Delay of colony formation is ultimately the result of inability to attain a suitable nutritional state since food supply is the primary factor in the initiation of nesting. Many of the complex food associations of the wood stork remain to be explained.

Florida↗

USGS2021

Global cropland-extent product at 30-m resolution (GCEP30) derived from Landsat satellite time-series data for the year 2015 using multiple machine-learning algorithms on Google Earth Engine cloud

Executive Summary Global food and water security analysis and management require precise and accurate global cropland-extent maps. Existing maps have limitations, in that they are (1) mapped using coarse-resolution remote-sensing data, resulting in the lack of precise mapping location of croplands and their accuracies; (2) derived by collecting and collating national statistical data that are often subjective, leading to substantial uncertainties in cropland-area estimates, as well as their locations; and (3) extracted from one or more classes of a land use–land cover product in which cropland classes are not the focus of mapping, leading to their mixing with other classes and creating significant errors of omission and commission. These limitations can be overcome by producing high-resolution cropland-extent maps using satellite-sensor data, such as Landsat 30-m resolution or higher. The most fundamental cropland product is the high-resolution cropland-extent map because all higher level cropland products, such as crop-watering method (that is, whether crops are irrigated or rainfed), crop types, cropping intensities, cropland fallows, crop productivity, and crop-water productivity, are dependent on a precise and accurate cropland-extent product. Given these realities, the overarching goal of this study was to produce a Landsat satellite-derived global cropland-extent product at 30-m resolution. The work, which involved a paradigm shift in how global cropland-extent maps are produced, involved the following five key steps: (1) petabyte-scale computing that involved multiyear, 8- to 16-day, time-series Landsat 30-m resolution data for the global land surface; (2) composition of analysis-ready data (ARD) cubes; (3) creation of a large global-reference data hub for machine learning; (4) use of multiple machine-learning algorithms (MLAs) by writing software and computing in the cloud; and (5) Google Earth Engine (GEE) cloud computing. The five key steps involved nine distinct phases. First, the world was segmented into 74 agroecological zones (AEZs). Second, Landsat 8- to 16-day data were used to time-composite 10-band (blue, green, red, near-infrared, short-wave infrared band 1, short-wave infrared band 2, thermal infrared, enhanced vegetation index, normalized difference water index, and normalized difference vegetation index) Landsat 30-m resolution data cubes for every 2- to 4-month time period during 3- to 4-year periods (stated as nominal-year 2015 or, simply, 2015), along with two additional 30-m resolution bands (Shuttle Radar Topography Mission elevation, and slope) in each of the 74 AEZs. Third, more than 100,000 reference-training data samples were collected using ground data (some of which were collected using a mobile application), as well as submeter- to 5-m-resolution, very high-resolution imagery sourced from other reliable sources. Fourth, reference-training data were used to create a knowledge base for separating cropland from noncropland. Fifth, MLAs such as the pixel-based supervised random forest and support-vector machines were written on the GEE using Python and JavaScript. Sixth, object-based recursive hierarchical segmentation algorithm was used, in addition to MLAs, to overcome uncertainties. Seventh, MLAs used the knowledge base to classify and separate cropland from noncropland. Eighth, accuracy assessment was conducted by generating error matrices for each of the 74 AEZs using 19,171 independent validation-data samples. Ninth, cropland areas were computed for all countries of the world and compared with United Nation’s (UN’s) Food and Agricultural Organization (FAO) and other national statistics. The outcome was a Landsat-derived global cropland-extent product at 30-m resolution (GCEP30), which has an overall accuracy of 91.7 percent. For the cropland class, producer’s accuracy was 83.4 percent, and user’s accuracy was 78.3 percent. GCEP30 calculated (using direct pixel count) the global net-cropland area (GNCA) for the year 2015 as 1.873 billion hectares (~12.6 percent of the Earth’s terrestrial area). The continental cropland distribution as a percentage of GNCA was Asia, 33 percent; Europe, 25.5 percent; Africa, 16.7 percent; North America, 14.4 percent; South America, 8.1 percent; and Australia and Oceania, 2.4 percent. The worldwide cropland areas in GCEP30 for 2015 were higher by 236 to 299 million hectares (Mha) compared to national statistics reported elsewhere for the same year (for example, in Food and Agriculture Organization’s corporate statistical database [FAOSTAT] and in the monthly irrigated and rainfed crop areas [MIRCA] database). The global cropland area reported for 2015 increased by 344 Mha (22.5 percent), compared to the year 2000. During the same period (2000–2015), the world’s population increased by 20 percent. Whereas some of these areal increases are real increases in cropland areas, others are due to the types of data, methods, and approaches used. Using the highest known resolution (compared to previous coarse-resolution global products) enabled this study to capture fragmented croplands. Coarse-resolution data compute areas on the basis of subpixels, which, for a large proportion of certain land use–land cover classes, will show only a certain percentage of the total pixel area as actual area. Subpixel areas can lead to substantial uncertainties in area computation, as determining the exact fraction of cropland areas within a coarse-resolution pixel is resource intensive and subject to errors. Other innovations in GCEP30 include reference-data hubs, machine learning, and cloud computing. Cropland areas in 214 countries, territories, departments, and regions were calculated for the year 2015 using GCEP30, on the basis of UN’s global administrative unit layers (GAUL) boundaries. The 10 leading countries in terms of cropland area (as a percentage of the GNCA) were India (9.6 percent), United States (8.95 percent), China (8.82 percent), Russia (8.32 percent), Brazil (3.42 percent), Ukraine (2.32 percent), Canada (2.29 percent), Argentina (2.05 percent), Indonesia (2 percent), and Nigeria (1.91 percent). Together, these 10 countries occupy 50 percent of the global cropland, and they have 52 percent of the global population. Their combined cropland area increased by 2 percent between 2000 and 2015, compared to the substantial increase in population of 517 million (15.5 percent). Together, India, United States, China, and Russia encompass 36 percent of the total area. In the United States and Canada, from 2000 to 2015, cropland decreased by about 2 percent, whereas their populations increased by 14 and 13 percent, respectively. The additional food requirements in these 10 countries, which are caused by increased populations, as well as increasing nutritional demands, are met by production increases in existing cropland or through virtual food trade, or both. More than 18 countries, territories, departments, or regions had 60 percent or more of their geographic area as cropland: Republic of Moldova, San Marino, and Hungary had more than 80 percent of the country’s area as cropland; Denmark, Ukraine, Ireland, and Bangladesh, 70 to 80 percent; and Uruguay, Netherlands, United Kingdom, Spain, Lithuania, Poland, Gaza Strip, Czechia, Italy, India, and Azerbaijan, 60 to 70 percent. Europe and South Asia can be considered agricultural capitals of the world, on the basis of their percentages of geographic area as cropland. United States, China, and Russia, which all have high cropland areas, are ranked second, third, and fourth in the world; India is ranked first. However, the amount of cropland as a percentage of the country’s geographic area is relatively very low for United States (18.3 percent), China (17.7 percent), and Russia (9.5 percent), whereas it is 60.5 percent for India. Most African and South American countries, territories, departments, or regions have less than 15 percent of their geographic area as cropland. China and India together house 36 percent of the world’s population; however, between 2000 and 2015, the amount of China’s cropland area fell by 18.9 percent, owing to urban expansion and the abandonment of farmlands caused by demographic changes (that is, the movement of population from villages to cities). In contrast, China’s population grew by 10 percent. The amount of India’s cropland increased by 8.5 percent, whereas its population grew by 20 percent. This study showed that, out of the 10 leading cropland countries, Ukraine, Nigeria, Russia, and Indonesia showed an 18 to 31 percent increase in cropland areas, on the basis of GCEP30 by the year 2015, compared to 2000. Nigeria’s cropland area increased by 25 percent, and its population increased by 31 percent in the same period. In these countries, food security is maintained by cropland expansion, productivity increases, and virtual food trade. Nevertheless, this trend of increasing net-cropland area and productivity will likely become difficult to maintain, owing to diminishing arable lands and plateauing of 50 years of continual yield increases, requiring policymakers to explore novel and data-supported approaches to solving future food security issues. The GCEP30 product, which can be browsed at full resolution at www.croplands.org , has been released for public download and use through U.S. Geological Survey (USGS)–National Aeronautics and Space Administration (NASA) Land Processes Distributed Active Archive Center (see https://lpdaac.usgs.gov/news/release-of-gfsad-30-meter-cropland-extent-products/ ).

Professional Paper↗

USGS2012

Bioaccumulation and toxicity of selenium during a life-cycle exposure with desert pupfish (Cyprinodon macularius)

Populations of desert pupfish ( Cyprinodon macularius ; pupfish), a federally-listed endangered species, inhabit irrigation drains in the Imperial Valley agricultural area of southern California. These drains have varying degrees of selenium (Se) contamination of water, sediment, and aquatic biota. Published Se toxicity studies suggest that these levels of Se contamination may pose risk of chronic toxicity to Se-sensitive fish, but until recently there have been no studies of the chronic toxicity of Se to desert pupfish. A life-cycle Se exposure with pupfish was conducted to estimate dietary and tissue thresholds for toxic effects of Se on all life stages. The dietary exposure was based on live oligochaete worms ( Lumbriculus variegatus ) dosed with Se by a laboratory food chain based on selenized yeast. Oligochaetes readily accumulated Se from mixtures of selenized and control yeasts. The protocol for dosing oligochaetes for pupfish feeding studies included long-term (at least 28 days) feeding of a low-ration of yeast mixtures to large batches of oligochaetes. Oligochaetes were dosed at five Se levels in a 50-percent dilution series. Pupfish were simultaneously fed Se-dosed oligochaetes and exposed to a series of Se concentrations in water (consisting of 85 percent selenate and 15 percent selenite) to produce exposures that were consistent with Se concentrations and speciation in pupfish habitats. The nutritional characteristics of oligochaete diets were consistent across the range of oligochaete Se concentrations tested. The life-cycle exposure started with laboratory-cultured juvenile pupfish that were exposed to Se through sexual maturation and reproduction (150 days; F0 exposure). The Se exposure continued with eggs, larvae, and juveniles produced by Se-exposed parents (79 days; F1 exposure). Selenium exposure (water and diets), Se bioaccumulation (whole-body and eggs), and toxicity endpoints (juvenile and adult survival and growth; egg production and hatching success, larval survival and deformities) were documented throughout the life-cycle study. Selenium concentrations in water (as much as 52 micrograms per liter [μg/L]) and diets (as much as 53 micrograms per gram [μg/g], on a dry weight basis) bracketed concentrations reported in pupfish habitats. Juvenile F0 pupfish rapidly accumulated Se and bioaccumulation models indicated that pupfish had reached more than 97 percent of maximum whole-body Se concentrations by the time they reached reproductive maturity. Adult pupfish accumulated whole-body Se concentrations that averaged about 40 percent of those in the oligochaete diets. Selenium concentrations in eggs and F1 juveniles were similar to or slightly greater than Se concentrations in F0 adults. Juvenile F0 pupfish contained selenomethionine fractions (62–71 percent of whole-body Se) greater than the average reported for wild pupfish from the Imperial Valley (53 percent). Selenium exposure had minimal effects on survival or growth of juvenile and adult pupfish. There was evidence of toxic effects on pupfish in the highest Se treatment (Se–5), including reduced growth of F0 and F1 juvenile pupfish (17–21 percent less than controls) on some sampling dates. These growth reductions did not persist to subsequent sampling dates, but reduced growth of F1 pupfish in the Se–5 treatment was associated with reduced survival (12 percent less than controls). Egg production was greatest in the controls and decreased with increasing Se exposure, reaching a minimum (51 percent less than controls) in the Se–4 treatment, but egg production was reduced by only 24 percent in the Se–5 treatment, a lesser reduction than in other Se treatments except Se–1. There was no statistically significant overall effect of Se treatment on mean pupfish egg production, reflecting large variation among replicates and among sampling dates. However, comparisons of daily mean egg production for 23 sampling dates indicated that egg production in each of 5 Se treatments was significantly less than controls on multiple (3–7) sampling dates, but no mean for any Se treatment was significantly greater than controls on any date. Significant reductions in daily egg production occurred mainly during the middle of the study and egg production increased in several Se treatments during the final 2 weeks of the study. These results suggest that pupfish egg production, although a highly variable endpoint, was adversely affected by elevated Se exposure. Neither egg hatching success nor survival of F1 larvae indicated clear evidence of Se toxicity. Egg hatching success did not differ significantly among treatments, with means ranging from 84–91 percent. The frequency of morphological deformities (primarily spinal deformities) was greater in larvae 10 days post-fertilization (dpf) from a preliminary reproduction study than in older larvae (14 dpf) from the main reproduction study. The frequency of larval deformities was generally greater in Se treatments than controls, but mean frequencies did not differ significantly among treatments. Survival of F1 larvae to 21 dpf was not reduced significantly by parental Se exposure, but the Se–5 treatment had the lowest larval survival (84 percent), and lowest combined egg hatching and larval survival (76 percent). Results of the Se treatments indicate that pupfish were insensitive to Se toxicity through most of their life cycle. Consistent toxic effects on survival and growth of juvenile and adult pupfish (defined as at least 10 percent reduction compared to controls) occurred only in treatment Se–5, which had a mean dietary Se concentration of 52 μg/g and a mean pupfish whole-body Se concentration of 27 μg/g. These apparent toxicity thresholds for growth and survival rank among the least sensitive chronic Se toxicity values reported for nonreproductive endpoints in freshwater fish. Comparisons of these thresholds to surveys of Se concentrations in the Imperial Valley suggest that risks of Se toxicity are low in pupfish habitats. The dietary threshold was about twice as high as the greatest mean Se concentrations reported in midge larvae from seven sites in the Imperial Valley. Whole-body thresholds were greater than mean whole-body Se concentrations reported for field-collected pupfish from three sites and for the sailfin molly (Poecilia latipinna), a potential bioaccumulation surrogate for pupfish, from seven sites. Reduced egg production, although highly variable, was the most sensitive response of pupfish to Se exposure. Toxic effects on egg production (reductions of 24–51 percent relative to controls) occurred in the four highest Se treatments, corresponding to reproductive toxicity thresholds of 7.3 μg/g for Se in diet, 3.4 μg/g in pupfish (whole body), and 4.4 μg/g in pupfish eggs. These thresholds are substantially lower than published Se toxicity values for reproductive effects in other freshwater fish (for example, 17–24 μg/g in eggs). Reduced egg production has not been reported as a sensitive endpoint in Se toxicity studies, although abnormal ovarian development has been reported in Se-exposed fish, and reduced egg production has been reported as a sensitive response of other Cyprinodon pupfish to other environmental stressors. Selenium concentrations in tissues of pupfish, mollies, and diet items from Imperial Valley sites frequently exceeded concentrations associated with reduced pupfish egg production in the laboratory study. Reduced egg production may limit the ability of pupfish populations to persist and recover in Se-contaminated habitats in the Imperial Valley and elsewhere in their limited range. However, these apparent risks of Se toxicity are not supported by recent surveys of desert pupfish populations in the Imperial Valley. These surveys indicated that desert pupfish made up a small, but variable, component of fish communities in Imperial Valley habitats, including sites with increased levels of Se exposure, and that pupfish distribution and population density indicated no clear relationships with Se concentrations in diets or fish tissues. Additional studies could determine the role of egg production in the maintenance and recovery of desert pupfish populations in Se-contaminated habitats.

Scientific Investigations Report↗

USGS2016

Ecological requirements for pallid sturgeon reproduction and recruitment in the Missouri River—A synthesis of science, 2005 to 2012

This report is intended to synthesize the state of the scientific understanding of pallid sturgeon ecological requirements to provide recommendations for future science directions and context for Missouri River restoration and management decisions. Recruitment of pallid sturgeon has been low to non-existent throughout its range. Emerging understanding of the genetic structure of pallid sturgeon populations sets a broad framework for species and river management decisions, including decisions about managing the future genetic diversity of the species, but also decisions about where and what type of river restoration actions will be effective for subpopulations of this highly migratory species. Adult pallid sturgeon may migrate hundreds of kilometers (km) to spawn and their progeny may disperse even greater distances downstream as drifting free embryos. As a result of their complex life history pallid sturgeon naturally exploit a wide range of habitats during their life cycles. The construction of dams and reservoirs has fragmented habitats and may have shifted Missouri River subpopulations downstream. Research has not identified one primary biological or ecological constraint that appears to limit populations of the pallid sturgeon. With the present (2013) state of knowledge many life stages and life-stage transitions cannot be ruled out as contributing to recruitment failure. Biological opinions in 2000 (and amended in 2003) presented the dominant hypotheses for recruitment failure that existed at that time. Emphasis was on the role of the flow regime, specifically spring flow pulses (“spring rises”), to condition spawning substrate and cue reproductive aggregations and migrations, and on low flows and additional slow, shallow-water area to serve as rearing habitat for age-0 to juvenile pallid sturgeon. Studies on spawning habitat dynamics have documented that habitat patches selected for spawning by fish in the Lower Missouri River (Missouri River downstream from Gavins Point Dam to the confluence with the Mississippi River) are dominantly on outside, revetted bends in the deepest, fastest, and most turbulent water. Studies in more natural habitat on the Yellowstone River have documented spawning in convergent flow in the middle of the channel on discrete patches of gravel within a sand-dominated channel, an arrangement that may be more effective in attracting aggregations of reproductive fish compared to the nearly continuous revetment on the Lower Missouri River. Pallid sturgeon spawn in the spring and early summer during periods of increasing day length. Water temperature consistently exerts a threshold effect for spawning at 16–18 °C. In addition, the role of water temperature is indicated by pauses and reversals in upstream migrations that have been associated with cold weather fronts that create a transient decrease in water temperature. From 2005 to 2012 on the Lower Missouri River, no obvious relations between flow pulses and fish movements and spawning behaviors have been apparent. However, pallid sturgeon tracking at the Upper Missouri–Yellowstone confluence indicates that in most years, most telemetered pallid sturgeon migrate out of the Missouri River and into the Yellowstone River in the June–July timeframe in association with the spring pulse. This pattern was disrupted in 2011 when a high flow pulse with warm temperatures and high turbidity emanated from the Milk River, followed by record releases from Fort Peck Dam, and 36–39 percent of the telemetered population migrated up the Upper Missouri. This result supports the hypothesis that sufficiently large flow pulses may trigger migration and aggregation but it is not clear that functional pulses are within reservoir management authorities. Notably, a pallid sturgeon free embryo was captured on the Upper Missouri River in 2011 and another single, genetically confirmed embryo was captured on the Yellowstone River in 2012. Research on free-embryo drift has indicated the potential for hundreds of miles of downstream dispersal. Lack of distance to accommodate the extended downstream dispersal period of free embryos on the Upper Missouri and Yellowstone Rivers is the predominant hypothesis for recruitment failure in the upper basin. Long drift distances in the Lower Missouri River may be responsible for shifting Lower Missouri River sub-populations further into the Middle Mississippi River. Physical understanding of drift processes indicates that mean velocities could be slowed through decreased discharges or increased channel hydraulic radius (width and topographic diversity) to reduce free-embryo dispersal distances. In addition, the probability that free embryos are transported into and retained in channel-margin habitats is theoretically amenable to channel re-engineering that would increase cross-channel secondary currents in bends or channel expansions. Considerable uncertainty persists, however, about whether extended drift of Lower Missouri River larvae is responsible for recruitment failure. If drift distance is limiting, it is important to discern whether it would be advisable to retain larvae within the Missouri River, and where along the river restoration projects should be placed to optimize survival and growth of age-0 and juvenile sturgeon. Longitudinal differences in female pallid sturgeon fecundity lend support to the hypothesis that recruitment failure may be due, in part, to fish having insufficient nutrition to produce the numbers of gametes needed for the population to grow, perhaps because of simultaneous declines in prey-fish populations and their habitats. Establishing a chain of causality from habitat decline, to prey-fish populations, to sturgeon diets, to sturgeon fecundity, and to pallid sturgeon population growth presents a considerable scientific challenge. In addition to the dominant hypotheses relating pallid sturgeon populations to changes in flow regime and channel morphology, other factors have been identified that might be sources of stress and contribute to recruitment failure. Among these are water quality and contaminants. Ambient water-quality monitoring on the Missouri River has demonstrated summer episodes when dissolved oxygen dips below 5 milligrams per liter, a threshold that may be stressful especially to age-0 and juvenile sturgeon. Documented cases of intersex in shovelnose and pallid sturgeon indicate that agricultural and municipal sources of endocrine disrupting chemicals also may have a role in pallid sturgeon recruitment failure. Scientific understanding of the ecological requirements of pallid sturgeon has increased almost exponentially in the last two decades, and efforts are now turning from understanding fundamental biology of the species to quantifying how population dynamics relate to potential management actions. Progress in developing the science needed to inform management actions on the Missouri River may benefit from continuation of monitoring of reproductive cycles, reproductive movements, growth, and survival of telemetry tagged adults, increased emphasis on focused, complementary field and laboratory studies of factors influencing early life history, implementation of studies to resolve the role of food limitations in growth, survival, and reproductive condition, and implementation of studies designed specifically to parameterize models linking management to populations.

Missouri River↗

USGS2016

Response of periphyton fatty acid composition to supplemental flows in the upper Esopus Creek, Catskill Mountains, New York

Fatty acid analysis of periphyton is an emerging tool for assessing the condition of a stream ecosystem on the basis of its water quality. The study presented in this report was designed to test the hypothesis that periphyton communities have a fatty acid profile that can detect excessive turbidity and suspended sediment. The fatty acid composition of periphyton was assessed during two seasons upstream and downstream from an underground aqueduct that provides supplemental flows, which are a potential source of turbidity and suspended sediment on the upper Esopus Creek, New York. These data were compared with measurements of periphyton standing crop, diatom community structure and integrity, and basic water-quality parameters. Periphyton standing crop and diatom community integrity indicated little evidence of impairment from the supplemental flows. The relative abundances of two physiologically important fatty acids, γ-linolenic acid (18:3ω6) and eicosapentaenoic acid (20:5ω3), were significantly lower downstream from the supplemental flows and multivariate analyses of fatty acid profiles identified significant differences between sites upstream and downstream from the supplemental flows. Individual fatty acids and summary metrics, however, were not significantly correlated with turbidity or suspended sediment. Together, these results indicate that the supplemental flows may cause some measurable effects but they do not constitute a major disturbance to the periphyton community on the upper Esopus Creek. Fatty acid analysis may have potential as a tool for monitoring changes in periphyton nutritional composition that may reflect water quality and ecosystem health but needs to be further evaluated around a more definitive source of water-quality impairment.

New York↗

USGS2018

Concentrations of nutrients at the water table beneath forage fields receiving seasonal applications of manure, Whatcom County, Washington, autumn 2011–spring 2015

The U.S. Geological Survey, in cooperation with the Whatcom Conservation District (WCD), collected groundwater-quality data for roughly 3 years (October 2011–May 2015) from near the water table beneath forage fields receiving regular seasonal applications of liquid dairy manure in Whatcom County, Washington. The work was done as part of an evaluation of WCD’s prototypical Application Risk Management (ARM) decision support system. The ARM system uses a combination of field-specific hydrology, stage of crop-growth, manure management practices, soil conditions, and precipitation forecast to evaluate the timing of manure application via a set of decision support tools (Manure Spreading Advisory, ARM Worksheet, manure application setback distances) in order to reduce the risk of contamination of surface water and groundwater. The ARM system’s effectiveness in reducing leaching of nitrate to groundwater was evaluated by monitoring nitrate concentrations in recently recharged groundwater beneath paired test plots receiving manure application scheduled using either conventional (CON) manure scheduling procedures, which utilize fixed start and end dates for manure application along with projected crop nutrient requirements or ARM manure scheduling procedures using an approach to manure application timing based on projected crop nutrient needs, field conditions, and weather forecast. Water-quality samples from the surface of the water table were collected synoptically from paired test plots (2–5 monitoring wells per test plot) at approximately monthly intervals at three different dairy field sites. Water-quality samples from near the water table were isolated from the underlying aquifer using a combination of an inflatable packer and a fine-grained sand pack encompassing the well-screen interval. Concentrations of nitrate and chloride measured at the water table beneath test plots were highly variable. Concentrations of nitrate ranged from non-detectable to 116 milligrams nitrogen per liter (mg-N/L), and chloride ranged from 1.15 to 153 mg/L. In each test plot, seasonal variations were much greater than spatial variations. Differences in nitrate concentrations in groundwater between the two treatments were inconclusive. Nitrate concentrations in groundwater at paired treatment plots (Mann Whitney, p<0.05) were significantly lower beneath the ARM treatment plot at site B, yet significantly higher beneath the ARM treatment plot at site C. Nitrate concentrations in ground water varied significantly among individual wells at each site (Kruskal-Wallis, p<0.05), indicating that leaching of nitrates from soil following manure application is spatially variable at the field scale tested regardless of manure application strategy. At all three paired test plots, average concentrations of nitrate and chloride at the water table were lowest near the end of the growing season (September) and increased rapidly with the onset of autumn rains (October–December). Under both the conventional (calendar-based) and treatment (ARM-based) manure application scheduling systems, high soil nitrate concentrations in autumn were coincident with rising groundwater levels, suggesting that nitrate and chloride were flushed from soil to groundwater by recharge from the seasonal rains. Under both treatments, concentrations of nitrate in shallow (10–25 feet) groundwater beneath forage fields receiving manure applications were greater than the nitrate drinking water standard of 10 mg-N/L in approximately 85 percent of samples. Yearly mass loading of nitrogen to the groundwater system calculated from nitrate concentrations at the water table and estimates of recharge volume ranged from 86 to 196 pounds-N per acre, which was equivalent to approximately 16–37 percent of the recommended manure application rate for projected forage production yield of 7 dry tons per acre per year. Manure nitrogen applied in the autumn, when crop nutrient needs decrease due to reduced sunlight and cooler temperatures and commensurate with ongoing mineralization of soil organic-nitrogen and increased seasonal precipitation, are more likely to exceed the immediate plant nutritional requirements and hence be flushed to groundwater than manure applications occurring near the peak of the growing season.

Washington↗

USGS1982

Algal conditions in the Caloosahatchee River (1975-79), Lake Okeechobee to Franklin Lock, Florida

Maximum numbers of suspended algae occurred in late spring and early summer, in each of the years 1975-79, in the Caloosahatchee River. Numbers exceeded 100,000 cells per milliliter at all stations sometime during the study. Concentrations decreased during late summer and autumn and were low during winter, except in January 1979 when numbers at most sites exceeded 100,000 cells per milliliter. The January 1979 bloom coincided with large discharges from Lake Okeechobee. During previous winters, discharges and algal numbers were lower. During other seasons, algal blooms occurred most frequently under low-flow or stagnant conditions. The upstream site at Moore Haven, which had the least discharge and was most stagnant, had consistently higher algal concentrations than downstream sites. Blue-green algae were dominant in the river during the summer at the upstream site throughout the year. The percentage of blue-green algae decreased downstream. Concentrations of nitrite plus nitrate nitrogen were inversely correlated with concentrations of algae and decreased to near zero during algal blooms. The low concentrations of these forms of inorganic nitrogen relative to other major nutrients probably favor blue-green algae and limit growth of other algae. Contributions by the basin tributaries to the nutritive condition of the river were small because concentrations of nutrients, algal growth potential, and algae in the tributaries were generally less than those in the river. (USGS)

Florida↗

USGS2015

Causes of mortality in green turtles from Hawaii and the insular Pacific exclusive of fibropapillomatosis

Fibropapillomatosis (FP) comprises a majority of green turtle stranding in Hawaii; however, green turtles in the Pacific are also susceptible to non-FP related causes of death. We present here necropsy findings from 230 free-ranging green turtles originating from Hawaii, the Mariana archipelago, Palmyra Atoll, American Samoa, and Johnston Atoll that died from non-FP related causes. Most turtles died from fishing-induced or boat strike trauma followed by infectious/inflammatory diseases, nutritional problems (mainly cachexia), and an array of physiologic problems. Infectious/inflammatory problems included bacterial diseases of the lungs, eyes, liver or intestines, spirorchid fluke infection, or polyarthritis of unknown origin. Likelihood of a successful diagnosis of cause of death was a function of post-mortem decomposition. Fibropapillomatosis was not seen in turtles submitted from outside Hawaii. The preponderance of anthropogenic causes of mortality offers some management opportunities to mitigate causes of death in these animals by, for example, implementing measures to decrease boating and fishing interactions.

Diseases of Aquatic Organisms↗

USGS2017

Collar temperature sensor data reveal long-term patterns in southern Beaufort Sea polar bear den distribution on pack ice and land

In response to a changing climate, many species alter habitat use. Polar bears Ursus maritimus in the southern Beaufort Sea have increasingly used land for maternal denning. To aid in detecting denning behavior, we developed an objective method to identify polar bear denning events using temperature sensor data collected by satellite-linked transmitters deployed on adult females between 1985 and 2013. We then applied this method to determine whether southern Beaufort Sea polar bears have continued to increase land denning with recent sea-ice loss and examined whether sea-ice conditions affect the distribution of dens between pack-ice and coastal substrates. Because land use in summer and autumn has also increased, we examined potential associations between summering substrate and denning substrate. Statistical process control methods applied to temperature-sensor data identified denning events with 94.5% accuracy in comparison to direct observations (n = 73) and 95.7% accuracy relative to subjective classifications based on temperature, location, and activity sensor data (n = 116). We found an increase in land-based denning during the study period. The frequency of land denning was directly related to the distance that sea ice retreated from the coast. Among females that denned, all 14 that summered on land subsequently denned there, whereas 29% of the 69 bears summering on ice denned on land. These results suggest that denning on land may continue to increase with further loss of sea ice. While the effects that den substrate have on nutrition, energetics, and reproduction are unclear, more polar bears denning onshore will likely increase human-bear interactions.

Alaska↗

USGS2022

Survival and reproduction in Arctic caribou are associated with summer forage and insect harassment

Investigators have speculated that the climate-driven “greening of the Arctic” may benefit barren-ground caribou populations, but paradoxically many populations have declined in recent years. This pattern has raised concerns about the influence of summer habitat conditions on caribou demographic rates, and how populations may be impacted in the future. The short Arctic summer provides caribou with important forage resources but is also the time they are exposed to intense harassment by insects, factors which are both being altered by longer, warmer growing seasons. To better understand the effects of summer forage and insect activity on Arctic caribou demographic rates, we investigated the influence of estimated forage biomass, digestible energy (DE), digestible nitrogen (DN), and mosquito activity on the reproductive success and survival of adult females in the Central Arctic Herd on the North Slope of Alaska. We tested the hypotheses that greater early summer DN would increase subsequent reproduction (parturition and late June calving success) while greater biomass and DE would increase adult survival (September–May), and that elevated mosquito activity would reduce both demographic rates. Because the period when abundant forage DN is limited and overlaps with the period of mosquito harassment, we also expected years with low DN and high harassment to synergistically reduce caribou reproductive success. Examining these relationships at the individual-level, using GPS-collared females, and at the population-level, using long-term monitoring data, we generally found support for our expectations. Greater early summer DN was associated with increased subsequent calving success, while greater summer biomass was associated with increased adult survival. Mosquito activity was associated with reductions in adult female parturition, late June calving success, and survival, and in years with low DN, had compounding effects on subsequent late June calving success. Our findings indicate that summer nutrition and mosquito activity collectively influence the demographic rates of Arctic caribou, and may impact the dynamics of populations in the future under changing environmental conditions.

Alaska↗

USGS2025

Spatiotemporal risk avoidance varies seasonally, relative to risk intensity, in a reestablishing predator–prey system

Predation establishes risk, which can indirectly influence prey behavior and ecology. We evaluated the influence of Mexican gray wolves ( Canis lupus baileyi ) on habitat selection and spatiotemporal predator avoidance strategies of elk ( Cervus canadensis ). We fit 866 adult female elk with GPS collars across areas of varying wolf densities within the Mexican wolf experimental population area of eastern Arizona and western New Mexico between 2019−2021. Using step-selection functions we examined relative intensity of elk use in relation to landscape attributes, estimated predator/prey diel activity, and measures of risk. Risk metrics included predicted wolf presence, habitat openness, and predicted risky places modeled from attributes of locations where wolves killed elk. Wolf activity varied across seasons and increased midday and night in fall and monsoon seasons. Relative use by elk was best explained by incorporating an interaction between diel period and predicted risky places across all seasons. Elk utilized risky places more in times of nutritional deficit associated with high energetic demands of the third trimester pregnancy and lactation and when forage quality was best, during spring and monsoon season. Particularly, use of risky places increased at less risky times in areas with more established wolf presence, suggesting use of risky places varied relative to exposure to Mexican wolves. These behaviors highlight the importance of temporal avoidance when predators and prey are highly mobile and largely overlap in space. Our research suggests temporally responding to predictable and relatively static environmental characteristics associated with encounter and kill rates may better balance energetic trade-offs than anticipating changes in wolf activity or spatially avoiding areas with higher wolf presence. Thus, elk appear to be more willing to take chances and mitigate cursorial predation risk with a more immediate, reactive approach and make proactive trade-offs during the seasons they can best increase fitness.

Arizona, New Mexico↗

USGS2016

Hydrothermal vents and methane seeps: Rethinking the sphere of influence

Although initially viewed as oases within a barren deep ocean, hydrothermal vent and methane seep communities are now recognized to interact with surrounding ecosystems on the sea floor and in the water column, and to affect global geochemical cycles. The importance of understanding these interactions is growing as the potential rises for disturbance from oil and gas extraction, seabed mining and bottom trawling. Here we synthesize current knowledge of the nature, extent and time and space scales of vent and seep interactions with background systems. We document an expanded footprint beyond the site of local venting or seepage with respect to elemental cycling and energy flux, habitat use, trophic interactions, and connectivity. Heat and energy are released, global biogeochemical and elemental cycles are modified, and particulates are transported widely in plumes. Hard and biotic substrates produced at vents and seeps are used by “benthic background” fauna for attachment substrata, shelter, and access to food via grazing or through position in the current, while particulates and fluid fluxes modify planktonic microbial communities. Chemosynthetic production provides nutrition to a host of benthic and planktonic heterotrophic background species through multiple horizontal and vertical transfer pathways assisted by flow, gamete release, animal movements, and succession, but these pathways remain poorly known. Shared species, genera and families indicate that ecological and evolutionary connectivity exists among vents, seeps, organic falls and background communities in the deep sea; the genetic linkages with inactive vents and seeps and background assemblages however, are practically unstudied. The waning of venting or seepage activity generates major transitions in space and time that create links to surrounding ecosystems, often with identifiable ecotones or successional stages. The nature of all these interactions is dependent on water depth, as well as regional oceanography and biodiversity. Many ecosystem services are associated with the interactions and transitions between chemosynthetic and background ecosystems, for example carbon cycling and sequestration, fisheries production, and a host of non-market and cultural services. The quantification of the sphere of influence of vents and seeps could be beneficial to better management of deep-sea environments in the face of growing industrialization.

Frontiers in Marine Science↗

USGS2019

Global observational needs and resources for marine biodiversity

The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models.

Frontiers in Marine Science↗

USGS2021

Gut microbiota associated with different sea lamprey (Petromyzon marinus) life stages

Sea lamprey (SL; Petromyzon marinus ), one of the oldest living vertebrates, have a complex metamorphic life cycle. Following hatching, SL transition into a microphagous, sediment burrowing larval stage, and after 2–10+ years, the larvae undergo a dramatic metamorphosis, transforming into parasitic juveniles that feed on blood and bodily fluids of fishes; adult lamprey cease feeding, spawn, and die. Since gut microbiota are critical for the overall health of all animals, we examined the microbiota associated with SLs in each life history stage. We show that there were significant differences in the gut bacterial communities associated with the larval, parasitic juvenile, and adult life stages. The transition from larval to the parasitic juvenile stage was marked with a significant shift in bacterial community structure and reduction in alpha diversity. The most abundant SL-associated phyla were Proteobacteria, Fusobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Firmicutes, with their relative abundances varying among the stages. Moreover, while larval SL were enriched with unclassified Fusobacteriaceae, unclassified Verrucomicrobiales and Cetobacterium, members of the genera with fastidious nutritional requirements, such as Streptococcus , Haemophilus , Cutibacterium , Veillonella , and Massilia , were three to four orders of magnitude greater in juveniles than in larvae. In contrast, adult SLs were enriched with Aeromonas , Iodobacter , Shewanella , and Flavobacterium . Collectively, our findings show that bacterial communities in the SL gut are dramatically different among its life stages. Understanding how these communities change over time within and among SL life stages may shed more light on the role that these gut microbes play in host growth and fitness.

Michigan, Ontario↗

USGS2021

Implications of zoonoses from hunting and use of wildlife in North American arctic and boreal biomes: Pandemic potential, monitoring, and mitigation

The COVID-19 pandemic has re-focused attention on mechanisms that lead to zoonotic disease spillover and spread. Commercial wildlife trade, and associated markets, are recognized mechanisms for zoonotic disease emergence, resulting in a growing global conversation around reducing human disease risks from spillover associated with hunting, trade, and consumption of wild animals. These discussions are especially relevant to people who rely on harvesting wildlife to meet nutritional, and cultural needs, including those in Arctic and boreal regions. Global policies around wildlife use and trade can impact food sovereignty and security, especially of Indigenous Peoples. We reviewed known zoonotic pathogens and current risks of transmission from wildlife (including fish) to humans in North American Arctic and boreal biomes, and evaluated the epidemic and pandemic potential of these zoonoses. We discuss future concerns, and consider monitoring and mitigation measures in these changing socio-ecological systems. While multiple zoonotic pathogens circulate in these systems, risks to humans are mostly limited to individual illness or local community outbreaks. These regions are relatively remote, subject to very cold temperatures, have relatively low wildlife, domestic animal, and pathogen diversity, and in many cases low density, including of humans. Hence, favorable conditions for emergence of novel diseases or major amplification of a spillover event are currently not present. The greatest risk to northern communities from pathogens of pandemic potential is via introduction with humans visiting from other areas. However, Arctic and boreal ecosystems are undergoing rapid changes through climate warming, habitat encroachment, and development; all of which can change host and pathogen relationships, thereby affecting the probability of the emergence of new (and re-emergence of old) zoonoses. Indigenous leadership and engagement in disease monitoring, prevention and response, is vital from the outset, and would increase the success of such efforts, as well as ensure the protection of Indigenous rights as outlined in the United Nations Declaration on the Rights of Indigenous Peoples. Partnering with northern communities and including Indigenous Knowledge Systems would improve the timeliness, and likelihood, of detecting emerging zoonotic risks, and contextualize risk assessments to the unique human-wildlife relationships present in northern biomes.

Frontiers in Public Health↗

USGS2022

Divergent gene expression profiles in Alaskan sea otters: An indicator of chronic domoic acid exposure?

An opportunistic investigation into ecosystem instability in Kachemak Bay (KBay), Alaska, has led us to investigate exposure to toxic algae in sea otters. We used gene expression to explore the physiological health of sea otters sampled in KBay in May 2019. We found altered levels of gene transcripts in comparison with reference sea otters from clinically normal, oil-exposed, and nutritionally challenged populations sampled over the past decade. KBay sea otters were markedly divergent from the other groups for five genes, which indicated the involvement of neurological, cardiac, immune, and detoxification systems. Further, analyses of urine and fecal samples detected domoic acid in the KBay sea otters. In combination, these results may point to chronic, low-level exposure to an algal toxin, such as domoic acid. With a warming climate, the frequency and severity of harmful algal blooms in marine environments is anticipated to increase, and novel molecular technologies to detect sublethal or chronic exposure to algal toxins will help provide an early warning of threats to the stability of populations and ecosystems.

Alaska↗