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At least 1,765 records · Page 98Linked to original sources
USGS1999

Surface-water-quality assessment of the Yakima River basin, Washington: Overview of major findings, 1987-91

Surface-water-quality conditions were assessed in the Yakima River Basin, which drains 6,155 square miles of mostly forested, range, and agricultural land in Washington. The Yakima River Basin is one of the most intensively farmed and irrigated areas in the United States, and is often referred to as the “Nation’s Fruitbowl.” Natural and anthropogenic sources of contaminants and flow regulation control water-quality conditions throughout the basin. This report summarizes the spatial and temporal distribution, sources, and implications of the dissolved oxygen, water temperature, pH, suspended sediment, nutrient, organic compound (pesticide), trace element, fecal indicator bacteria, radionuclide, and aquatic ecology data collected during the 1987–91 water years. The Yakima River descends from a water surface altitude of 2,449 feet at the foot of Keechelus Dam to 340 feet at its mouth downstream from Horn Rapids Dam near Richland. The basin can be divided into three distinct river reaches on the basis of its physical characteristics. The upper reach, which drains the Kittitas Valley, has a high gradient, with an average streambed slope of 14 feet per mile (ft/mi) over the 74 miles from the foot of Keechelus Dam (river mile [RM] 214.5) to just upstream from Umtanum. The middle reach, which drains the Mid Valley, extends a distance of 33 miles from Umtanum (RM 140.4) to just upstream from Union Gap and also has a high gradient, with an average streambed slope of 11 ft/mi. The lower reach of the Yakima River drains the Lower Valley and has an average streambed slope of 7 ft/mi over the 107 miles from Union Gap (RM 107.2) to the mouth of the Yakima River. These reaches exhibited differences in water-quality conditions related to the differences in geologic sources of contaminants and land use. Compared with the rest of the basin, the Kittitas Valley and headwaters of the Naches River Subbasin had relatively low concentrations and loads of suspended sediment, nutrients, organic compounds, and fecal indicator bacteria. There were very few failures to meet the Washington State dissolved oxygen standard or exceedances of the water temperature and pH standards in this reach. In general, these areas are considered to be areas of lessdegraded water quality in the basin. The preTertiary metamorphic and intrusive rocks of the Cle Elum and Teanaway River Subbasins, however, were found to be significant geologic sources of antimony, arsenic, chromium, copper, mercury, nickel, selenium, and zinc. As a result, the arsenic, chromium, and nickel concentrations measured in the streambed sediment of the Kittitas Valley were 13 to 74 times higher than those measured in the Lower Valley. The Mid and Lower Valleys had similar water-quality conditions, governed by the intensive agricultural and irrigation activities, highly erosive landscapes, and flow regulation. Most of the failures to meet the Washington State standards for dissolved oxygen and exceedances of the standards for water temperature and pH occurred in the Mid and Lower Valleys. Agricultural drains in the Mid and Lower Valleys were found to be significant sources of nutrients, suspended sediment, pesticides, and fecal indicator bacteria. Downstream from the irrigation diversions near Union Gap, summertime streamflow in the Yakima River was drastically reduced to only a few hundred cubic feet per second. In the lower Yakima River, agricultural return flow typically accounts for as much as 80 percent of the main stem summertime flow near the downstream terminus of the basin. Therefore, the water-quality characteristics of the lower Yakima River resemble those of the agricultural drains. The highest fecal bacteria concentrations (35,000 colonies of Escherichia coli per 100 milliliters of water) were measured in the Granger/Sunnyside area, the location of most of the livestock in the basin. The east side area of the Lower Valley (area east of the Yakima River) was the predominant source area for suspended sediment and pesticides in the basin. This area had the largest acreage of irrigated land and generally received the largest application of pesticides. Owing to the highly erosive soils of the area, the suspended sediment load from the east side in June 1989 (320 kilograms per day) was five or more times larger than from any other area, and the loads of several of the more hydrophobic organic compounds were four or more times larger. An ecological assessment of the Yakima River Basin ranked physical, chemical, and biological conditions at impaired (degraded) sites against reference sites in an effort to understand how land use changes physical and chemical site characteristics and how biota respond to these changes. For this assessment, the basin was divided into four natural ecological categories: (1) Cascades ecoregion, (2) Eastern Cascades Slopes and Foothills ecoregion, (3) Columbia Basin ecoregion, and (4) large rivers. Each of these categories has a unique combination of climate and landscape features that produces a distinctive terrestrial vegetation assemblage. In the combined Cascades and Eastern Cascades site group, which had the fewest impaired sites, the metals index was the only physical and chemical index that indicated any impairment. The moderate levels of impairment noted in the invertebrate and algal communities were not, however, associated with metals, and may have been related to the effects of logging, although the intensity of logging was not directly quantified in this study. Sites in the Columbia Basin site group were all moderately or severely impaired with the exception of the two reference sites (Umtanum Creek and Satus Creek below Dry Creek), which showed no physical, chemical, or biological impairment. Three sites were heavily affected by agriculture (Granger Drain, Moxee Drain, and Spring Creek) and were listed as severely impaired by most of the physical, chemical, and biological condition indices. Agriculture was the primary cause of the impairment of biological communities in this site group. The primary physical and chemical indicators of agricultural effects were nutrients, pesticides, dissolved solids, and substrate embeddedness, which all tended to increase with agricultural intensity. The biological effects of agriculture were manifested by a decrease in the abundance and number of native species of fish and invertebrates, a shift in algal communities to species indicative of eutrophic conditions, and higher abundances. There was also an increase in the abundance and number of nonnative fish species due to the prevalence of fish that are largely tolerant of nutrient-rich conditions. Main stem (large river) sites downstream from the city of Yakima exhibited severe impairment of fish communities associated with high levels of pesticides in fish tissues and the presence of external anomalies on fish.

Washington↗
USGS2006

Mapping existing vegetation composition and structure for the LANDFIRE Prototype Project

The Landscape Fire and Resource Management Planning Tools Prototype Project, or LANDFIRE Prototype Project, required the mapping of existing vegetation composition (cover type) and structural stages at a 30-m spatial resolution to provide baseline vegetation data for the development of wildland fuel maps and for comparison to simulated historical vegetation reference conditions to develop indices of ecological departure. For the LANDFIRE Prototype Project, research was conducted to develop a vegetation mapping methodology that could meet the following general requirements: Cover types (species composition) must be characterized at a scale suitable for subsequent mapping of wildland fuel and fire regime condition class (FRCC). The vegetation map unit classification used for mapping cover types must be based on existing national systems, such as the United States National Vegetation Classification System (NVCS; Grossman and others 1998). The alliance (a community with multiple dominant species) or association (a community with a single dominant species) levels of this standard must provide a clearly defined list of map units that can be used as a basis for mapping vegetation classes that are both scaleable and representative of suitable units for modeling historical fire regimes (see Long and others, Ch. 6 for details on the LANDFIRE vegetation map units). The mapping of existing vegetation structure must be based on the relative composition of forest, shrub, and herbaceous canopy cover and average forest, shrub, and herbaceous canopy height. Although structural stages are discrete map units describing unique combinations of canopy cover and canopy height by life form, mapping individual canopy cover and height variables as continuous variables is desired to provide additional information for mapping and modeling vegetation and flexibility for setting threshold values.

General Technical Report↗
USGS2023

Coral restoration for coastal resilience: Integrating ecology, hydrodynamics, and engineering at multiple scales

The loss of functional and accreting coral reefs reduces coastal protection and resilience for tropical coastlines. Coral restoration has potential for recovering healthy reefs that can mitigate risks from coastal hazards and increase sustainability. However, scaling up restoration to the large extent needed for coastal protection requires integrated application of principles from coastal engineering, hydrodynamics, and ecology across multiple spatial scales, as well as filling missing knowledge gaps across disciplines. This synthesis aims to identify how scientific understanding of multidisciplinary processes at interconnected scales can advance coral reef restoration. The work is placed within the context of a decision support framework to evaluate the design and effectiveness of coral restoration for coastal resilience. Successfully linking multidisciplinary science with restoration practice will ensure that future large-scale coral reef restorations maximize protection for at-risk coastal communities.

Ecosphere↗
USGS2009

Impacts of acidification on macroinvertebrate communities in streams of the western Adirondack Mountains, New York, USA

Limited stream chemistry and macroinvertebrate data indicate that acidic deposition has adversely affected benthic macroinvertebrate assemblages in numerous headwater streams of the western Adirondack Mountains of New York. No studies, however, have quantified the effects that acidic deposition and acidification may have had on resident fish and macroinvertebrate communities in streams of the region. As part of the Western Adirondack Stream Survey, water chemistry from 200 streams was sampled five times and macroinvertebrate communities were surveyed once from a subset of 36 streams in the Oswegatchie and Black River Basins during 2003-2005 and evaluated to: (a) document the effects that chronic and episodic acidification have on macroinvertebrate communities across the region, (b) define the relations between acidification and the health of affected species assemblages, and (c) assess indicators and thresholds of biological effects. Concentrations of inorganic Al in 66% of the 200 streams periodically reached concentrations toxic to acid-tolerant biota. A new acid biological assessment profile (acidBAP) index for macroinvertebrates, derived from percent mayfly richness and percent acid-tolerant taxa, was strongly correlated (R2 values range from 0.58 to 0.76) with concentrations of inorganic Al, pH, ANC, and base cation surplus (BCS). The BCS and acidBAP index helped remove confounding influences of natural organic acidity and to redefine acidification-effect thresholds and biological-impact categories. AcidBAP scores indicated that macroinvertebrate communities were moderately or severely impacted by acidification in 44-56% of 36 study streams, however, additional data from randomly selected streams is needed to accurately estimate the true percentage of streams in which macroinvertebrate communities are adversely affected in this, or other, regions. As biologically relevant measures of impacts caused by acidification, both BCS and acidBAP may be useful indicators of ecosystem effects and potential recovery at the local and regional scale.

Ecological Indicators↗
USGS2011

The fecal bacteria

The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This new volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

Book↗
USGS2009

Fire rehabilitation effectiveness: a chronosequence approach for the Great Basin

Federal land management agencies have invested heavily in seeding vegetation for emergency stabilization and rehabilitation (ES&R) of non-forested lands. ES&R projects are implemented to reduce post-fire dominance of non-native annual grasses, minimize probability of recurrent fire, quickly recover lost habitat for sensitive species, and ultimately result in plant communities with desirable characteristics including resistance to invasive species and resilience or ability to recover following disturbance. Land managers lack scientific evidence to verify whether seeding non-forested lands achieves their desired long-term ES&R objectives. The overall objective of our investigation is to determine if ES&R projects increase perennial plant cover, improve community composition, decrease invasive annual plant cover and result in a more desirable fuel structure relative to no treatment following fires while potentially providing habitat for Greater Sage-Grouse, a species of management concern. In addition, we provide the locations and baseline vegetation data for further studies relating to ES&R project impacts. We examined effects of seeding treatments (drill and broadcast) vs. no seeding on biotic and abiotic (bare ground and litter) variables for the dominant climate regimes and ecological types within the Great Basin. We attempted to determine seeding effectiveness to provide desired plant species cover while restricting non-native annual grass cover relative to post-treatment precipitation, post-treatment grazing level and time-since-seeding. Seedings were randomly sampled from all known post-fire seedings that occurred in the four-state area of Idaho, Nevada, Oregon and Utah. Sampling locations were stratified by major land resource area, precipitation, and loam-dominated soils to ensure an adequate spread of locations to provide inference of our findings to similar lands throughout the Great Basin. Nearly 100 sites were located that contained an ES&R project. Of these sites, 61 were seeded by using a drill, 27 were broadcast aerially, and 12 had a combination of both. We randomly sampled three burned and seeded, burned and unseeded, and unburned and unseeded locations in the vicinity of the fire, each within the same ecological site. We measured foliar cover of all plant functional groups (perennial or annual, shrub, grass, forb, native or introduced), biological soil crusts, and abiotic (bare soil and litter) variables using the line-point intercept protocol. Fuel loads and horizontal fuel continuity were measured. We applied linear mixed models to response variables (cover and density of plant groups) relative to the dependent variables (seeding treatments and precipitation/temperature relationships. Post-fire strengths with native perennial grasses or shrubs in mixes did not increase density or cover of these groups significantly relative to unseeded, burned areas. Seeded non-native perennial grasses and the shrub Bassia prostrata were effective in providing more cover in aerial and drill seedings. Seeded non-native perennial grass cover increased with increased annual precipitation regardless of seeding type. Seeding native shrubs, particularly Artemisia tridentata, did not significantly increase shrub cover in burned areas. Cover of undesirable non-native annual grasses was lower in drill seedings relative to unseeded areas but only at higher elevations. Seeding effectiveness after wildfire is unpredictable in drier, low elevation environments, and our findings indicate management objectives are more likely met when focusing efforts on higher elevation or higher precipitation locations where establishment of perennial grasses is more likely. On sites where potential for invasion and dominance of non-native annuals is high, such as lower and drier sites, intensive methods of restoration that include invasive plant control before seeding may be required. Where establishment of native perennial plants is the goal, managers might consider using native-only seed mixtures, because we found that the non-native perennials typically used in Great Basin restoration efforts are selected for their competitive nature and may reduce establishment of less competitive native species. Although we attempted to include information on livestock grazing history after seedings, we were unable to extract sufficient data from files to address this topic that may play an additional role in understanding native plant abundance post-fire seeding. Evaluation of drill and aerial seeding effects on fuel characteristics focused on two metrics that are standard inputs for fire behavior models, fuel load and fuel continuity. Fuel loads were evaluated separately for total fuel load biomass, and the individual components that sum to total biomass, namely herbaceous, shrub, shrub:herbaceous ratio, litter, 10-hour, and 100-hour fuel biomasses. Fuel continuity was evaluated using the following cover categories, total, annual grass, annual forb, perennial forb perennial grass, shrub, litter, vegetative interspace, and perennial interspace. Drill seeding did not affect fuel loads, except to reduce 10-hour fuels, probably due to mechanical destruction of dead and down fuels by the drill seeding equipment. Drill seeding did affect fuel continuity, specifically decreasing total plant cover by increasing perennial grass cover which suppressed annual grass and litter production resulting in a net decrease in continuity, but only at the elevations above approximately 1500m. Aerial seeding had no effect on any fuel load or fuel continuity category. For the Greater Sage-Grouse habitat study, we developed multi-scale empirical models of sage-grouse occupancy in 211 randomly located plots within a 40 million ha portion of the species’ range. We then used these models to predict sage-grouse habitat quality at 101 ES&R seeding projects. We compared conditions at restoration sites to published habitat guidelines. Sage-grouse occupancy was positively related to plot- and landscape-level dwarf sagebrush (Artemisia arbuscula, A. nova, A. tripartita) and big sagebrush steppe, and negatively associated with non-native grass and human development. The predicted probability of sage-grouse occupancy at treated plots was low on average (0.07–0.09) and was not significantly different from burned areas that had not been treated. Restoration was more often successful at higher elevation sites with low annual temperatures, high spring precipitation, and high plant diversity. No plots seeded after fire (n=313) met all overstory guidelines for breeding habitats, but approximately 50% met understory guidelines, particularly for perennial grasses. This trend was similar for summer habitat. Ninety-eight percent of treated plots did not meet winter habitat guidelines. Restoration actions in burned areas did not increase the probability of meeting most guideline criteria. The probability of meeting guidelines was influenced by a latitudinal gradient, local climate, and topography. Post-fire seeding treatments in Great Basin sagebrush shrublands generally have not created high quality habitat for sage-grouse. Understory conditions are more likely to be adequate than those of overstory, but in unfavorable climates, establishing forbs and reducing cheatgrass dominance is unlikely. Reestablishing sagebrush cover will require more than 20 years using the restoration methods of the past two decades. Given current fire frequencies and restoration capabilities, protection of landscapes containing a mix of dwarf sagebrush and big sagebrush steppe, minimal human development, and low non-native plant cover may provide the best opportunity for conservation of sage-grouse habitats. Our database of ES&R locations has used the Land Treatment Digital Library to archive data and location information regarding our study (see Pilliod and Welty 2013). This has contributed to two additional studies. One examined the potential spread of Bassia prostrata (aka Kochia prostrata; forage kochia) from ES&R project locations (Gray and Muir 2013). The second used remote sensing to determine the phenology of vegetation green-up on post-fire seeded sites (Sankey et al. 2013).

California;Idaho;Oregon;Utah↗
USGS1989

Potamocorbula amurensis discovered in San Francisco Bay

The small Asian clam, Potamocorbula amurensis , is now a major component of benthic communities in most areas of northern San Francisco Bay and some areas of South Bay. Because of its wide tolerance of salinity and other environmental variables and its high abundance in many areas, benthic ecologists believe this recent invasion may represent a major and permanent change in the bay system.

California↗
USGS2011

Development of a bioenergetics model for age-0 American shad

Bioenergetics modeling can be used as a tool to investigate the impact of non-native age-0 American shad ( Alosa sapidissima ) on reservoir and estuary food webs. The model can increase our understanding of how these fish influence lower trophic levels as well as predatory fish populations that feed on juvenile salmonids. Bioenergetics modeling can be used to investigate ecological processes, evaluate alternative research hypotheses, provide decision support, and quantitative prediction. Bioenergetics modeling has proven to be extremely useful in fisheries research (Ney et al. 1993,Chips and Wahl 2008, Petersen et al. 2008). If growth and diet parameters are known, the bioenergetics model can be used to quantify the relative amount of zooplankton or insects consumed by age-0 American shad. When linked with spatial and temporal information on fish abundance, model output can guide inferential hypothesis development to demonstrate where the greatest impacts of age-0 American shad might occur. Bioenergetics modeling is particularly useful when research questions involve multiple species and trophic levels (e.g. plankton communities). Bioenergetics models are mass-balance equations where the energy acquired from food is partitioned between maintenance costs, waste products, and growth (Winberg 1956). Specifically, the Wisconsin bioenergetics model (Hanson et al. 1997) is widely used in fisheries science. Researchers have extensively tested, reviewed, and improved on this modeling approach for over 30 years (Petersen et al. 2008). Development of a bioenergetics model for any species requires three key components: 1) determine physiological parameters for the model through laboratory experiments or incorporate data from a closely related species, 2) corroboration of the model with growth and consumption estimates from independent research, and 3) error analysis of model parameters. Wisconsin bioenergetics models have been parameterized for many of the salmonids and predatory fishes encountered in the lower Columbia River (Petersen and Ward 1999). The Wisconsin bioenergetics model has not been developed for American shad, however Limburg (1996) parameterized a simplified bioenergetics growth model for this species. A common application for the Wisconsin bioenergetics model is to estimate the consumption or growth of a fish population under different temperature and feeding scenarios (Ney 1993). One advantage of the bioenergetics approach is that consumption can be estimated without direct field measurements of predation rate (prey·predator -1 · day -1 ; Petersen and Ward 1999). Field estimates of fish consumption are time consuming and costly to determine, and estimates may show wide variance due to environmental and sampling variability. However, the consumption parameters used in a newly developed bioenergetics model must be verified with field and laboratory estimates of consumption (Ney 1993). The objective of this research was to parameterize a Wisconsin bioenergetics model for age-0 American shad using published physiological data on American shad and closely related alosine species. The American shad bioenergetics model will be used as a tool to explore various hypotheses about how age-0 American shad directly and indirectly affect Columbia River salmon through ecological interactions in lower Columbia River food webs. One over-arching focus of the larger research project was to identify potential interactions between age-0 American shad and juvenile salmonids, addressing potential outcomes through bioenergetics modeling scenarios. This report contains two bioenergetics modeling applications to demonstrate how these models can be used to address management questions and direct research effort. The first modeling application uses the American shad bioenergetics model described in this report to explore prey consumption by age-0 American shad (Chapter 1, this report). Dietary data on age-0 American shad and previously published reports on the diet of juvenile fall Chinook salmon (Rondorf et al. 1990, USGS unpublished data) suggested there might be considerable dietary overlap between these species in the lower Columbia River. The U.S. Geological Survey (USGS) was interested in using the American shad bioenergetics model to explore hypotheses concerning dietary overlap between age-0 American shad and emigrating fall Chinook salmon. The second modeling application uses the fall Chinook salmon bioenergetics model (Koehler et al. 2006) to explore the growth potential of juvenile fall Chinook salmon predating on age-0 American shad in the lower Columbia River. This modeling was based dietary information on a small number of age-0 fall Chinook salmon (n = 13) collected in John Day Reservoir in 1994 - 1996 (unpublished USGS data). Analysis of this dietary data found that these salmonids were feeding primarily on age-0 American shad (> 75% by weight).

Oregon↗
USGS2023

Taxonomic identity, biodiversity, and antecedent disturbances shape the dimensional stability of stream invertebrates

The “dimensional stability” approach measures different components of ecological stability to investigate how they are related. Yet, most empirical work has used small-scale and short-term experimental manipulations. Here, we apply this framework to a long-term observational dataset of stream macroinvertebrates sampled between the winter flooding and summer monsoon seasons. We test hypotheses that relate variation among stability metrics across different taxa, the magnitude of antecedent (monsoon) and immediate (winter) floods to stability metrics, and the relative importance of disturbance magnitude and taxonomic richness on community dimensional stability. Cluster analysis revealed four distinct stability types, and we found that the magnitude of floods during the prior monsoon was more important in influencing stability than the winter flood itself. For dimensional stability at the community level, taxonomic richness was more important than disturbance magnitude. This work demonstrates that abiotic and biotic factors determine dimensional stability in a natural ecosystem.

Limnology and Oceanography Letters↗
USGS2025

Between a rock and a hard place: Experiences of the chronic wasting disease management community

Chronic wasting disease (CWD) is a widespread and incurable cervid disease. Despite continuing investments, the logistical challenges of CWD have required wildlife managers and researchers to navigate changing priorities with conflicting public perceptions. When overcoming difficult management problems, leveraging exploratory methods may identify previously unrecognized hypotheses. In this study, we interviewed wildlife managers and researchers to describe the diverse experiences of experts in the CWD management community. Our study asked about common management strategies used, challenges experienced, and attempted to understand how decision-making in CWD management is shaped and constrained. Our study participants experienced a wide range of constraining factors, primarily related to external influences. We also identified connections between these constraints and a common concern for staff and public burnout. The results of this study provide insight on constraints limiting CWD management success and possible explanations for some commonly recognized challenges resulting from social and ecological interactions.

Journal of Society and Natural Resources↗
USGS2021

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

Microbiome↗
USGS2011

USGS research on Florida's isolated freshwater wetlands

The U.S. Geological Survey (USGS) has studied wetland hydrology and its effects on wetland health and ecology in Florida since the 1990s. USGS wetland studies in Florida and other parts of the Nation provide resource managers with tools to assess current conditions and regional trends in wetland resources. Wetland hydrologists in the USGS Florida Water Science Center (FLWSC) have completed a number of interdisciplinary studies assessing the hydrology, ecology, and water quality of wetlands. These studies have expanded the understanding of wetland hydrology, ecology, and related processes including: (1) the effects of cyclical changes in rainfall and the influence of evapotranspiration; (2) surface-water flow, infiltration, groundwater movement, and groundwater and surfacewater interactions; (3) the effects of water quality and soil type; (4) the unique biogeochemical components of wetlands required to maintain ecosystem functions; (5) the effects of land use and other human activities; (6) the influences of algae, plants, and invertebrates on environmental processes; and (7) the effects of seasonal variations in animal communities that inhabit or visit Florida wetlands and how wetland function responds to changes in the plant community.

Florida↗
USGS1999

Water-use patterns of woody species in pineland and hammock communities of South Florida

Rockland pine forests of south Florida dominated by Pinus elliottii var. densa characteristically have poor soil development in relation to neighboring hardwood hammocks. This has led to the hypothesis that Everglades hammock trees are more reliant on soil moisture derived from local precipitation whereas pineland plants must depend more on groundwater linked to broader regional hydrologic patterns. Because soil moisture sources are likely to vary more than groundwater sources, we hypothesized that hammock plants would exhibit correspondingly higher levels of dry season water stress. This was examined by measuring predawn water potentials, and by analyzing water uptake in representative hammock and pineland woody species using stable isotopes of plant water and that of potential sources during wet and dry seasons. Two species typical of each of the two communities were selected; a fifth species which was found in both communities, Lysiloma latisiliqua Benth., was also analyzed. Water content of soils in both communities decreased from wet to dry season. Consistent with our hypothesis, the change in predawn water potentials between the wet and dry season was less in pineland species than that of hammock species. Water potential changes in L. latisiliqua in both communities resembled that of hammock species more than pineland plants. Isotopic data showed that pineland species rely proportionately more on groundwater than hammock species. Nevertheless, unlike hammock species in the Florida Keys, mainland hammock species utilized a substantial amount of groundwater during the dry season.

Florida↗
USGS2011

Responses of plankton communities to the introduction of grass carp into some Georgia ponds

Net plankton community structure and numbers were studied in soft-water, acidic ponds containing aquatic macrophytes, after introduction of the herbivorous grass carp ( Ctenopharyngodon idella ). The plankton communities in ponds with grass carp consisted of significantly fewer individuals, genera, and orders than did the communities in control ponds. Expected shifts from desirable to undesirable species of plankton did not occur. These results demonstrate that plankton blooms are not an inevitable result of stocking grass carp, and support the suggestion that macrophytes may be especially significant in nutrient cycling in soft-water, acidic systems.

Georgia↗
USGS2023

Divergent community trajectories with climate change across a fine-scale gradient in snow depth

Fine-scale microclimate variation due to complex topography can shape both current vegetation distributional patterns and how vegetation responds to changing climate. Topographic heterogeneity in mountains is hypothesized to mediate responses to regional climate change at the scale of metres. For alpine vegetation especially, the interplay between changing temperatures and topographically mediated variation in snow accumulation will determine the overall impact of climate change on vegetation dynamics. We combined 30 years of co-located measurements of temperature, snow and alpine plant community composition in Colorado, USA, to investigate vegetation community trajectories across a snow depth gradient. Our analysis of long-term trends in plant community composition revealed notable directional change in the alpine vegetation with warming temperatures. Furthermore, community trajectories are divergent across the snow depth gradient, with exposed parts of the landscape that experience little snow accumulation shifting towards stress-tolerant, cold- and drought-adapted communities, while snowier areas shifted towards more warm-adapted communities. Synthesis : Our findings demonstrate that fine-scale topography can mediate both the magnitude and direction of vegetation responses to climate change. We documented notable shifts in plant community composition over a 30-year period even though alpine vegetation is known for slow dynamics that often lag behind environmental change. These results suggest that the processes driving alpine plant population and community dynamics at this site are strong and highly heterogeneous across the complex topography that is characteristic of high-elevation mountain systems.

Journal of Ecology↗
USGS2023

Inferring pathogen presence when sample misclassification and partial observation occur

Surveillance programmes are essential for detecting emerging pathogens and often rely on molecular methods to make inference about the presence of a target disease agent. However, molecular methods rarely detect target DNA perfectly. For example, molecular pathogen detection methods can result in misclassification (i.e. false positives and false negatives) or partial detection errors (i.e. detections with ‘ambiguous’, ‘uncertain’ or ‘equivocal’ results). Then, when data are to be analysed, these partial observations are either discarded or censored; this, however, disregards information that could be used to make inference about the true state of the system. There is a critical need for more direction and guidance related to how many samples are enough to declare a unit of interest ‘pathogen free’. Here, we develop a Bayesian hierarchal framework that accommodates false negative, false positive and uncertain detections to improve inference related to the occupancy of a pathogen. We apply our modelling framework to a case study of the fungal pathogen Pseudogymnoascus destructans (Pd) identified in Texas bats at the invasion front of white-nose syndrome. To improve future surveillance programmes, we provide guidance on sample sizes required to be 95% certain a target organism is absent from a site. We found that the presence of uncertain detections increased the variability of resulting posterior probability distributions of pathogen occurrence, and that our estimates of required sample size were very sensitive to prior information about pathogen occupancy, pathogen prevalence and diagnostic test specificity. In the Pd case study, we found that the posterior probability of occupancy was very low in 2018, but occupancy probability approached 1 in 2020, reflecting increasing prior probabilities of occupancy and prevalence elicited from the site manager. Our modelling framework provides the user a posterior probability distribution of pathogen occurrence, which allows for subjective interpretation by the decision-maker. To help readers apply and use the methods we developed, we provide an interactive RShiny app that generates target species occupancy estimation and sample size estimates to make these methods more accessible to the scientific community ( https://rmummah.shinyapps.io/ambigDetect_sampleSize ). This modelling framework and sample size guide may be useful for improving inferences from molecular surveillance data about emerging pathogens, non-native invasive species and endangered species where misclassifications and ambiguous detections occur.

Methods in Ecology and Evolution↗
USGS2021

New faunal records from a World Heritage Site in danger: Rennell Island, Solomon Islands

Remote oceanic islands have high potential to harbor unique fauna and flora, but opportunities to conduct in-depth biotic surveys are often limited. Furthermore, underrepresentation of existing biodiversity in the literature has the potential to detract from conservation planning and action. Between 18 and 29 October 2018, we surveyed the terrestrial vertebrates of East Rennell, a UNESCO World Heritage Site in Solomon Islands. We documented 56 species, including 15 squamates, 13 mammals, and 38 birds, and present four new vertebrate records for the island: Stephan's emerald dove ( Chalcophaps stephani ), Maluku myotis ( Myotis moluccarum ), littoral skink ( Emoia atrocostata ) and brahminy blindsnake ( Indotyphlops braminus ). East Rennell was designated a World Heritage site for its significant on-going ecological and biological processes, and importance for the study of island biogeography. The new records presented here provide evidence that continued field studies combined with DNA analysis will continue to uncover even greater endemic biodiversity. Rennell is currently experiencing major habitat destruction in parts of the island that are not under World Heritage protection, and we anticipate collateral damage will likely extend into protected areas. Our survey also underscores the incredible vertebrate biodiversity that stands to be lost unless conservation actions and local community needs are intertwined to promote beneficial outcomes on both fronts.

Pacific Science↗
USGS2007

Altered mangrove wetlands as habitat for estuarine nekton: are dredged channels and tidal creeks equivalent?

Hasty decisions are often made regarding the restoration of "altered" habitats, when in fact the ecological value of these habitats may be comparable to natural ones. To assess the "value" of altered mangrove-lined habitats for nekton, we sampled for 1 yr within three Tampa Bay wetlands. Species composition, abundance, and spatial distribution of nekton assemblages in permanent subtidal portions of natural tidal creeks and wetlands altered by construction of mosquito-control ditches and stormwater-drainage ditches were quantified through seasonal seine sampling. Results of repeated-measures analysis of variance and ordination of nekton community data suggested differences in species composition and abundance between natural and altered habitat, though not consistently among the three wetlands. In many cases, mosquito ditches were more similar in assemblage structure to tidal creeks than to stormwater ditches. In general, mosquito ditches and stormwater ditches were the most dissimilar in terms of nekton community structure. These dissimilarities were likely due to differences in design between the two types of ditches. Mosquito ditches tend to fill in over time and are thus more ephemeral features in the landscape. In contrast, stormwater ditches are a more permanent altered habitat that remain open due to periodic flushing from heavy runoff. Results indicate that environmental conditions (e.g., salinity, current velocity, vegetative structure) may provide a more useful indication of potential habitat "value" for nekton than whether the habitat has been altered. The type of ditching is therefore more important than ditching per se when judging the habitat quality of these altered channels for fishes, shrimps and crabs. Planning should entail careful consideration of environmental conditions rather than simply restoring for restoration's sake.

Florida↗