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USGS2008

Development, Testing, and Sensitivity and Uncertainty Analyses of a Transport and Reaction Simulation Engine (TaRSE) for Spatially Distributed Modeling of Phosphorus in South Florida Peat Marsh Wetlands

Alterations to the predevelopment delivery of water and nutrients into the Everglades of southern Florida have been occurring for nearly a century. Major regional drainage projects, large-scale agricultural development, and changes to the hydrology of the Kissimmee River-Lake Okeechobee watershed have resulted in substantial phosphorus transport increases by surface waters. Excess phosphorus has accumulated in the soils of northern Everglades marshes to levels that have impaired the natural resources of the region. Regulations now limit the amount of phosphorous that enters the Everglades through an extensive network of water-control structures. This study involved the development and application of water-quality modeling components that may be applied to existing hydrologic models of southern Florida to evaluate the effects of different management scenarios. The result of this work is a spatially distributed water-quality model for phosphorus transport and cycling in wetlands. The model solves the advection-dispersion equation on an unstructured triangular mesh and incorporates a wide range of user-selectable mechanisms for phosphorus uptake and release parameters. In general, the phosphorus model contains transfers between stores; examples of stores that can be included are soil, water column (solutes), pore water, macrophytes, suspended solids (plankton), and biofilm. Examples of transfers are growth, senescence, settling, diffusion, and so forth, described with first order, second order, and Monod types of transformations. Local water depths and velocities are determined from an existing two-dimensional, overland-flow hydrologic model. The South Florida Water Management District Regional Simulation Model was used in this study. The model is applied to three case studies: intact cores of wetland soils with water, outdoor mesocosoms, and a large constructed wetland; namely, Cell 4 of Stormwater Treatment Area 1 West (STA-1W Cell 4). Different levels of complexity in the phosphorus cycling mechanisms were simulated in these case studies using different combinations of phosphorus reaction equations. Changes in water column phosphorus concentrations observed under the controlled conditions of laboratory incubations, and mesocosm studies were reproduced with model simulations. Short-term phosphorus flux rates and changes in phosphorus storages were within the range of values reported in the literature, whereas unknown rate constants were used to calibrate the model output. In STA-1W Cell 4, the dominant mechanism for phosphorus flow and transport is overland flow. Over many life cycles of the biological components, however, soils accrue and become enriched in phosphorus. Inflow total phosphorus concentrations and flow rates for the period between 1995 and 2000 were used to simulate Cell 4 phosphorus removal, outflow concentrations, and soil phosphorus enrichment over time. This full-scale application of the model successfully incorporated parameter values derived from the literature and short-term experiments, and reproduced the observed long-term outflow phosphorus concentrations and increased soil phosphorus storage within the system. A global sensitivity and uncertainty analysis of the model was performed using modern techniques such as a qualitative screening tool (Morris method) and the quantitative, variance-based, Fourier Amplitude Sensitivity Test (FAST) method. These techniques allowed an in-depth exploration of the effect of model complexity and flow velocity on model outputs. Three increasingly complex levels of possible application to southern Florida were studied corresponding to a simple soil pore-water and surface-water system (level 1), the addition of plankton (level 2), and of macrophytes (level 3). In the analysis for each complexity level, three surface-water velocities were considered that each correspond to residence times for the selected area (1-kilometer long) of 2, 10, and 20

Scientific Investigations Report↗

USGS2015

A spatial individual-based model predicting a great impact of copious sugar sources and resting sites on survival of Anopheles gambiae and malaria parasite transmission

Background Agent-based modelling (ABM) has been used to simulate mosquito life cycles and to evaluate vector control applications. However, most models lack sugar-feeding and resting behaviours or are based on mathematical equations lacking individual level randomness and spatial components of mosquito life. Here, a spatial individual-based model (IBM) incorporating sugar-feeding and resting behaviours of the malaria vector Anopheles gambiae was developed to estimate the impact of environmental sugar sources and resting sites on survival and biting behaviour. Methods A spatial IBM containing An. gambiae mosquitoes and humans, as well as the village environment of houses, sugar sources, resting sites and larval habitat sites was developed. Anopheles gambiae behaviour rules were attributed at each step of the IBM: resting, host seeking, sugar feeding and breeding. Each step represented one second of time, and each simulation was set to run for 60 days and repeated 50 times. Scenarios of different densities and spatial distributions of sugar sources and outdoor resting sites were simulated and compared. Results When the number of natural sugar sources was increased from 0 to 100 while the number of resting sites was held constant, mean daily survival rate increased from 2.5% to 85.1% for males and from 2.5% to 94.5% for females, mean human biting rate increased from 0 to 0.94 bites per human per day, and mean daily abundance increased from 1 to 477 for males and from 1 to 1,428 for females. When the number of outdoor resting sites was increased from 0 to 50 while the number of sugar sources was held constant, mean daily survival rate increased from 77.3% to 84.3% for males and from 86.7% to 93.9% for females, mean human biting rate increased from 0 to 0.52 bites per human per day, and mean daily abundance increased from 62 to 349 for males and from 257 to 1120 for females. All increases were significant (P < 0.01). Survival was greater when sugar sources were randomly distributed in the whole village compared to clustering around outdoor resting sites or houses. Conclusions Increases in densities of sugar sources or outdoor resting sites significantly increase the survival and human biting rates of An. gambiae mosquitoes. Survival of An. gambiae is more supported by random distribution of sugar sources than clustering of sugar sources around resting sites or houses. Density and spatial distribution of natural sugar sources and outdoor resting sites modulate vector populations and human biting rates, and thus malaria parasite transmission.

Malaria Journal↗

USGS2025

Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation

Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus ) and a venomous spider (golden silk orb weaver, Trichonephila clavipes ), and haplotyping humans ( Homo sapiens ) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.

Nature Ecology & Evolution↗

USGS2008

Validation of daily ring deposition in the otoliths of age-0 channel catfish

We developed and validated methods for estimating the daily age of age-0 channel catfish Ictalurus punctatus. Two clutches of channel catfish eggs were hatched in the laboratory; subsequently, one was stocked in a 186-m2 earthen nursery pond and the other in a 757-L outdoor circular tank. Before stocking, subsamples of fish were collected at swim-up and 3 d after swim-up to evaluate early ring formation. Fish were sampled from the pond and tank on eight occasions ranging from 30 to 119 d posthatch. Distinct differences in early ring formation were found between yolk sac and free-swimming larval stages. Mean ring count and known age were closely related for tank- and pond-raised fish, indicating that daily ring deposition occurred in the otoliths of age-0 channel catfish up to 119 d posthatch. The accuracy of daily age estimation was similar between tank and pond samples, and daily ring counts were considerably accurate up to 60 d posthatch. Pond-raised fish were more difficult to age than tank-raised fish, which we attributed to ring compression resulting from slower growth among pond-raised fish after 30 d. The total length of tank- and pond-raised fish was positively related to otolith size; however, the slopes of the relationships between fish length and otolith radius were different between treatments. Therefore, we could not confirm that the relationship between fish length and otolith size was directly proportional for age-0 channel catfish. We encourage researchers to use this aging technique to determine how abiotic and biotic factors influence early life history characteristics and ultimately the population dynamics of catfishes (Ictaluridae). ?? Copyright by the American Fisheries Society 2008.

North American Journal of Fisheries Management↗

USGS1996

Effects of nutrients and hydroperiod on Typha, Cladium, and Eleocharis: Implications for everglades restoration

The recent expansion of Typha domingensis ( Typha ) into areas of the Everglades previously dominated by Cladium jamaicense ( Cladium ) communities has led to competing hypotheses about the importance of nutrient concentration vs. hydroperiod in controlling the distribution of these species. In this study, experimental mixtures of Typha domingensis , Cladium jamaicense , and Eleocharis interstincta ( Eleocharis ), a member of the Cladium community, were subjected to two levels of nutrient concentration and three contrasting hydroperiods to determine how these variables might affect Typha 's ability to displace the Cladium community. Mixtures of the three species were established in outdoor tanks containing soil from the northern Everglades region where the experiment was conducted. Nutrient treatments consisted of nutrient additions to adjust ambient water concentrations to either 50 μg/L phosphorus (P) or 100 μg/L P plus nitrogen (N). The three hydroperiods were achieved by maintaining water depths within ranges observed in the northern Everglades. Maximum water depths of 15, 30, and 60 cm were established throughout the wet season (May‐November) followed by lowering to 5 cm during the dry season. Over a 2‐yr period, biomass was monitored nondestructively and aboveground material was harvested at the end of the experiment. Analysis of the biomass changes over time showed that differences between the species developed by the end of the first growing season. Typha and Eleocharis had initial growth rates substantially higher than those observed for Cladium . Typha 's growth in mixtures responded positively to both elevated nutrients (by as much as 45%) as well as to increased water depth (by as much as 60%), while Cladium and Eleocharis did not increase in response to these variables. Tissue P concentrations were found to be higher for Typha and Eleocharis than for Cladium under nearly all conditions. Net accumulation of P in Typha shoots was 2‐3 times greater than in the other species. The enhancement of Typha by elevated nutrients and increased flooding is associated with a syndrome of life history characteristics that includes rapid growth rates, high tissue concentrations of P, tall leaves, and a greater response to contrasting environmental conditions. Cladium , in contrast, showed a slow growth rate, low tissue concentrations of P, a greater capacity to resist invasion by Typha in shallow waters, and less of a growth response to contrasting environmental conditions, traits that would seem to be well suited to the nutrient‐poor, hydrologically unstable conditions natural to the Everglades. Results from this study suggest that attempts to limit the spread of Typha should consider hydrologic restoration as well as reduction in surface water nutrients.

Florida↗

USGS2018

Baseline water quality of an area undergoing shale-gas development in the Muskingum River watershed, Ohio, 2015–16

In 2015–16, the U.S. Geological Survey, in cooperation with the Muskingum Watershed Conservancy District, led a study to assess baseline (2015–16) surface-water quality in six lake drainage basins within the Muskingum River watershed that are in the early years of shale-gas development. In 2015, 9 of the 10 most active counties in Ohio for oil and gas development were wholly or partially within the Muskingum River watershed. In addition to shale gas development, the area has a history of conventional oil and gas development and coal mining. In all, 30 surface-water sites were sampled: 20 in tributaries flowing to the lakes, 4 in lakes themselves, and 6 downstream of the lakes. At each of the 30 sites, 6 samples were collected to characterize surface-water chemistry throughout a range of hydrologic conditions. The sampling generally occurred during low flows (periods of greater groundwater contribution) rather than during runoff events (periods of high stream stage). Trilinear diagrams of major ion chemistry revealed three main types of water in the study area―sulfate-dominated waters, bicarbonate-dominated waters, and waters with mixed bicarbonate and chloride anions. Most sites produced samples of bicarbonate-dominated water, and 11 sites produced samples with sulfate-type waters. Mixed bicarbonate and chloride waters were found in samples from two of the six lake drainage basins studied. The baseline (2015–16) assessment of surface-water quality in the study area indicated that few water-chemistry constituents and properties occurred at concentrations or levels that would adversely affect aquatic organisms. Chemical-specific, aquatic life use criteria were not met in only three instances: two were for total dissolved solids at sites likely impacted by coal mining in their drainage basins (hereafter referred to as “mine-impacted sites”), and one was for dissolved oxygen. Mine drainage from historical coal mining in the region likely affected the quality of about one-third of the streams sampled. To simplify interpretation of water-chemistry results, 11 sites with sulfate-type water were identified as mine-impacted sites based on water-quality criteria established by Ohio Department of Natural Resources, Division of Mineral Resources Management, and separated out for subsequent statistical analysis. Concentrations or levels of bicarbonate, boron, calcium, carbonate, total dissolved solids, fluoride, magnesium, lithium, pH, potassium, sodium, specific conductance, strontium, sulfate, and suspended sediment in water were higher (significance level of 0.05) at mine-impacted stream sites than at non-mine-impacted stream sites. An accidental release of oil- and gas-related brines could increase salinity (sodium and chloride), the concentration of total dissolved solids in shallow groundwater and streams, and specific conductance. For this study, chloride concentrations in the study area ranged from 2.12 to 76.1 milligrams per liter. Sources of chloride in water samples were evaluated using binary mixing curves and ratios of chloride to bromide. These ratios indicated that 13 samples from 3 sites in the drainage basin that contained the highest density of conventional oil and gas wells in the study, as well as 4 samples collected from other drainage basins, likely contained a component of brine. Concentrations or levels of barium, bromide, chloride, iron, lithium, manganese, and sodium were significantly higher (alpha = 0.05) in samples with a component of brine than in samples without a component of brine. Benzene, toluene, ethylbenzene and xylene (BTEX), compounds that occur naturally in crude oil, made up 24 of the 45 detections (53 percent) of volatile organic compounds in the study area. The BTEX detections were not associated with sites containing a component of brine. The only volatile organic compound detected in any of the 17 samples that contained a component of brine was acetone, detected in 3 (18 percent) of these samples and in 11 percent of samples not containing a component of brine. Considering that BTEX are gasoline hydrocarbons and that most of the detections occurred during warmer months in and around the lakes, the BTEX detections likely are associated with increases in outdoor activities such as automobile and boating traffic. Radium-226 and radium-228 were included in the list of analytes for this study because production water from shale-gas drilling can contain these naturally occurring radioactive materials. Concentrations of radium-226 exceeded background levels in only two surface-water samples. Concentrations of radium-228 exceeded background levels in one surface-water sample. A brine signature potentially indicative of oil and gas contamination was detected in samples collected at two sites that contained active or plugged waste injection wells, or both. Results from the study indicated significant differences in the median concentrations of bromide, chloride, lithium, manganese, sodium, and total dissolved nitrogen between sites with and without injection wells in their drainage areas. Median concentrations of bromide, chloride, lithium, and sodium, which are common oil- and gas-related contaminants, were higher at sites with injection wells in their drainage areas compared to sites without injection wells. Historical (1960s, 1970s, and 1980s) chloride concentrations and streamflow data at or near five of the six sampling sites downstream from each lake dam were compared to current (2015–16) values. An analysis of covariance was done to test the effects of streamflow, time (decade), and the combined effects (cross product) of streamflow and time on chloride concentrations. Those analyses indicated that streamflow was not significant in explaining the variation in chloride concentration, likely because streamflow in those locations is controlled by dam operations; therefore, association between runoff-generating events and streamflow is less direct than in unregulated streams. From the 1980s to the study period (2015–16), data for three of the five lakes indicated an increase in chloride concentrations. The comparison of historical and current (2015–16) study data from samples collected at another lake indicated that chloride concentrations increased from the 1960s to the 1970s, but concentrations in the 1970s and 2015–16 were similar even though 13 samples from this lake drainage basin were classified as having a component of brine. Median chloride concentrations for the fifth lake, however, seemed to decrease from the 1980s to 2015–16.

Ohio↗

USGS1998

Hydrology of Central Florida Lakes - A Primer

INTRODUCTION Lakes are among the most valued natural resources of central Florida. The landscape of central Florida is riddled with lakeswhen viewed from the air, it almost seems there is more water than land. Florida has more naturally formed lakes than other southeastern States, where many lakes are created by building dams across streams. The abundance of lakes on the Florida peninsula is a result of the geology and geologic history of the State. An estimated 7,800 lakes in Florida are greater than 1 acre in surface area. Of these, 35 percent are located in just four counties (fig. 1): Lake, Orange, Osceola, and Polk (Hughes, 1974b). Lakes add to the aesthetic and commercial value of the area and are used by many residents and visitors for fishing, boating, swimming, and other types of outdoor recreation. Lakes also are used for other purposes such as irrigation, flood control, water supply, and navigation. Residents and visitors commonly ask questions such as Whyare there so many lakes here?, Why is my lake drying up (or flooding)?, or Is my lake spring-fed? These questions indicate that the basic hydrology of lakes and the interaction of lakes with ground water and surface water are not well understood by the general population. Because of the importance of lakes to residents of central Florida and the many questions and misconceptions about lakes, this primer was prepared by the U.S. Geological Survey (USGS) in cooperation with the St. Johns River Water Management District and the South Florida Water Management District. The USGS has been collecting hydrologic data in central Florida since the 1920s, obtaining valuable information that has been used to better understand the hydrology of the water resources of central Florida, including lakes. In addition to data collection, as of 1994, the USGS had published 66 reports and maps on central Florida lakes (Garcia and Hoy, 1995). The main purpose of this primer is to describe the hydrology of lakes in central Florida, the interactions between lakes and ground- and surface-waters, and to describe how these interactions affect lake water levels. Included are descriptions of the basic geology and geomorphology of central Florida, origins of central Florida lakes, factors that affect lake water levels, lake water quality, and common methods of improving water quality. The geographic area discussed in this primer is approximate (fig. 1) and includes west and east-central Florida, extending from the Gulf of Mexico to the Atlantic Ocean coastlines, northward into Marion, Putnam, and Flagler Counties, and southward to Lake Okeechobee. The information presented here was obtained from the many publications available on lakes in central Florida, as well as from publications on Florida geology, hydrology, and primers on ground water, surface water, and water quality. Many publications are available that provide more detailed information on lake water quality, and this primer is not intended as an extensive treatise on that subject. The reader is referred to the reference section of this primer for sources of more detailed information on lake water quality. Lakes discussed in this report are identified in figure 2. Technical terms used in the report are shown in bold italics and are defined in the glossary. The classification of some water bodies as lakes is highly subjective. What one individual considers a lake another might consider a pond. Generally, any water- filled depression or group of depressions in the land surface could be considered a lake. Lakes differ from swamps or wetlands in the type and amount of vegetation, water depth, and some water-quality characteristics. Lakes typically have emergent vegetation along the shoreline with a large expanse of open water in the center. Swamps or wetlands, on the other hand, are characterized by a water surface interrupted by the emergence of many varieties of plant life, from saw grasses to cypress trees. Lakes may be na

Circular↗