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USGS2012

Weathering processes in the Rio Icacos and Rio Mameyes watersheds in Eastern Puerto Rico: Chapter I in Water quality and landscape processes of four watersheds in eastern Puerto Rico

Streams draining watersheds of the two dominant lithologies (quartz diorite and volcaniclastic rock) in the Luquillo Experimental Forest of eastern Puerto Rico have very high fluxes of bedrock weathering products. The Río Blanco quartz diorite in the Icacos watershed and the Fajardo volcaniclastic rocks in the Mameyes watershed have some of the fastest documented rates of chemical weathering of siliceous rocks in the world. Rapid weathering produces thick, highly leached saprolites in both watersheds that lie just below the soil and largely isolate subsurface biogeochemical and hydrologic processes from those in the soil. The quartz diorite bedrock in the Icacos watershed weathers spheroidally, leaving large, relatively unweathered corestones that are enveloped by slightly weathered rock layers called rindlets. The rindlets wrap around the corestones like an onionskin. Within the corestones, biotite oxidation is thought to induce the spheroidal fracturing that leads to development of rindlets; plagioclase in the rindlets dissolves, creating additional pore spaces. Near the rindlet-saprolite interface, the remaining plagioclase dissolves, hornblende dissolves to completion, and precipitation of kaolinite, gibbsite, and goethite becomes pervasive. In the saprolite, biotite weathers to kaolinite and quartz begins to dissolve. In the soil layer, both quartz and kaolinite dissolve. The volcaniclastic bedrock of the Mameyes watershed weathers even faster than the quartz diorite bedrock of the Icacos watershed, leaving thicker saprolites that are devoid of all primary minerals except quartz. The quartz content of volcaniclastic bedrock may help to control watershed geomorphology; high-quartz rocks form thick saprolites that blanket ridges. Hydrologic flow paths within the weathering profiles vary with total fluid flux, and they influence the chemistry of streams. Under low-flow conditions, the Río Icacos and its tributaries are fed by rainfall and by groundwater from the fracture zones; during storm events, intense rainfall rapidly raises stream levels and water is flushed through the soil as shallow flow. As a result, weathering constituents that shed into streamwaters are dominated by rindlet-zone weathering processes during base flow and by soil weathering processes during stormflow. The upper reaches of the Mameyes watershed are characterized by regolith more than 35 meters thick in places that contains highly fractured rock embedded in its matrix. Weathering contributions to stream chemistry at base flow are predicted to be more spatially variable in the Mameyes watershed than in the Icacos watershed owing to the more complex subsurface weathering profile of the volcaniclastic bedrocks of the Mameyes watershed.

Professional Paper↗

USGS1999

Petrology and geochemistry of late-stage intrusions of the A-type, mid-Proterozoic Pikes Peak batholith (Central Colorado, USA): Implications for petrogenetic models

The ~1.08 Ga anorogenic, A-type Pikes Peak batholith (Front Range, central Colorado) is dominated by coarse-grained, biotite ?? amphibole syenogranites and minor monzogranites, collectively referred to as Pikes Peak granite (PPG). The batholith is also host to numerous small, late-stage plutons that have been subdivided into two groups (e.g. Wobus, 1976. Studies in Colorado Field Geology, Colorado School of Mines Professional Contributions, Colorado): (1) a sodic series (SiO2= ~44-78 wt%; K/Na=0.32-1.36) composed of gabbro, diabase, syenite/quartz syenite and fayalite and sodic amphibole granite; and (2) a potassic series (SiO2= ~ 70-77 wt%; K/Na=0.95-2.05), composed of biotite granite and minor quartz monzonite. Differences in major and trace element and Nd isotopic characteristics for the two series indicate different petrogenetic histories. Potassic granites of the late-stage intrusions appear to represent crustal anatectic melts derived from tonalite sources, based on comparison of their major element compositions with experimental melt products. In addition, Nd isotopic characteristics of the potassic granites [??(Nd)(1.08 Ga) = -0.2 to -2.7] overlap with those for tonalites/granodiorites [ca 1.7 Ga Boulder Creek intrusions; ??(Nd)(1.08 Ga) = -2.4 to -3.6] exposed in the region. Some of the partial melts evolved by fractionation dominated by feldspar. The late-stage potassic granites share geochemical characteristics with most of the PPG, which is also interpreted to have an anatectic origin involving tonalitic crust. The origin of monzogranites associated with the PPG remains unclear, but mixing between granitic and mafic or intermediate magmas is a possibility. Syenites and granites of the sodic series cannot be explained as crustal melts, but are interpreted as fractionation products of mantle-derived mafic magmas with minor crustal input. High temperature and low oxygen fugacity estimates (e.g. Frost et al., 1988. American Mineralogist 73, 727-740) support a basalt fractionation origin, as do ??(Nd) values for sodic granitoids [??(Nd)(1.08 Ga) = +2.2 to -0.7], which are higher than ??(Nd) values for Colorado crust at 1.08 Ga (ca -1.0 to -4.0). Enrichments in incompatible elements (e.g. rare earth elements, Rb, Y) and depletions in compatible elements (e.g. Cr, Sr, Ba) in the sodic granitoids compared to coeval mafic rocks are also consistent with fractionation. Accessory mineral fractionation, release of fluorine-rich volatiles and/or removal of pegmatitic fluids could have modified abundances of Ce, Nb, Zr and Y in some sodic granitoid magmas. Gabbros and mafic dikes associated with the sodic granitoids have ??(Nd)(1.08 Ga) of -3.0 to +3.5, which are lower than depleted mantle at 1.08 Ga, and their trace element characteristics suggest derivation from mantle sources that were previously affected by subduction-related processes. However, it is difficult to characterize the mantle component in these magmas, because assimilation of crust during magma ascent could also result in their observed geochemical features. The Pikes Peak batholith is composed of at least two petrogenetically different granite types, both of which exhibit geochemical characteristics typical of A-type granites. Models proposed for the petrogenesis of the granitoids imply the existence of mafic rocks at depth and addition of juvenile material to the crust in central Colorado at ~ 1.1 Ga.

Precambrian Research↗

USGS2013

Geochemical changes and fracture development in Woodford Shale cores following hydrous pyrolysis under uniaxial confinement

A uniaxial confinement clamp was used on Woodford Shale cores in hydrous pyrolysis experiments to study fracture development during thermal maturation. The clamp simulates overburden in that it prevents cores from expanding perpendicular to bedding fabric during the volume-increasing reactions associated with petroleum generation. Cores were cut from a slab of immature Woodford Shale and subjected to hydrous pyrolysis under confinement at 300, 330, and 365 °C for 72 hours to induce thermal maturities ranging from early bitumen to maximum expelled-oil generation. Two additional cores were used as experimental controls: (1) a confined core was saturated with water by heating it to 100 °C under hydrous pyrolysis conditions for 72 hours to use for characterization of the original rock, and (2) an unconfined core was heated at 365 °C for 72 hours to evaluate the effects of confinement on petroleum generation and expulsion. X-ray computed tomography (X-CT) imaging and other analyses identified five distinct beds within the cored interval. Using a tentative classification system, beds 1, 2, and 3 are described as dolomitic marlstone (DM) with total organic carbon (TOC) contents of 7.7, 5.8, and 7.7 wt. %, respectively; bed 4 is a cherty quartzose claystone (CQC) with TOC content of 5.5 wt. %; and bed 5 is a quartzose claystone with TOC content of 10.9 wt. %. Bed samples all had similar Rock-Eval hydrogen indices (600 ± 46 mg S2/g-TOC) and Tmax values (433 ± 2 °C), demonstrating organic matter uniformity and low thermal maturity. The X-CT scan of the core heated to 100 °C showed preexisting fractures that were nearly perpendicular to the bedding fabric primarily in the low-TOC DM bed 2 and CQC bed 4. Heating led to enhancement of preexisting fractures in the confined cores with the greatest enhancement occurring in CQC bed 4. The fractures increased in size and intensity with temperature. This is attributed to the internal pressure generated by volume-increasing reactions during the conversion of kerogen to bitumen and bitumen to oil and gas. The unconfined core heated to 365 °C showed no enhanced fracturing and its X-CT-scan resembled that of the 100 °C confined core. Comparison of the oil and gas yields from the confined and unconfined cores heated to 365 °C showed no significant differences, indicating that product expulsion is not inhibited by the procedure used in this study. These results also indicate that fracturing during thermal maturation is driven primarily by the enhancement of existing fractures.

Conference Paper↗

USGS2018

Interaction between hydraulic fracture and a preexisting fracture under triaxial stress conditions

Enhanced reservoir connectivity generally requires maximizing the intersection between hydraulic fracture (HF) and preexisting underground natural fractures (NF), while having the hydraulic fracture cross the natural fractures (and not arrest). We have studied the interaction between a hydraulic fracture and a polished saw-cut fault. The experiments include a hydraulic fracture initiating from a pressurized axial borehole (using water) that approaches a dry fault that is inclined at an angle θ with respect to the borehole axis. The experiments are conducted on Poly(methyl) Meta Acrylate (PMMA) and Solnhofen limestone, a finely grained (<5 μm grain), low permeability (<10 nD) carbonate. The confining pressure in all experiments is 5 MPa, while the differential stress (1-80 MPa) and approach angle, θ (30, 45, 60, 90°) are experimental variables. During the hydraulic fracture, acoustic emissions (AE), slip velocity, slip magnitude, stress drop and pore pressure are recorded at a 5 MHz sampling rate. A Doppler laser vibrometer measures piston velocity outside the pressure vessel to infer fault slip duration and a strain gauge adjacent to the saw-cut provides a near-field measure of axial stress. For PMMA, the coefficient of friction was 0.30 and sliding was unstable (stick-slip). The approaching HF in PMMA created a tensile fracture detected by AE transducers ~100 μs before the significant stick-slip event (45% stress drop and slip velocity of ~60 mm/s) and was arrested by the fault at all fault orientations and differential stresses, even at 90° fault orientation and 80 MPa differential stress. For Solnhofen limestone, we observed stable sliding at a coefficient of friction of 0.12. In contrast to PMMA, the HF in Solnhofen consistently crossed to the other side of the fault. When the HF crossed the fault, it produced a small stress drop (<10%) and slip velocity of only 0.5 mm/s. Theoretical models by Blanton (1986) and Renshaw and Pollard (1995) predict that HF will be arrested for Solnhofen limestone and cross PMMA 90° fault at 80 MPa differential stress. Although the exact cause for the discrepancy between experiments and the theory is not known, one feature present in the experiments but not considered in the models, is the diffusion of fluid driven by the fault slip. Thus, the formation of a "fluid-filled patch" on the fault surface as it is intersected by the HF may substantially impact the crossing/arrest behavior. The approach angle and differential stress also influence the HF initiation azimuth and breakdown pressure. In most cases, the HF initiation azimuth was normal to the fault strike. These observations suggest that the presence of natural fractures could result in rotation of hydraulic fractures to be more normal to their strike and a subsequent change in the downhole pressure recordings. The latter could be used as a diagnostic tool for predicting this interaction.

Conference Paper↗

USGS2012

Hood River PIT-tag interrogation system efficiency study. Annual report of U.S. Geological Survey activities: November 2010-October 2011

Introduction During summer 2010, an agreement was made between the US Geological SurveyColumbia River Research Laboratory (USGS-CRRL) and the Confederated Tribes of the Warm Springs (CTWS) to operate an experimental Passive Integrated Transponder (PIT)-tag interrogation system (PTIS) near the mouth of the Hood River for a year and provide fishdetection efficiency estimates (Bonneville Power Administration (BPA) project number 1988- 053-03, contract number 50150). A previous agreement between Oregon Department of Fish and Wildlife (ODFW) and USGS-CRRL had funded materials acquisition, construction, and installation of the PTIS (BPA project number 1988-053-04, contract number 48684). The primary purpose of the project was to test the efficacy of a PTIS in the lower Hood River for providing data on returning adult salmonids to the Hood River as part of the Hood River Production Monitor and Evaluation project (HRPME). Because PIT tags are small, relatively inexpensive, carry no internal battery, and last through the lifespan of most fishes, they are commonly used in long term fish monitoring projects. They have been extensively used in the Columbia River basin to monitor salmonid behavior and survival through life stages and migration routes in the mainstem Columbia River (Skalski et al. 1998; Zabel and Achord 2004). Increasingly, PIT-tag detection equipment has been deployed in streams to investigate salmonid behavior (Zydlewski et al. 2001, 2006; Riley et al. 2003; Bond et al. 2007). Most of the detection systems deployed and evaluated to date have been in much smaller streams than the mainstem of the Hood River (Zydlewski et al. 2001, 2006; Bond et al. 2007; Horton et al. 2007; Connolly et al. 2008), but researchers are attempting to expand detection abilities to larger streams and rivers. Large streams and rivers can prove extremely challenging to monitor. Some systems have showed promise for contributing valuable detection data, others have proved less successful. A detection system in the Klamath River (Beeman et al. 2012), a site similar in size to the Hood River, suffered problems from cables being dislodged and high water that resulted in a detection efficiency estimate for juvenile coho salmon of less than 0.05. An additional USGS-CRRL task, under contract number 50150, was to build three antennas for use with Destron-Fearing 2001F-ISO PIT tag readers. These antennas would be 5 used at the East Fork Hood River Acclimation site. They would be placed in the outflow channel to inform managers about the number of PIT tagged steelhead smolts released to the Hood River after a period of acclimation when some mortality and predation might occur.

Oregon↗

USGS2000

Structure and composition of oligohaline marsh plant communities exposed to salinity pulses

The response of two oligohaline marsh macrophyte communities to pulses of increased salinity was studied over a single growing season in a greenhouse experiment. The plant communities were allowed a recovery period in freshwater following the pulse events. The experimental treatments included: (1) salinity influx rate (rate of salinity increase from 0 to 12 gl-1); (2) duration of exposure to elevated salinity; and (3) water depth. The communities both included Sagittaria lancifolia L.; the codominant species were Eleocharis palustris (L.) Roemer and J.A. Schultes in community 1 and Schoenoplectus americanus (Pers.) Volk. ex Schinz and R. Keller in community 2. Effects of the treatments on sediment chemical characteristics (salinity, pH, redox potential, and sulfide and ammonium concentrations) and plant community attributes (aboveground and belowground biomass, stem density, leaf tissue nutrients, and species richness) were examined. The treatment effects often interacted to influence sediment and plant communities characteristics following recovery in fresh water. Salinity influx rate per se, however, had little effect on the abiotic or biotic response variables; significant influx effects were found when the 0 gl-1 (zero influx) treatment was compared to the 12 gl-1 treatments, regardless of the rate salinity was raised. A salinity level of 12 gl-1 had negative effects on plant community structure and composition; these effects were usually associated with 3 months of salinity exposure. Water depth often interacted with exposure duration, but increased water depth did independently decrease the values of some community response measures. Community 1 was affected more than community 2 in the most extreme salinity treatment (3 months exposure/15-cm water depth). Although species richness in both communities was reduced, structural changes were more dramatic in community 1. Biomass and stem density were reduced in community 1 overall and in both dominant species. Structural changes in community 2 consisted of reduced biomass and stem density in the community overall and in S. lancifolia; S. americanus was not affected by salinity. In this most extreme treatment, community 2 tended to change to a monospecific S. americanus stand while community 1 was reduced to a few surviving stems of secondary species. Our results suggest that vegetation recovery or establishment of new species following a temporary increase in soil water salinity will vary with exposure duration and water depth. (C) 2000 Elsevier Science B.V.

Aquatic Botany↗

USGS2004

Changes in ground-water quality near two granular-iron permeable reactive barriers in a sand and gravel aquifer, Cape Cod, Massachusetts, 1997-2000

Two experimental permeable reactive barriers (PRBs) of granular zero-valent iron were emplaced in the path of a tetrachloroethene plume (the Chemical Spill-10 plume) at the Massachusetts Military Reservation, Cape Cod, Massachusetts, in June 1998. The goal of the field experiment was to achieve emplacement of a granular-iron PRB deeper than attempted before. The PRBs were expected to create a reducing environment and degrade the tetrachloroethene by reductive dechlorination. The goal of the work presented in this report was to observe temporary and sustained changes to the ground-water chemistry downgradient from the PRBs. A hydraulic-fracturing method involving injection of the granular iron with a guar-biopolymer and enzyme slurry was used to install the parallel 30- to 33-foot-wide wall-shaped barriers at a depth of 82 to 113 feet below land surface. An acetic acid and enzyme mixture was subsequently injected in wells near the barriers to degrade the guar biopolymer. Prior to the emplacement, tetrachloroethene concentrations in the Chemical Spill-10 plume at the study area were as high as 250 micrograms per liter. Other water properties in the plume generally were similar to the properties of uncontaminated ground water in the area, which typically has dissolved oxygen concentrations of 250 to 375 micromoles per liter, pH of 5.5 to 6.0, and specific conductance of 60 to 90 microsiemens per centimeter. Water-quality samples were collected periodically from monitoring wells near the PRBs to determine how the emplacement of the granular-iron walls altered the ground-water quality. In addition, an automated well-sampling device measured temperature, specific conductance, pH, and dissolved oxygen every 1–4 days for 16 months in a well downgradient from the two parallel PRBs. Temporary increases (lasting about 5 to 6 months) in specific conductance were observed downgradient from the PRBs as a result of the sodium chloride, potassium carbonate, and other salts included in the slurry and the acetic acid and enzyme mixture that was subsequently injected to degrade the guar biopolymer. Temporary increases in the concentrations of major cations (sodium, potassium, magnesium, and calcium) were observed downgradient from the PRBs, as were temporary but substantial increases in the dissolved and total organic carbon concentrations. Methane was detected, sulfate concentrations decreased temporarily, and concentrations of dissolved inorganic carbon increased in samples from wells downgradient from the PRBs. A sustained (longer than 12 months) reducing environment, in which dissolved oxygen concentrations decreased to zero, the pH increased to about 6.8, and dissolved iron concentrations increased substantially, developed as a result of the oxidation (corrosion) of the granular iron; this zone persisted at least 65 feet downgradient from the PRBs. The pH and dissolved iron concentrations increased with distance from the granular-iron walls. Concentrations of arsenic, cobalt, manganese, and phosphorus increased, and nitrate concentrations were reduced to below the detection limit downgradient from the walls. A sustained decrease of tetrachloroethene concentrations was not observed; however, reductive dechlorination products were observed at wells downgradient from the PRBs during several rounds of sampling. The emplacement of zero-valent iron in the aquifer to remove tetrachloroethene from the ground water caused changes in the water chemistry that persisted farther downgradient from the PRBs than has been observed at other sites because of the low chemical reactivity of the quartz-dominated aquifer sediments and the low ambient dissolved chemical concentrations in the ground water. The small transverse dispersion in the aquifer and the probable long-term persistence of the iron indicate that the chemically altered zone probably will extend a substantial distance downgradient from the PRBs for a substantial period of time (years); further investigation would be needed to determine this distance.

Massachusetts↗

USGS2004

Effects of the fungicides mancozeb and chlorothalonil on fluxes of CO2, N2O, and CH4 in a fertilized Colorado grassland soil

[1] Management of agricultural soil plays an important role in present and future atmospheric concentrations of the greenhouse gases carbon dioxide (CO 2 ), nitrous oxide (N 2 O), and methane (CH 4 ). Pesticides are used as management tools in crop production, but little is known about their effects on soil‐atmosphere exchange of CO 2 , N 2 O, and CH 4 . Field studies described in this paper determined the effect of two commonly used fungicides, mancozeb and chlorothalonil, on trace gas exchange. Separate experimental plots, 1 m 2 , were established in nitrogen fertilized no‐tilled native grassland and tilled soils with and without fungicide application. Two studies were conducted. The first study was initiated in June 1999 and lasted for 1 year with monthly flux measurements from tilled and no‐till soils. The second study commenced in August 2001 with twelve weekly measurements from tilled soils only. From both studies mancozeb suppressed emissions of CO 2 and N 2 O in the tilled soil by an average of 28% and 47%, respectively. This suppression corresponded with efficacy periods of 14–29 and 56–77 days, respectively. From the no‐till soils mancozeb decreased CO 2 and N 2 O emissions by 33% and 80% for periods of 29 and 94 days, respectively. Mancozeb inhibited CH 4 consumption in the first study by 46% and 71% in the tilled and no‐till soil for periods of 8 and 29 days, respectively, but had no effect in the second study. From both studies chlorothalonil initially suppressed CO 2 and N 2 O emissions and enhanced CH 4 uptake in the tilled soil by an average of 37%, 40%, and 115%, respectively. These effects corresponded with efficacy periods of 14–29, 21–56, and 1–14 days, respectively. In the no‐till soil chlorothalonil inhibited CO 2 and N 2 O emissions and enhanced CH 4 uptake by 29%, 48%, and 86% for periods of 29, 56, and 56 days, respectively. Following the initial period of suppression, chlorothalonil subsequently enhanced N 2 O emissions in the tilled soil by an average of 51% and in the no‐till soil by 81% before returning to near background levels. The beginning of increased N 2 O emissions from the chlorothalonil‐amended plots corresponded with a maximum soil concentration of the chlorothalonil degradate, 4‐hydroxy‐2, 5, 6‐trichloroisophthalonitrile. The site specific global warming potential (GWP) resulting from the fluxes of CO 2 , N 2 O, and CH 4 from all soils was determined to decrease by an average 26% and 21% as a result of a single application of mancozeb or chlorothalonil, respectively. The decrease in CO 2 emissions in the fungicide‐amended plots potentially could result in the conservation of as much as 1200 and 2400 kg C ha −1 yr −1 organic carbon in the tilled and no‐till plots, respectively. Therefore it is feasible that application of certain fungicides to agricultural soil might lead to enhanced soil carbon sequestration and thus have additional positive effects on atmospheric CO 2 concentrations.

Journal of Geophysical Research D: Atmospheres↗

USGS1997

The roles of time and displacement in velocity-dependent volumetric strain of fault zones

The relationship between measured friction μ A and volumetric strain during frictional sliding was determined using a rate and state variable dependent friction constitutive equation, a common work balance relating friction and volume change, and two types of experimental faults: initially bare surfaces of Westerly granite and rock surfaces separated by a 1 mm layer of less than 90 μm Westerly granite gouge. The constitutive equation is the sum of a constant term representing the nominal resistance to sliding and two smaller terms: a rate dependent term representing the shear viscosity of the fault surface (direct effect), and a term which represents variations in the area of contact (evolution effect). The work balance relationship requires that μ A differs from the frictional resistance that leads to shear heating by the derivative of fault normal displacement with respect shear displacement, d δ n / d δ s . An implication of this relationship is that the rate dependence of d δ n / d δ s contributes to the rate dependence of μ A . Experiments show changes in sliding velocity lead to changes in both fault strength and volume. Analysis of data with the rate and state equations combined with the work balance relationship preclude the conventional interpretation of the direct effect in the rate and state variable constitutive equations. Consideration of a model bare surface fault consisting of an undeformable indentor sliding on a deformable surface reveals a serious flaw in the work balance relationship if volume change is time-dependent. For the model, at zero slip rate indentation creep under the normal load leads to time-dependent strengthening of the fault surface but, according to the work balance relationship, no work is done because compaction or dilatancy can only be induced by shearing. Additional tests on initially bare surfaces and gouges show that fault normal strain in experiments is time-dependent, consistent with the model. This time-dependent fault normal strain, which is not accounted for in the work balance relationship, explains the inconsistency between the constitutive equations and the work balance. For initially bare surface faults, all rate dependence of volume change is due to time dependence. Similar results are found for gouge. We conclude that μ A reflects the frictional resistance that results in shear heating, and no correction needs to be made for the volume changes. The result that time-dependent volume changes do not contribute to μ A is a general result and extends beyond these experiments, the simple indentor model and particular constitutive equations used to illustrate the principle.

Journal of Geophysical Research B: Solid Earth↗

USGS2014

Impacts of white-tailed deer on red trillium ( Trillium recurvatum ): defining a threshold for deer browsing pressure at the Indiana Dunes National Lakeshore

Overabundant white-tailed deer ( Odocoileus virginianus ) have been a concern for land managers in eastern North America because of their impacts on native forest ecosystems. Managers have sought native plant species to serve as phytoindicators of deer impacts to supplement deer surveys. We analyzed experimental data about red trillium ( Trillium recurvatum ), large flowered trillium ( T. grandiflorum ), nodding trillium ( T. cernuum ), and declined trillium ( T. flexipes ) growth in paired exclosure (fenced) plots and control (unfenced) plots from 2002 to 2010 at the Indiana Dunes National Lakeshore. The latter two species lacked replication, so statistical analysis was not possible. All red trillium plants were surveyed for height-to-leaf, effects of browsing, and presence of flowers. Data from individuals in 2009 demonstrated a sigmoidal relationship between height-to-leaf and probability of flowering. The relationship on moraine soils was shifted to taller plants compared to those on sand substrates, with respectively 50 percent flowering at 18 and 16 cm and 33 percent flowering at 16 and 14 cm height-to-leaf. On a plot basis, the proportion of plants flowering was influenced by height to leaf, duration of protection, and deviation in rainfall. The proportion of plants flowering increased ninefold in exclosures (28 percent) compared to control plots (3 percent) over the 8 years of protection. The mean height-to-leaf was a function of the interaction between treatment and duration, as well as red trillium density. Changes in height-to-leaf in control plots from year to year were significantly influenced by an interaction between change in deer density and change in snowfall depth. There was a significant negative correlation between change in deer density and snowfall depth. Plants in the exclosures increased in height at a rate of 1.5 cm yr −1 whereas control plants decreased in height by 0.9 cm yr −1 . In all, 78 percent of the control plots lacked flowering individuals over the 9 years of study, indicating that red trillium is being negatively affected by deer throughout the East Unit of the park. Of the five deer management zones studied, only one showed pre-impact height-to-leaf and flowering percentages in control plots that then declined after 2005. The results of this study demonstrate that Trillium species growing in the lands of the Indiana Dunes National Lakeshore are being suppressed reproductively by deer browsing. Specifically, we demonstrate, for the first time, the utility of using red trillium ( Trillium recurvatum ) height-to-leaf and percentage of flowering as indicators of the impacts of deer browsing. Application of the recommended thresholds demonstrates their utility in adopting red trillium as a phytoindicator of deer impact. Responses of plants to protection from deer suggest that deer culling might be necessary for 6 or more years for red trillium populations and rare trillium species to recover.

Indiana↗

USGS2025

Mammalian responses to select Type 3 Watershed Experiment prescriptions in the Olympic Experimental State Forest: A camera-based monitoring approach

The Type 3 Watershed Experiment is a landscape-scale management experiment designed to assess the ecological, economic, and social benefits of timber harvest and post-harvest management prescriptions in upland and riparian systems of the Washington Coast Range ecoregion. The experiment is being conducted on state trust lands in the Olympic Experimental State Forest (OESF), which are managed by the Washington Department of Natural Resources (WADNR). A wide variety of abiotic and biotic responses are being studied for the experiment, but no current studies include mammalian responses. The goal of this study is to use camera traps to assess patterns of medium and large mammal use of treatment blocks associated with the Type 3 Watershed Experiment, including the Complex Early Seral (CES) prescription and Variable Retention Harvest (VRH) prescription, in comparison to unharvested second growth forests. We are using a block design to assess responses of the medium and large mammal community to the CES and VRH prescriptions. Target taxa include Columbia black-tailed deer, Roosevelt elk, black bear, cougar, coyote, bobcat, fisher, and other medium sized mammals of interest. Mammalian use at the management prescription sites will be compared to use at the unharvested control sites (second growth forest stands). We will conduct an initial study in 2024─2025 for proof of concept after a pilot period of camera deployment. We anticipate that the cameras will be deployed continuously year-round for at least three years and possibly longer to assess longer-term patterns of use of these prescriptions. The project includes 48 cameras deployed evenly across CES, VRH, and control units. All our camera deployments are collocated at sites where avian monitoring is also occurring, and several also overlap with areas where the amphibian community is being surveyed, providing spatial linkages among different wildlife datasets. We will assess mammal community responses to forest management prescriptions using a variety of approaches. For the different prescriptions, we will examine the occurrence of a suite of species, measure species richness (alpha and beta diversity), estimate relative use, and quantify species persistence (i.e., the amount of time a species spends in a given prescription). We will estimate the influence of select habitat conditions on individual species use and on total species richness using mixed-effects models. The results of this study will provide estimates of initial responses of the mammalian community to the focal management prescriptions and serve as baseline data for long-term monitoring. This research will provide natural resource managers with a better understanding of how the mammalian community responds to and uses different types of habitats after timber harvest operations and will assess how those patterns change over time as vegetation develops under different silviculture prescriptions.

Washington↗

USGS2016

Evaluation of the biological and hydraulic performance of the portable floating fish collector at Cougar Reservoir and Dam, Oregon, September 2015–January 2016

The biological and hydraulic performance of a portable floating fish collector (PFFC) located in the cul-de-sac of Cougar Dam and Reservoir, Oregon, was evaluated during 2015–16. The PFFC, first commissioned in May 2014, was modified during winter 2014–15 to address several deficiencies identified during operation and testing in 2014. These modifications included raising the water inflow structures to reduce the depth and volume of inflow to improve the internal hydraulic profiles, and moving the anchors so the PFFC could be positioned closer to the existing reservoir outlet, a water temperature control tower. The PFFC was positioned about 18 meters (m) upstream of the intake of the water temperature control tower and faced into the prevailing water current. Like several floating surface collectors operating in the Pacific Northwest at the time, the PFFC used pumps to draw water and fish over an inclined plane, past dewatering screens, and into a collection area. The portable and experimental nature of the PFFC required a smaller size, shallower entrance (about 2.5-m deep), and smaller inflow rate (72 cubic feet per second [ft 3 /s] inflow during the Low treatment, 122 ft 3 /s during the High treatment) than other collectors in the region. The collection of the target species, juvenile Chinook salmon ( Oncorhynchus tshawytscha ) , during 2015–16 was an order of magnitude larger than in 2014. Subyearling-age Chinook salmon comprised most of the catch (2,616 subyearling compared to 258 yearling) and was greatest during the spring during the High inflow treatment. Bycatch consisted predominantly of cyprinids and centrarchids. Trap mortality (fish found dead in the trap) of juvenile Chinook salmon, at 9.2 percent of the subyearlings and 5.0 percent of yearlings, was about 30 percent of the level in 2014. Fish mortality from handling the live catch was about 1 percent. Data from fish tagged with passive integrated transponder (PIT) tags and those with acoustic+PIT tags released near the head of the reservoir indicated the catch rates of the PFFC were low. Eight of the 1,497 PIT-tagged fish and 5 of the 534 acoustic+PIT-tagged fish were collected by the PFFC. Fish collection efficiencies—the number collected by the PFFC out of the number detected at the head of the forebay (FCE FB ) or in the cul-de-sac (FCE CDS ) —were 0.002 and 0.003 during the Low treatment and 0.008 and 0.009 during the High treatment. The low FCEs were attributed to the following factors: Few acoustic+PIT-tagged fish were detected within 10 m of the PFFC entrance, Most fish were detected between the stern of the PFFC and the entrance to the tower, Fish depths commonly were several times greater than the PFFC entrance depth, and Surface water temperatures were warm. The data suggest that the shallow entrance and low inflow rate reduced fish guidance near the PFFC entrance and the hydraulic characteristics resulting from the outflow plumes (and perhaps water entering the temperature control tower) attracted fish to that area. Catch of juvenile Chinook salmon likely would increase if the collector entrance were deepened, the inflow rate were increased, and measures were taken to constrain fish presence to the area upstream of the trap entrance.

Oregon↗

USGS2001

Green fluorescent protein is lighting up fungal biology

Prasher ( 42 ) cloned a cDNA for the green fluorescent protein (GFP) gene from the jellyfish Aequorea victoria in 1992. Shortly thereafter, to the amazement of many investigators, this gene or derivatives thereof were successfully expressed and conferred fluorescence to bacteria and Caenorhabditis elegans cells in culture ( 10 , 31 ), followed by yeast ( 24 , 39 ), mammals ( 40 ), Drosophila ( 66 ), Dictyostelium ( 23 , 30 ), plants ( 28 , 49 ), and filamentous fungi ( 54 ). The tremendous success of GFP as a reporter can be attributed to unique qualities of this 238-amino-acid, 27-kDa protein which absorbs light at maxima of 395 and 475 nm and emits light at a maximum of 508 nm. The fluorescence of GFP requires only UV or blue light and oxygen, and therefore, unlike the case with other reporters (β-glucuronidase, β-galacturonidase, chloramphenicol acetyltransferase, and firefly luciferase) that rely on cofactors or substrates for activity, in vivo observation of gfp expression is possible with individual cells, with cell populations, or in whole organisms interacting with symbionts or environments in real time. Complications caused by destructive sampling, cell permeablization for substrates, or leakage of products do not occur. Furthermore, the GFP protein is extremely stable in vivo and has been fused to the C or N terminus of many cellular and extracellular proteins without a loss of activity, thereby permitting the tagging of proteins for gene regulation analysis, protein localization, or specific organelle labeling. The mature protein resists many proteases and is stable up to 65°C and at pH 5 to 11, in 1% sodium dodecyl sulfate or 6 M guanidinium chloride (reviewed in references 17 and 67 ), and in tissue fixed with formaldehyde, methanol, or glutaraldehyde. However, GFP loses fluorescence in methanol-acetic acid (3:1) and can be masked by autofluorescent aldehyde groups in tissue fixed with glutaraldehyde. Fluorescence is optimal at pH 7.2 to 8.0 ( 67 ). Limitations on GFP as a reporter for some applications are its low turnover rate, 2-h lag time for autoactivation of its chromophore, improper folding at high temperatures (37°C), which results in nonfluorescent and insoluble forms of the protein, and requirement for oxygen, which is not present in equal concentrations in all subcellular locations or cell types (reviewed in references 17 and 67 ). These characteristics of GFP, however, have not posed a problem for many applications, and mutant forms of GFP that have an ability to fold properly at high temperatures, increased solubility and fluorescence, reduced photobleaching ( 16 , 17 , 51 ), and reduced half-lives ( 1 ) have been developed. Coupled with fluorescence-activated cell sorting, confocal microscopy or quantitative image analysis techniques, GFP technology can be used to isolate transformed cells or specific cell types from populations of cells ( 14 ), to quantify gene expression of individual cells within whole organisms ( 8 ), or to assess the dispersal and biomass of organisms in complex environments, such as in animal or plant hosts ( 38 , 59 ), in biofilms ( 55 ), in fermentors ( 41 ), on leaf surfaces ( 53 , 61 ), or in soils ( 2 ). The vast majority of studies utilizing GFP expression in fungi have been with yeast (reviewed in reference 13 ). Ustilago maydis was the first filamentous fungus for which successful expression of gfp was reported ( 54 ), followed closely by Aspergillus nidulans ( 22 , 57 ) and Aureobasidium pullulans ( 61 ). Presently, gfp expression has been reported for 16 species comprising 12 genera of filamentous fungi, including Colletotrichum ( 21 , 44 ), Mycosphaerella ( 52 ), Magnaporthe ( 32 , 35 ), Cochliobolus ( 38 ), Trichoderma ( 2 , 70 ), Podospora ( 5 ), Sclerotinia ( 63 ), Schizophyllum ( 37 ), Aspergillus ( 20 , 47 , 50 ) and Phytophthora ( 7 , 62 ). In this review we draw on published reports, with the goal of providing an overview of GFP technology as it applies to the biology of filamentous fungi. These reports are not exhaustive of potential applications of GFP technology, as examples of genomic approaches to utilizing GFP in bacterial and yeast systems attest ( 4 , 46 , 60 , 65 ). Expression of gfp in filamentous fungi requires a gfp variant that is efficiently translated in fungi, a transformation system, and a fungal promoter that satisfies the requirements of a given experimental objective. Transformation of fungi has recently been reviewed by Gold et al. ( 26 ). Robinson and Sharon ( 44 ) suggest that GFP can actually be used to optimize transformation protocols. In addition to reporting the construction of a new fungal transformation vector that expresses SGFP under the control of the ToxA gene promoter from Pyrenophora tritici-repentis ( 12 ) and demonstrating its use in plant pathogens belonging to eight different genera of filamentous fungi ( Fusarium, Botrytis, Pyrenophora, Alternaria, Cochliobolus, Sclerotinia, Colletotrichum , and Verticillium ), in this review we also enumerate and describe a comprehensive list of vectors for expressing GFP in fungi.

Applied and Environmental Microbiology↗

USGS2014

Survival of hatchery Gulf sturgeon ( Acipenser oxyrinchus desotoi Mitchill, 1815) in the Suwannee River, Florida: a 19-year evaluation

An experimental release of 1192 hatchery-reared, individually PIT tagged, 220 days old (296–337 mm TL) Gulf sturgeon, Acipenser oxyrinchus desotoi , was undertaken in 1992 in the Suwannee River, Florida. The original objectives of the 1992 release experiment were to: (1) evaluate survival rate of cultured Gulf sturgeon in the wild vs survival rate of their wild 1992 cohort counterparts, (2) determine the differential effect of release site within the river upon long-term survival, and (3) evaluate comparative growth rates of recaptured hatchery vs captured wild 1992 cohort Gulf sturgeon. The present investigation addressed those original objectives, plus an additional fourth objective: (4) evaluation of hatchery fish recapture rate change over the 19-year experiment. The primary objective was to determine efficacy of potential conservation aquaculture for this species in terms of long-term survival in the wild. Follow-up 1993–2011 gill net sampling in freshwater reaches (rkm 4–237) and the estuarine river mouth (rkm −6 to 4) yielded recaptures representing 13.0% of the total released. Mean annual hatchery fish mortality (including emigration) rate estimated for the 19-year period (1993–2011) was more than twice that for same cohort wild fish. Mark-recapture survival probability (phi) for hatchery fish, 1993–2011, was substantially lower (0.733) than for their wild counterparts (0.888). Mean annual hatchery fish recapture rate, as a percentage of all 1992 cohort fish recaptures, declined significantly after age-7, coinciding with age of onset of migration into the open Gulf of Mexico. Hypothesized causal factors may be differentially lower fitness in the marine habitat or permanent outmigration due to natal river imprinting failure. Hatchery fish recapture rates varied significantly for fish from the ten release sites, being highest near the river mouth, and lowest for the furthest upriver sites in the Suwannee River and its Santa Fe River tributary. Hatchery fish also displayed a significantly lower growth rate than their wild counterparts through age 3000 days. Cumulative hatchery fish mortality of 99.87% over 19 years predicts <3 individuals would have survived through 2011. From the results of the 1992 release experiment, hatchery supplementation as a Gulf sturgeon conservation measure does not appear to be an effective option.

Florida↗

USGS2016

Depth calibration of the Experimental Advanced Airborne Research Lidar, EAARL-B

Introduction The original National Aeronautics and Space Administration (NASA) Experimental Advanced Airborne Research Lidar (EAARL) was extensively modified to increase the spatial sampling density and to improve performance in water ranging from 3 to 44 meters (m). The new (EAARL-B) sensor features a higher spatial density that was achieved by optically splitting each laser pulse into three pulses spatially separated by 1.6 m along the flight track and 2.0 m across the flight track, on the water surface when flown at a nominal altitude of 300 m (984 feet). The sample spacing can be optionally increased to 1.0 m across the flight track. Improved depth capability was achieved by increasing the total peak laser power by a factor of 10 and by designing a new “deep-water” receiver, which is optimized to exclusively receive refracted and scattered light from deeper water (15–44 m). Two different clear-water flight missions were conducted over the U.S. Navy's South Florida Testing Facility (SFTF) to determine the EAARL-B calibration coefficients. The SFTF is an established lidar calibration range located in the coastal waters southeast of Fort Lauderdale, Florida. We used 23 selected polygons at 23 distinct depths to compare a reference dataset from this site to determine EAARL-B calibration constants over the depth range of 6.5 to 34 m. We also conducted a near-simultaneous single-beam jet-ski-based sonar survey of selected transects ranging from 1 to 33 m depth in the same area. The near-concurrent jet ski data were used to evaluate the EAARL-B performance over the depth range from 0.9 to 10 m. The more timely jet ski data were necessary because the primary reference dataset was 9 years old, and areas shallower than 6.5 m are dominated by shifting sand. We determined the jet ski data were not useful as a calibration reference in water deeper than 10 m due to large uncertainty in the vertical measurement introduced by the lack of any sensor orientation data, that is, for pitch, roll, and heading to correct the measured slant range to a vertical measurement. The resulting calibrated EAARL-B data were then analyzed and compared with the original reference dataset, the jet-ski-based dataset from the same Fort Lauderdale site, as well as the depth-accuracy requirements of the International Hydrographic Organization (IHO). We do not claim to meet all of the IHO requirements and standards. The IHO minimum depth-accuracy requirements were used as a reference only and we do not address the other IHO requirements such as “ Full Seafloor Search”. Our results show good agreement between the calibrated EAARL-B data and all reference datasets, with results that are within the 95 percent depth accuracy of the IHO Order 1 (a and b) depth-accuracy requirements.

Open-File Report↗

USGS1998

Experimental analysis and simulation modeling of forest management impacts on wood thrushes, Hylocichla mustelina

North American Breeding Bird Survey data show that wood thrush (Hylocichla mustelina) populations in eastern U.S. forests have declined 1.8% per year during 1966-95. The declining quality of breeding forest tracts in North America is one possible cause for the apparent decline of some neotropical migratory birds, such as the wood thrush. In Georgia, however, wood thrush populations have declined during a period of increasing pine forest area and larger patch sizes. We hypothesized that forest management practices such as thinning and prescribed burning might create unsuitable habitat for wood thrushes. We conducted a four-year before/after, treatment/control experiment at the Piedmont National Wildlife Refuge in central Georgia to study to the effects of a treatment of thinning and prescribed burning on wood thrush demographic parameters. We simultaneously monitored wood thrush adults and juveniles with mark-recapture, radio-telemetry, nest searches, and plot-map surveys. Our analyses showed that wood thrushes were less likely to emigrate from the study compartments after the treatment, and wood thrushes exhibited some tendency to increase preference for hardwood habitats and decrease preference for pine habitats following the treatment. However, we observed no effects of treatment on nest success, adult survival, and adult and juvenile dispersal distances. We also found that female wood thrushes had lower survival rates than males during the breeding season, and we documented large-scale, within-year dispersal movements of adult (up to 17 km) and juvenile (up to 7 km) wood thrushes. We conclude that landscape level habitat quantity and quality must be considered during songbird management decisions. The documentation of sex- and age-specific wood thrush survival and movement rates was critical for construction of a set of population models. We used three stochastic models to learn more about wood thrush population dynamics and make predictions about population growth rates, reproductive success, and the effect of habitat changes on wood thrush populations. The simplest source/sink population model suggests that the Piedmont National Wildlife Refuge's wood thrush population is probably stable or increasing, and wood thrush populations in treated areas had higher growth rates than birds in untreated areas. We were able to use the individual-based model of wood thrush productivity to predict fecundity, a parameter that we could not measure directly in the field. Again, females on treated areas had higher fecundity than birds on untreated areas. Our spatially-based model predicted that wood thrush populations should respond positively to predicted changes in the age/size class structure of the Refuge's pine forests. Our model also showed that most wood thrushes leave the Refuge's forest compartments during the breeding season, and these dispersal movements are extremely important to understanding and managing wood thrush populations. The use of prescribed burning and retention shelterwood silviculture at the Piedmont National Wildlife Refuge does not appear to negatively affect the local wood thrush population. Continued use of the current management regime should result in adequate nesting, foraging, and escape habitats for wood thrushes. However, landscape-level habitat availability and quality, including lands outside the Refuge, must be considered when making management decisions that may affect wood thrushes.

Book↗

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↗

USGS2012

Effects of prescribed burning on marsh-elevation change and the risk of wetland loss

Marsh-elevation change is the net effect of biophysical processes controlling inputs versus losses of soil volume. In many marshes, accumulation of organic matter is an important contributor to soil volume and vertical land building. In this study, we examined how prescribed burning, a common marsh-management practice, may affect elevation dynamics in the McFaddin National Wildlife Refuge, Texas by altering organic-matter accumulation. Experimental plots were established in a brackish marsh dominated by Spartina patens , a grass found throughout the Gulf of Mexico and Atlantic marshes. Experimental plots were subjected to burning and nutrient-addition treatments and monitored for 3.5 years (April 2005 – November 2008). Half of the plots were burned once in 2006; half of the plots were fertilized seasonally with nitrogen, phosphorus, and potassium. Before and after the burns, seasonal measurements were made of soil physicochemistry, vegetation structure, standing and fallen plant biomass, aboveground and belowground production, decomposition, and accretion and elevation change (measured with Surface Elevation Tables (SET)). Movements in different soil strata (surface, root zone, subroot zone) were evaluated to identify which processes were contributing to elevation change. Because several hurricanes occurred during the study period, we also assessed how these storms affected elevation change rates. The main findings of this study were as follows: 1. The main drivers of elevation change were accretion on the marsh surface and subsurface movement below the root zone, but the relative influence of these processes varied temporally. Prior to Hurricanes Gustav and Ike (September 2008), the main driver was subsurface movement; after the hurricane, both accretion and subsurface movement were important. 2. Prior to Hurricanes Gustav and Ike, rates of elevation gain and accretion above a marker horizon were higher in burned plots compared to nonburned plots, whereas nutrient addition had no detectable influence on elevation dynamics. 3. Burning decreased standing and fallen plant litter, reducing fuel load. Hurricanes Gustav and Ike also removed fallen litter from all plots. 4. Aboveground and belowground production rates varied annually but were unaffected by burning and nutrient treatments. 5. Decomposition (of a standard cellulose material) in upper soil layers was increased in burned plots but was unaffected by nutrient treatments. 6. Soil physicochemistry was unaffected by burning or nutrient treatments. 7. The elevation deficit (difference between rate of submergence and vertical land development) prior to hurricanes was less in burned plots (6.2 millimeters per year [mm yr -1 ]) compared to nonburned plots (7.2 mm yr -1 ). 8. Storm sediments delivered by Hurricane Ike raised elevations an average of 7.4 centimeters (cm), which countered an elevation deficit that had accrued over 11 years. Our findings provide preliminary insights into elevation dynamics occurring in brackish marshes of the Texas Chenier Plain under prescribed fire management. The results of this study indicate that prescribed burning conducted at 3- to 5-year intervals is not likely to negatively impact the long-term sustainability of S. patens -dominated brackish marshes at McFaddin National Wildlife Refuge and may offset existing elevation deficits by ≈ 1 mm yr -1 . The primary drivers of elevation change varied in time and space, leading to a more complex situation in terms of predicting how disturbances may alter elevation trajectories. The potential effect of burning on elevation change in other marshes will depend on several site-specific factors, including geomorphic/ sedimentary setting, tide range, local rate of relative sea level rise, plant species composition, additional management practices (for example, for flood control), and disturbance types and frequency (for example, hurricanes or herbivore grazing). Increasing the scope of inference would require installation of SETs in replicate marshes undergoing different prescribed fire intervals and in different geomorphic settings (with different hurricane frequencies and/or different sedimentary settings). Multiple locations along the Gulf and Atlantic coasts where prescribed fire is used as a management tool could provide the appropriate setting for these installations.

Open-File Report↗