Selected procedures for biological and microbiological investigations
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Open-File Report↗
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Accelerometer-derived activity correlates with volitional swimming speed in lake sturgeon (Acipenser fulvescens)
Quantifying fine-scale locomotor behaviours associated with different activities is challenging for free-swimming fish. Biologging and biotelemetry tools can help address this problem. An open channel flume was used to generate volitional swimming speed (Us) estimates of cultured lake sturgeon (Acipenser fulvescens Rafinesque, 1817) and these were paired with simultaneously recorded accelerometer-derived metrics of activity obtained from three types of data-storage tags. This study examined whether a predictive relationship could be established between four different activity metrics (tail-beat frequency (TBF), tail-beat acceleration amplitude (TBAA), overall dynamic body acceleration (ODBA), and vectorial dynamic body acceleration (VeDBA)) and the swimming speed of A. fulvescens. Volitional Us of sturgeon ranged from 0.48 to 2.70 m·s−1 (0.51–3.18 body lengths (BL) · s−1). Swimming speed increased linearly with all accelerometer-derived metrics, and when all tag types were combined, Us increased 0.46 BL·s−1 for every 1 Hz increase in TBF, and 0.94, 0.61, and 0.94 BL·s−1 for every 1g increase in TBAA, ODBA, and VeDBA, respectively. Predictive relationships varied among tag types and tag-specific parameter estimates of Us are presented for all metrics. This use of acceleration data-storage tags demonstrated their applicability for the field quantification of sturgeon swimming speed.
Canadian Journal of Zoology↗
A water-quality assessment of the Muddy Fork Silver Creek watershed, Clark, Floyd, and Washington counties, Indiana
Data collected for a wide range of flow conditions from September 8, 1975, to July 13, 1976, reveal that human and animal waste loading of streams and pesticide use in the watershed are probably the most significant water-quality problems. Generally, the type(s) of water in tributary streams in the south and southwest parts of the watershed was calcium bicarbonate and in other tributaries were calcium sulfate and magnesium sulfate. Dissolved-solids concentrations of discharge from top-spill reservoirs were lower and more consistent over a range of flows than concentrations from uncontrolled streams. Chemical characteristics of discharges from bottom-draw reservoirs differed from those of discharges from the other reservoirs. More than half the manganese concentrations equaled or exceeded 0.05 milligrams per liter, the maximum concentration recommended for domestic water supplies. Leaf fall in forested parts of the watershed are probably a source of this manganese. Nitrate (as nitrogen) concentration of streams ranged from 0.00 to 2.5 milligrams per liter; orthophosphate (as phosphorus), from 0.00 to 0.29 milligrams per liter, and total organic carbon, from 2.0 to 14 milligrams per liter. Concentrations of fecal coliform bacteria and fecal streptococcal bacteria ranged from 5 to 65,000 colonies per 100 milliliters and from 5 to 24,000 colonies per 100 milliliters, respectively. Occasional human-waste contamination is indicated downstream from the towns of Borden and Speed. Data on periphyton, phytoplankton, and benthic communities collected during low flow in September 1975 indicate organic loading of Muddy Fork downstream from the town of Speed. Phytoplankton community structures varied temporally and spatially. Ranges of concentration of various chlorinated hydrocarbons in samples of bed materials (in micrograms per kilogram) were: chlordane, from 0 to 14; DDT, from 0 to 19; and PCB's, from 0 to 11. Concentrations of aldrin, DDD, DDE, heptachlor, and heptachlor epoxide of 5.1 micrograms per kilogram or less were also detected. The presence of these compounds makes them potentially available for accumulation in the biological food chain.
Indiana↗
Unlocking ecological insights from sub-seasonal visible-to-shortwave infrared imaging spectroscopy: The SHIFT campaign
We stand at the threshold of a transformative era in Earth observation, marked by space-borne visible-to-shortwave infrared (VSWIR) imaging spectrometers that promise consistent global observations of ecosystem function, phenology, and inter- and intra-annual change. However, the full value of repeat spectroscopy, the information embedded within different temporal scales, and the reliability of existing algorithms across diverse ecosystem types and vegetation phenophases have remained elusive due to the absence of suitable sub-seasonal spectroscopy data. In response, the Surface Biology and Geology (SBG) High-Frequency Time Series (SHIFT) campaign was initiated during late February 2022 in Santa Barbara County, California. SHIFT, designed to support NASA's SBG mission, addressed mission scoping, scientific advancement, applications development, and community building. This ambitious endeavor included weekly Airborne Visible InfraRed Imaging Spectrometer-Next Generation (AVIRIS-NG) imagery acquisitions for 13 weeks (spanning February 24 to May 29, 2022), accompanied by coordinated terrestrial vegetation and coastal aquatic data collection. We describe the rich datasets collected and illustrate how the complex sub-seasonal patterns of change can be linked to biological science and applications, surpassing insights from multispectral observations. Leveraging open-source processing methods and cloud-based analysis tools, the SHIFT campaign showcases the readiness of the scientific community to harness ecological insights from remotely sensed hyperspectral time series. We provide an overview of SHIFT's goals, data collections, preliminary results, and the collaborative efforts of early career scientists committed to unlocking the transformative potential of high-frequency time series data from space-borne VSWIR imaging spectrometers.
Ecosphere↗
Seven recommendations to make your invasive alien species data more useful
Science-based strategies to tackle biological invasions depend on recent, accurate, well-documented, standardized and openly accessible information on alien species. Currently and historically, biodiversity data are scattered in numerous disconnected data silos that lack interoperability. The situation is no different for alien species data, and this obstructs efficient retrieval, combination, and use of these kinds of information for research and policy-making. Standardization and interoperability are particularly important as many alien species related research and policy activities require pooling data. We describe seven ways that data on alien species can be made more accessible and useful, based on the results of a European Cooperation in Science and Technology (COST) workshop: (1) Create data management plans; (2) Increase interoperability of information sources; (3) Document data through metadata; (4) Format data using existing standards; (5) Adopt controlled vocabularies; (6) Increase data availability; and (7) Ensure long-term data preservation. We identify four properties specific and integral to alien species data (species status, introduction pathway, degree of establishment, and impact mechanism) that are either missing from existing data standards or lack a recommended controlled vocabulary. Improved access to accurate, real-time and historical data will repay the long-term investment in data management infrastructure, by providing more accurate, timely and realistic assessments and analyses. If we improve core biodiversity data standards by developing their relevance to alien species, it will allow the automation of common activities regarding data processing in support of environmental policy. Furthermore, we call for considerable effort to maintain, update, standardize, archive, and aggregate datasets, to ensure proper valorization of alien species data and information before they become obsolete or lost.
Frontiers in Applied Mathematics and Statistics↗
Envisioning, quantifying, and managing thermal regimes on river networks
Water temperatures fluctuate in time and space, creating diverse thermal regimes on river networks. Temporal variability in these thermal landscapes has important biological and ecological consequences because of nonlinearities in physiological reactions; spatial diversity in thermal landscapes provides aquatic organisms with options to maximize growth and survival. However, human activities and climate change threaten to alter the dynamics of riverine thermal regimes. New data and tools can identify particular facets of the thermal landscape that describe ecological and management concerns and that are linked to human actions. The emerging complexity of thermal landscapes demands innovations in communication, opens the door to exciting research opportunities on the human impacts to and biological consequences of thermal variability, suggests improvements in monitoring programs to better capture empirical patterns, provides a framework for suites of actions to restore and protect the natural processes that drive thermal complexity, and indicates opportunities for better managing thermal landscapes.
Washington↗
Molecular contributions to conservation
Recent advances in molecular technology have opened a new chapter in species conservation efforts, as well as population biology. DNA sequencing, MHC (major histocompatibility complex), minisatellite, microsatellite, and RAPD (random amplified polymorphic DNA) procedures allow for identification of parentage, more distant relatives, founders to new populations, unidentified individuals, population structure, effective population size, population-specific markers, etc. PCR (polymerase chain reaction) amplification of mitochondrial DNA, nuclear DNA, ribosomal DNA, chloroplast DNA, and other systems provide for more sophisticated analyses of metapopulation structure, hybridization events, and delineation of species, subspecies, and races, all of which aid in setting species recovery priorities. Each technique can be powerful in its own right but is most credible when used in conjunction with other molecular techniques and, most importantly, with ecological and demographic data collected from the field. Surprisingly few taxa of concern have been assayed with any molecular technique. Thus, rather than showcasing exhaustive details from a few well-known examples, this paper attempts to present a broad range of cases in which molecular techniques have been used to provide insight into conservation efforts.
Ecology↗
Lakes of Oregon, Volume 4: Clackamas County
An inventory of lakes and reservoirs of Oregon is essential for a complete evaluation of the total surface-water supply of the State and to provide a basis for answering questions about Oregon's lakes. Much of the information on lakes and reservoirs previously collected by Federal and State agencies has never been published. Those data were compiled and used as a basis for collecting additional information. This report provides information for use by city, county, and State planning groups as well as for sportsmen, tourists, and others interested in preserving the recreational value of Oregon's lakes. Because of the large number of lakes and reservoirs in Oregon, a single report covering the State would be bulky. Therefore, the lake information is being issued in several volumes on a county or multicounty basis. Volume 1, released in 1973, covered Clatsop, Columbia, and Tillamook Counties; volume 2 (1974 included Benton, Lincoln, and Polk Counties; and volume 3 (1975) included Hood River, Multnomah, Washington, and Yamhill Counties. Clackamas County was selected for volume 4. (See figure 1.) In addition to office compilation of existing data, each lake was visited. Most visits were made in summer or early fall when lakes were most accessible and when water temperature and biological activity were near maximum.
Oregon↗
Water and sediment quality in the Yukon River basin, Alaska, during water year 2004
This report contains water-quality and sediment-quality data from samples collected in the Yukon River Basin from March through September during the 2004 water year (WY). Samples were collected throughout the year at five stations in the basin (three on the main stem Yukon River, one each on the Tanana and Porcupine Rivers). A broad range of physical, chemical, and biological analyses are presented.
Open-File Report↗
Water-quality data for the American River basin, California, February-October 1979
Data were collected in the American River basin from February to October 1979 for use in assessing the water quality in the basin and developing land-use/water-quality relations. The basin covers 2,163 square miles of the western slope of the central Sierra Nevada. Basin headwaters are located primarily between Donner Summit and Echo Summit. Water-quality data were collected at 14 stream sites and at 3 sites on Folsom Lake and include selected measurements and analyses for physical, chemical, and biological properties and constituents.
California↗
Hydrologic data for selected streams in the coal area of southeastern Oklahoma, July 1978 to September 1982
Hydrologic data on quantity and quality of surface waters were collected in the coal resource area of southeastern Oklahoma during an investigation of the effects of coal surface mining on the hydrology of the area. The objective of the study was to determine the characteristics of the regional hydrologic system and to detect and document changes in the system that may occur as the result of coal surface mining. This report presents data which were collected at 13 sites in 4 counties between July 1978 and September 1982. The data include: (1) mean daily stream discharge; (2) physical properties, selected field constituents, and concentration of suspended sediment of water samples; (3) concentration of selected common constituents, nutrients, and trace elements of water samples; (4) mean daily specific conductance, pH, water temperature, and dissolved oxygen; and (5) analyses of biological samples.
Open-File Report↗
The Ozark Highlands
The Ozark Highlands include diverse topographic, geologic, soil, and hydrologic conditions that support a broad range of habitat types. The landscape features rugged uplands - some peaks higher than 2,500 feet above sea level - with exposed rock and varying soil depths and includes extensive areas of karst terrain. The Highlands are characterized by extreme biological diversity and high endemism (uniqueness of species). Vegetation communities are dominated by open oak-hickory and shortleaf pine woodlands and forests. Included in this vegetation matrix is an assemblage of various types of fens, forests, wetlands, fluvial features, and carbonate and siliceous glades. An ever-growing human population in the Ozark Highlands has become very dependent on reservoirs constructed on major rivers in the region and, in some cases, groundwater for household and public water supply. Because of human population growth in the Highlands and increases in industrial and agricultural activities, not only is adequate water quantity an issue, but maintaining good water quality is also a challenge. Point and nonpoint sources of excessive nutrients are an issue. U.S. Geological Survey (USGS) partnership programs to monitor water quality and develop simulation tools to help stakeholders better understand strategies to protect the quality of water and the environment are extremely important. The USGS collects relevant data, conducts interpretive studies, and develops simulation tools to help stakeholders understand resource availability and sustainability issues. Stakeholders dependent on these resources are interested in and benefit greatly from evolving these simulation tools (models) into decision support systems that can be used for adaptive management of water and ecological resources. The interaction of unique and high-quality biological and hydrologic resources and the effects of stresses from human activities can be evaluated best by using a multidisciplinary approach that the USGS can provide. Information varying from defining baseline resource conditions to developing simulation models will help resource managers and users understand the human impact on resource sustainability. Varied expertise and experience in biological and water-resources activities across the entire Highlands make the USGS a valued collaborator in studies of Ozark ecosystems, streams, reservoirs, and groundwater. A large part of future success will depend on the involvement and active participation of key partners.
Fact Sheet↗
Use of physical blockers to control invasive red swamp crayfish in burrows
The red swamp crayfish Procambarus clarkii is native to the southeast United States but has successfully invaded nearly every continent around the world. Although physical, biological, and chemical controls are employed to reduce or eliminate populations in open-water systems, terrestrial burrows provide a potential refuge from aquatic control treatments. We conducted burrow trials to test whether two physical blocker treatments would kill P. clarkii in their burrows. Bentonite clay (a sealing agent) and expanding foam (an insulating sealant) were each applied to 37 crayfish burrows, and 36 burrows served as treatment controls (i.e., 110 total burrows). Burrows were excavated 48 hr after the application of the physical blockers to assess the status of crayfish in treated and control burrows. There was 74% mortality of crayfish in occupied burrows treated with bentonite clay, 62% in burrows treated with expanding foam, and 6% mortality in control burrows. We believe bentonite clay should continue to be field-tested; however, because expanding foam is toxic to aquatic organisms and is expected to persist in the environment, we do not believe it is a suitable physical blocker for the control of invasive crayfish in burrows. Bentonite clay applications likely will not need permits, will mitigate damage to banks and levees caused by burrowing crayfish, and can be used with other control agents such as pesticides. However, the use of physical blockers may be limited at field sites that have burrows with complex morphologies. We believe the use of bentonite clay to control invasive crayfish in terrestrial burrows will provide resource managers with an effective tool for their integrative pest management programs.
Management of Biological Invasions↗
Reconnaissance of six solid-waste disposal sites in Puerto Rico and effects on water quality
Five solid-waste landfills and an open burning dump were studied in Puerto Rico to obtain physical, chemical and biological data on leachates, give an overview of their pollution potential, and determine the adequacy of monitoring at these or similar sites. These sites are operated by the municipal governments of Arecibo, Caguas, Cayey, Humacao, Mayaguez and Guayama. The bulk of waste is of domestic origin but wastes from local industries and institutions are also handled. Data were collected between February and July 1976. Parameters measured included temperature, specific conductance, pH, color, common ions, cyanide, macronutrients (nitrogen and phosphorus species), total organic carbon, dissolved oxygen, BOD5 (biochemical oxygen demand), COD (chemical oxygen demand), total and fecal conform, trace metals, and phenols. The results obtained indicated that leachate from most sites is enriched in common ions, macronutrients, and trace metals. A sample obtained from runoff at the Cayey landfill was the only one with an acidic pH (5.8). It had a common ion concentration of 10,750 mg/L (milligrams per liter), or twice that found in leachate contained within the buried refuse. The leachate from the Caguas site had the highest common ion concentration (12,520 mg/L). Maximum values for other parameters were as follows: Temperature, 33°C (or about 10°C above ambient ground-water temperature); specific conductance, 19,200 micromhos per centimeter; color, 2,200 units; cyanide, 30 ug/L (micrograms per liter); total nitrogen, 600 mg/L; total phosphorus, 4.3 mg/L; total organic carbon, 500 mg/L; 5-day biochemical oxygen demand, 5,540 mg/L; chemical oxygen demand, 3,000 mg/L; total coliform bacteria, 410,000 colonies per 100 milliliters; fecal coliform bacteria, 14,000 colonies per 100 milliliters; total arsenic, 54 ug/L; total cadmium, 15 ug/L; total chromium, 1,600 ug/L; total lead, 1,10C ug/L; total mercury, 2.6 ug/L; total nickel, 1,300 ug/L; and total phenols, 1,100 ug/L. Pollution of water resources is limited to the periphery of the sites. A major problem throughout seems to be related to operating methods. Under the conditions found, large quantities of rainwater and runoff could be available for leachate production. Generation of leachate may not be significant at present probably because of the recent establishment of the landfills (less than 5 years). Monitoring at these or similar sites in Puerto Rico can be limited to defining present baseline water-quality conditions and implementation of a sampling program. Baseline data could be limited to specific conductance, pH, color, common ions, and dissolved oxygen. A scheduled sampling program could be limited to specific conductance readings and measurement of concentration of bicarbonate, chloride, and dissolved oxygen.
Puerto Rico↗
Using piecewise regression to identify biological phenomena in biotelemetry datasets
1. Technological advances in the field of animal tracking have greatly expanded the potential to remotely monitor animals, opening the door to exploring how animals shift their behavior over time or respond to external stimuli. A wide variety of animal-borne sensors can provide information on an animal’s location, movement characteristics, external environmental conditions, and internal physiological status. 2. Here, we demonstrate how piecewise regression can be used to identify the presence and timing of potential shifts in a variety of biological responses using GPS telemetry and other biologging data streams. Different biological latent states can be inferred by partitioning a time-series into multiple segments based on changes in modeled responses (e.g., their mean, variance, trend, degree of autocorrelation) and specifying a unique model structure for each interval. 3. We provide six example applications highlighting a variety of taxonomic species, data streams, timescales and biological phenomena. These examples include a short-term behavioural response (flee and return) by a trumpeter swan Cygnus buccinator following a GPS collar deployment; remote identification of parturition based on movements by a pregnant moose Alces alces ; a physiological response (spike in heart-rate) in a black bear Ursus americanus to a stressful stimulus(presence of a drone); a mortality event of a trumpeter swan signalled by changes in collar temperature and overall dynamic body acceleration; an unsupervised method for identifying the onset, return, duration and staging use of sandhill crane Antigone canadensis migration; and estimation of the transition between incubation and brood-rearing (i.e. hatching) for a breeding trumpeter swan. 4. We implement analyses using the MCP package in R, which provides functionality for specifying and fitting a wide variety of user-defined model structures in a Bayesian framework and methods for assessing and comparing models using information criteria and cross-validation measures.
Journal of Animal Ecology↗
Conservation of the yellow-shouldered blackbird Agelaius xanthomus, an endagered West Indian species
The yellow-shouldered blackbird Agelaius xanthomus , endemic to Puerto Rico and Mona Island, is endangered, mainly because of brood parasitism by the shiny cowbird Molothrus bonariensis , which reached Puerto Rico at least 30 years ago. The yellow-shouldered blackbird populations have since declined, about 770–1200 remaining (470–900 on Mona Island) by 1982–1986 compared to a population of about 2400 in 1975. Nearly all nests of blackbirds in most of its habitats are parasitized by cowbirds. This significantly reduces nesting success, but blackbirds have evolved no defenses against brood parasitism. Removal of cowbirds from the yellow-shouldered blackbird nesting grounds, modeled after similar programmes for the brown-headed cowbird Molothrus ater on Kirtland's warbler Dendroica kirtlandii nesting areas, significantly increased blackbird production. Blackbirds readily accept nest boxes, and breeding populations can be established in otherwise unusable sites and can be concentrated in mangrove habitats, were they are more easily protected by cowbird removal. Furthermore, yellow-shouldered blackbird pairs using cavities, including nest boxes, fledged more young per nest than pairs using open nests.
Boquerón Commonwealth Forest, Roosevelt Roads Nava↗
Lakes of Oregon, Volume 3: Hood River, Multnomah, Washington and Yamhill Counties
An inventory of lakes and reservoirs of Oregon is essential for a complete evaluation of the total surface-water supply of the State and to provide a basis for answering questions about Oregon's lakes. Much of the information on lakes and reservoirs previously collected by Federal and State agencies has never been published. These data were compiled and used as a basis for collecting additional information. This report provides information for use by city, county, and State planning groups as well as for sportsmen, tourists, and others interested in preserving the recreational value of Oregon's lakes. Because of the large number of lakes and reservoirs in Oregon, a single report covering the State would be bulky. Therefore, the lake information is being published in several volumes on a county or multicounty basis. Volume 1, published in 1973, covered Clatsop, Columbia, and Tillamook Counties; volume 2, published in 1974, included Benton, Lincoln, and Polk Counties. Hood River, Multnomah, Washington, and Yamhill Counties were selected for volume 3. (See fig. 1.) In addition to office compilation of existing data, each lake was also visited. Most visits were made in summer or early fall when lakes were most accessible and when water temperature and biological activitiy were at a maximum.
Oregon↗
Lakes of Oregon, Volume 5: Marion County
An inventory of lakes and reservoirs of Oregon is essential for a complete evaluation of the total surface-water supply of the State and to provide a basis for answering questions about Oregon's lakes. Much of the information on lakes and reservoirs previously collected by Federal and State agencies has never been published. Those data were compiled and used as a basis for collecting additional information. This report provides information for use by city, county, and State planning groups as a basis for designing more advanced interpretative studies. The information also will be useful to sportsmen, tourists, and others interested in preserving the recreational value of Oregon's lakes. Because of the large number of lakes and reservoirs in Oregon, a single report covering the State would be bulky. Therefore, the lake information is being issued in several volumes on a county or multicounty basis. Volume 1, released in 1973, covered Clatsop, Columbia, and Tillamook Counties; volume 2 (1974) included Benton, Lincoln, and Polk Counties; volume 3 (1975) included Hood River, Multnomah, Washing ton, and Yamhill Counties; and volume 4 (1976) included Clackamas County. Marion County was selected for volume 5. (See figure 1.) The southeast part of Marion County lies in a national wilderness area. Wilderness areas are protected under the National Wilderness Preservation System that directs management "for the use and enjoyment of the American people in such a manner as will leave them unimpaired for future use and enjoyment as wilderness." Regulations for wilderness use and entry permits may be obtained at U.S. Forest Service offices. In addition to office compilation of existing data, each lake was visited. Most visits were made in summer or early fall when lakes were most accessible and when water temperature and biological activitiy were near maximum.
Oregon↗