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DayCent is a biogeochemical model of intermediate complexity widely used to simulate greenhouse gases (GHG), soil organic carbon and nutrients in crop, grassland, forest and savannah ecosystems. Although this model has been applied to a wide range of ecosystems, it is still typically parameterized through a traditional “trial and error” approach and has not been calibrated using statistical inverse modelling (i.e. algorithmic parameter estimation). The aim of this study is to establish and demonstrate a procedure for calibration of DayCent to improve estimation of GHG emissions. We coupled DayCent with the parameter estimation (PEST) software for inverse modelling. The PEST software can be used for calibration through regularized inversion as well as model sensitivity and uncertainty analysis. The DayCent model was analysed and calibrated using N2O flux data collected over 2 years at the Iowa State University Agronomy and Agricultural Engineering Research Farms, Boone, IA. Crop year 2003 data were used for model calibration and 2004 data were used for validation. The optimization of DayCent model parameters using PEST significantly reduced model residuals relative to the default DayCent parameter values. Parameter estimation improved the model performance by reducing the sum of weighted squared residual difference between measured and modelled outputs by up to 67 %. For the calibration period, simulation with the default model parameter values underestimated mean daily N2O flux by 98 %. After parameter estimation, the model underestimated the mean daily fluxes by 35 %. During the validation period, the calibrated model reduced sum of weighted squared residuals by 20 % relative to the default simulation. Sensitivity analysis performed provides important insights into the model structure providing guidance for model improvement.
To document the environmental occurrence and persistence of fungicides, a robust and sensitive analytical method was used to measure 34 fungicides and an additional 57 current-use pesticides in bed sediments and suspended solids collected from areas of intense fungicide use within three geographic areas across the United States. Sampling sites were selected near or within agricultural research farms using prophylactic fungicides at rates and types typical of their geographic location. At least two fungicides were detected in 55% of the bed and 83% of the suspended solid samples and were detected in conjunction with herbicides and insecticides. Six fungicides were detected in all samples including pyraclostrobin (75%), boscalid (53%), chlorothalonil (41%) and zoxamide (22%). Pyraclostrobin, a strobilurin fungicide, used frequently in the United States on a variety of crops, was detected more frequently than p,p′ -DDE, the primary degradate of p,p′ -DDT, which is typically one of the most frequently occurring pesticides in sediments collected within highly agricultural areas. Maximum fungicide concentrations in bed sediments and suspended solids were 198 and 56.7 μg/kg dry weight, respectively. There is limited information on the occurrence, fate, and persistence of many fungicides in sediment and the environmental impacts are largely unknown. The results of this study indicate the importance of documenting the persistence of fungicides in the environment and the need for a better understanding of off-site transport mechanisms, particularly in areas where crops are grown that require frequent treatments to prevent fungal diseases.
Plot-scale experimentation can provide valuable insight into the effects of manure management practices on phosphorus (P) runoff, but whole-farm evaluation is needed for complete assessment of potential trade offs. Artificially-applied rainfall experimentation on small field plots and event-based and long-term simulation modeling were used to compare P loss in runoff related to two dairy manure application methods (surface application with and without incorporation by tillage) on contrasting Pennsylvania soils previously under no-till management. Results of single-event rainfall experiments indicated that average dissolved reactive P losses in runoff from manured plots decreased by up to 90% with manure incorporation while total P losses did not change significantly. Longer-term whole farm simulation modeling indicated that average dissolved reactive P losses would decrease by 8% with manure incorporation while total P losses would increase by 77% due to greater erosion from fields previously under no-till. Differences in the two methods of inference point to the need for caution in extrapolating research findings. Single-event rainfall experiments conducted shortly after manure application simulate incidental transfers of dissolved P in manure to runoff, resulting in greater losses of dissolved reactive P. However, the transfer of dissolved P in applied manure diminishes with time. Over the annual time frame simulated by whole farm modeling, erosion processes become more important to runoff P losses. Results of this study highlight the need to consider the potential for increased erosion and total P losses caused by soil disturbance during incorporation. This study emphasizes the ability of modeling to estimate management practice effectiveness at the larger scales when experimental data is not available.
We observed behavior consistent with nest-guarding in Agassiz's desert tortoise (Gopherus agassizii) at two nests in a large wind-energy-generation facility near Palm Springs, California, locally known as the Mesa Wind Farm. As researchers approached the nests, female desert tortoises moved to the entrance of their burrows and positioned themselves sideways, directly over their nests. One female stretched her limbs outward and wedged herself into the burrow (her plastron directly above the nest). Guarding of nests is rarely observed in Agassiz's desert tortoise but can occur as a result of attempted predation on eggs by Gila monsters (Heloderma suspectum) or in direct response to the perceived threat posed by researchers. This is the first report of nest-guarding for G. agassizii in the Sonoran Desert ecosystem of California.
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Agricultural lands are an important part of the economy and heritage of the Chesapeake Bay watershed and are a focus of conservation activities. Streams and rivers around farms provide communities with drinking water and recreational opportunities, but these local benefits can be impaired by elevated nutrient and sediment concentrations. Compared to inputs from the atmosphere, wastewater, and urban and suburban areas, agricultural lands are the largest source of nutrients and sediment in many Chesapeake Bay streams. Farmers are voluntary conservation partners and have an important role in improving water-quality conditions. This fact sheet summarizes recent scientific insights from the U.S. Geological Survey (USGS) that can help farmers use conservation practices and their knowledge of local site conditions to achieve cleaner water.
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Bovine tuberculosis is a bacterial disease caused by Mycobacterium bovis in livestock and wildlife with hosts that include Eurasian badgers ( Meles meles ), brushtail possum ( Trichosurus vulpecula ), and white-tailed deer ( Odocoileus virginianus ). Risk-assessment efforts in Michigan have been initiated on farms to minimize interactions of cattle with wildlife hosts but research on M. bovis on cattle farms has not investigated the spatial context of disease epidemiology. To incorporate spatially explicit data, initial likelihood of infection probabilities for cattle farms tested for M. bovis , prevalence of M. bovis in white-tailed deer, deer density, and environmental variables for each farm were modeled in a Bayesian hierarchical framework. We used geo-referenced locations of 762 cattle farms that have been tested for M. bovis , white-tailed deer prevalence, and several environmental variables that may lead to long-term survival and viability of M. bovis on farms and surrounding habitats (i.e., soil type, habitat type). Bayesian hierarchical analyses identified deer prevalence and proportion of sandy soil within our sampling grid as the most supported model. Analysis of cattle farms tested for M. bovis identified that for every 1% increase in sandy soil resulted in an increase in odds of infection by 4%. Our analysis revealed that the influence of prevalence of M. bovis in white-tailed deer was still a concern even after considerable efforts to prevent cattle interactions with white-tailed deer through on-farm mitigation and reduction in the deer population. Cattle farms test positive for M. bovis annually in our study area suggesting that the potential for an environmental source either on farms or in the surrounding landscape may contributing to new or re-infections with M. bovis . Our research provides an initial assessment of potential environmental factors that could be incorporated into additional modeling efforts as more knowledge of deer herd factors and cattle farm prevalence is documented.
Initial success in sperm cryopreservation came at about the same time for aquatic species and livestock. However, in the 50-plus years since then cryopreserved sperm of livestock has grown into a billion-dollar global industry, while despite work in some 200 species with well over 200 published reports, cryopreservation of aquatic species sperm remains essentially a research activity with little commercial application. Most research has focused on large-bodied culture and sport fishes, such as salmonids, carps, and catfishes, and mollusks such as commercially important oyster and abalone species. However, only a handful of studies have addressed sperm cryopreservation in small fishes, such as zebrafish, and in endangered species. Overall, this work has yielded techniques that are being applied with varying levels of success around the world. Barriers to expanded application include a diverse and widely distributed literature base, technical problems, small sperm volumes, variable results, a general lack of access to the technology, and most importantly, the lack of standardization in practices and reporting. The benefits of cryopreservation include at least five levels of improvements for existing industries and for creation of new industries. First, cryopreservation can be used to improve existing hatchery operations by providing sperm on demand and simplifying the timing of induced spawning. Second, frozen sperm can enhance efficient use of facilities and create new opportunities in the hatchery by eliminating the need to maintain live males, potentially freeing resources for use with females and larvae. Third, valuable genetic lineages such as endangered species, research models, or improved farmed strains can be protected by storage of frozen sperm. Fourth, cryopreservation opens the door for rapid genetic improvement. Frozen sperm can be used in breeding programs to create improved lines and shape the genetic resources available for aquaculture. Finally, cryopreserved sperm of aquatic species will at some point become an entirely new industry itself. A successful industry will require integrated practices for sample collection, refrigerated storage, freezing, thawing, rules for use and disposal, transfer agreements, and database development. Indeed the development of this new industry is currently constrained by factors including the technical requirements for scaling-up to commercial operations during the transition from research, and the absence of uniform quality control practices, industry standards, marketing and price structures, and appropriate biosecurity safeguards.
The use of winter cover crops and conservation tillage are agricultural practices promoted to reduce nutrient and sediment loss from cropland, improve soil health, increase infiltration, and support farm nutrient cycling and ecosystem services. However, environmental performance of these practices is variable in the working farm landscape. The Lower Chesapeake Bay research project within the USDA Long-Term Agroecosystem Research (LTAR) network has collaboratively developed satellite remote sensing algorithms to measure the performance and phenology of winter cover crops (aboveground biomass, nitrogen content, fractional cover, and emergence and termination dates) using no-cost Harmonized Landsat and Sentinel-2 multispectral satellite imagery. This research supports annual operational assessment of >28,000 fields per year in four states. Results document the impacts of agronomic management on conservation outcomes, support adaptive management of incentive payment structures, and can reduce the workload for conservation district staff by remotely verifying cover crop management. Additionally, super-spectral satellite applications have been developed to accurately map crop residue cover by measuring lignocellulose absorption in shortwave infrared wavelengths, producing a 7-year time series of tillage intensity maps for the Delmarva Peninsula. These remote sensing products can be used in decision support and modeling to estimate changes in nutrient, sediment, and carbon cycling resulting from conservation practice implementation in the working farm landscape. This manuscript provides an overview of remote sensing research findings and applications associated with the USDA LTAR and Conservation Effects Assessment Projects (CEAP), documenting a variety of previously published outcomes with update and expansion of techniques using additional unpublished data and analyses as appropriate.
We describe efforts to obtain access for research to 81 wetland basins on 69 farms in four zones of the Prairie Pothole Region of North Dakota, South Dakota, and Minnesota. Access was obtained to 54% of the farms in areas where land was intensively cropped and 87% of farms in areas of low cropping intensity. On average, 1.35 operators had to be contacted and 1.70 interviews were required to obtain a decision on access to a farm. On 77% of the farms, cooperators placed at least one restriction on access, most commonly requiring walking access only or notification before nighttime work. Cost of obtaining access averaged $265/farm in wages and travel expenses. No cooperators were willing to sign written access agreements. Operators rescinded access to four farms and drained three wetland basins during the first year; six of the seven sites lost were in the intensively cropped portion of a low-wetland-density zone. The difficulty of obtaining and retaining research access to privately owned wetland basins in intensively cropped areas may be related to landowner attitudes towards wetlands. Researchers may have to rely on remote sensing or consider payment for access to secure representative research sites in such areas. Unwillingness of cooperators to sign access agreements may jeopardize research by the newly formed National Biological Service and other resource management agencies.
Gridded multibeam bathymetry covers approximately 634 square kilometers of sea floor in Block Island Sound. Although originally collected for charting purposes during National Oceanic and Atmospheric Administration hydrographic surveys H12009, H12010, H12011, H12015, H12033, H12137, and H12139, these combined acoustic data and the sea-floor sediment sampling and photography stations subsequently occupied to verify them during U.S. Geological Survey cruise 2011-006-FA (1) show the composition and terrain of the seabed, (2) provide information on sediment transport and benthic habitat, and (3) are part of an expanding series of studies that provide a fundamental framework for research and management activities (for example, wind farms and fisheries) along the Rhode Island inner continental shelf.
Summary – We reviewed all the peer-reviewed scientific publications we could find on the known and potential effects of wind farm development, operation, maintenance, and decommissioning on reptiles and amphibians (collectively herpetofauna) worldwide. Both groups are declining globally due to a multitude of threats including energy development. Effect studies were limited to the long-term research by the authors on Agassiz’s Desert Tortoise ecology and behavior at single operational wind farm in California, US and an analysis of the effects of wind farm installation on species richness of vertebrates including reptiles and amphibians in northwestern Portugal. Research on Agassiz’s Desert Tortoise found few demonstrable differences in biological parameters between populations in the wind farm and those in more natural habitats. High reproductive output is due to the regional climate and not to the presence or operation of the wind farm. Site operations have resulted in death and injury to a small number of adult tortoises and over the long-term tortoises now appear to avoid the areas of greatest turbine concentration. Research in Portugal using models and simulations based on empirical data show that vertebrate species richness (including herpetofauna) decreased by almost 20% after the installation of only two large monopole turbines per 250 x 250 m plot. Knowledge of the known responses of herpetofauna to various disturbances allows identification of potential impacts from construction material acquisition in offsite areas, mortality and stress due to impacts of roads and related infrastructure, destruction and modification of habitat, habitat fragmentation and barriers to gene flow, noise, vibration, electromagnetic field generation, heat from buried high voltage transmission lines, alteration of local and regional climate, predator attraction, and increased risk of fire. Research on herpetofauna lags far behind what is needed and, in particular, before-after-control-impact studies are critically needed to identify cause and effect relationships in order to develop effective mitigation strategies for any negative impacts.