Department of Animal Science

Selenium (Se) deficiency occurs commonly in California grazing cattle and has been associated with reduced immune function and, in some studies, reduced weight gain. Multiple methods of supplementing Se are available, but little research has compared the effects of these methods on whole blood Se levels and weight gain. In two trials, we evaluated four methods of Se supplementation — an intrarumenal bolus, two injectable preparations and a loose salt containing 120 ppm Se — over an 85- to 90-day period in Se-deficient yearling cattle in Tehama County. The bolus treatment raised whole blood Se levels to an adequate level (0.08 ppm) for the entire study period. Whole blood Se concentrations in injected cattle initially reached adequate levels but then declined to deficient levels. The loose salt treatment acted slowly, with average whole blood Se concentration reaching adequate levels at the end of the study period. None of the treatments significantly affected weight gain and Se blood concentration was not correlated with weight gain. In growing cattle, it appears that Se supplementation may be viewed not as a direct driver of weight gain, but rather as similar to vaccination, in that it can prevent health problems that might otherwise lead to reduced weight gain.

The nutritious stems and leaves of broccoli often go to landfills as byproducts after harvesting and processing of the florets. The stems and leaves contain specific carotenoids that are noted to have anti-allergic, anti-cancer and anti-obesity bioactivity. Research has shown the stems and leaves could be made into a meal, small amounts of which could be added to poultry diets to increase the nutrients in eggs and also deepen the color of the yolks. We studied adding a relatively high percentage (15%) of broccoli stem and leaves meal to the corn-soy diets of White Leghorn inbred crosses. Compared to the control group of hens, fed the unenhanced corn-soy diet, feed consumption, body weight, feed conversion, egg production, egg weight, albumen height, Haugh units and eggshell thickness were statistically similar. No harmful effects of the glucosinolates in broccoli were observed. Yolk color scores were significantly higher with the addition of the meal. The results justify larger studies with various commercial lines of laying hens and various levels of meal added to the diets.

California summers are hot, compromising the welfare and productivity of dairy cows. To minimize negative effects, producers use shade, fans and sprayed water. However, little is known about how those heat abatement strategies are provided in commercial conditions, nor their effectiveness. Ten dairies with drylots, a common housing system in California, were assessed for strategies provided, and the cows' responses to heat load were observed for 3 days in the afternoon. Dairies were diverse in all aspects. Shade varied in terms of placement (at corral and feed bunk or at corral only) and amount (28 to 74 square feet, or 2.6 to 6.9 square meters, per cow). The quantity of water used to spray cows ranged from 0 to 6.8 gallons (0 to 25.6 liters) per hour per cow. Across dairies, there was a range in the cows' shade use (47% to 98% of herd) and feeding activity (7% to 33% of herd). Respiration rates ranged from 65 (normal) to 95 breaths per minute (very hot) and were positively related to inactivity. Our results indicate that there are opportunities to improve cooling, and consequently dairy cattle welfare, in drylots.

Legacy and current-use contaminants enter into and accumulate throughout the San Francisco Bay−Delta (Bay−Delta), and are present at concentrations with known effects on species important to this diverse watershed. There remains major uncertainty and a lack of focused research able to address and provide understanding of effects across multiple biological scales, despite previous and ongoing emphasis on the need for it. These needs are challenging specifically because of the established regulatory programs that often monitor on a chemical-by-chemical basis, or in which decisions are grounded in lethality-based endpoints. To best address issues of contaminants in the Bay−Delta, monitoring efforts should consider effects of environmentally relevant mixtures and sub-lethal impacts that can affect ecosystem health. These efforts need to consider the complex environment in the Bay−Delta including variable abiotic (e.g., temperature, salinity) and biotic (e.g., pathogens) factors. This calls for controlled and focused research, and the development of a multi-disciplinary contaminant monitoring and assessment program that provides information across biological scales. Information gained in this manner will contribute toward evaluating parameters that could alleviate ecologically detrimental outcomes. This review is a result of a Special Symposium convened at the University of California−Davis (UCD) on January 31, 2017 to address critical information needed on how contaminants affect the Bay−Delta. The UCD Symposium focused on new tools and approaches for assessing multiple stressor effects to freshwater and estuarine systems. Our approach is similar to the recently proposed framework laid out by the U.S. Environmental Protection Agency (USEPA) that uses weight of evidence to scale toxicological responses to chemical contaminants in a laboratory, and to guide the conservation of priority species and habitats. As such, we also aimed to recommend multiple endpoints that could be used to promote a multi-disciplinary understanding of contaminant risks in Bay−Delta while supporting management needs.

An extreme decline in Delta Smelt (Hypomesus transpacificus) abundance has led to a number of management actions to support this endangered species, including the development and refinement of culture techniques and the creation of a refuge population. The wild Delta Smelt population has diminished to the point that many in the scientific community believe population supplementation using cultured fish needs to be experimentally evaluated as a possible management tool. Concerns about supplementation include the effectiveness of this action, and its potential to divert attention and funding from other needed management actions such as habitat restoration. Here, we describe the outcomes of a 2-day workshop that described the current refuge population, and identified key issues for potential future use of cultured Delta Smelt for research and management. Expanded use of cultured Delta Smelt is controversial and requires consideration for complexities that include legal constraints and permitting requirements. Developing policies that allow for in situ experiments using cultured Delta Smelt appears to be a precursor for advancing policies that might allow supplementation actions. Releases of cultured fish, either experimentally or as a management action, clearly need to be conducted within an adaptive management program that is integrated with other strategies, including habitat restoration. We describe a general framework for evaluating the potential risks of supplementation and include suggestions for how to reduce risks and uncertainty. Overall, we conclude there is sufficient baseline information about Delta Smelt and the existing culture program to proceed with targeted field research that utilizes cultured fish. Finally, given the dire status of this species, we conclude that rapid progress toward the development of a viable and testable supplementation program must be a priority for Delta Smelt conservation.

Delta Smelt have collapsed demographically, but little is known about their current genetic status. We used 12 microsatellite loci to evaluate two measures of the effective population size (Ne) of Delta Smelt. Ne is a measure that offers predictive power regarding the loss of genetic diversity in a population over time, as well as the short and long-term genetic risks for loss of fitness resulting from low diversity. We found that the Ne of Delta Smelt is too high to accurately estimate with the data (upper 95% confidence intervals were infinity), but the lower confidence intervals of NeLD (linkage disequilibrium Ne) were above 1,000, while some of the lower confidence intervals of NeV (variance Ne) were below 1,000. We interpret this to indicate that Delta Smelt are not declining because of genetic factors, and are not at immediate risk of losing genetic diversity from low Ne. We caution that these estimates are from a short-term data set estimated from a population that has already been declining for decades, and that it is likely that Delta Smelt have lost diversity. We suggest continuing efforts to maximize abundance to prevent further loss of genetic diversity.

Agriculture in California contributes 8% of the state's greenhouse gas (GHG) emissions. To inform the state's policy and program strategy to meet climate targets, we review recent research on practices that can reduce emissions, sequester carbon and provide other co-benefits to producers and the environment across agriculture and rangeland systems. Importantly, the research reviewed here was conducted in California and addresses practices in our specific agricultural, socioeconomic and biophysical environment. Farmland conversion and the dairy and intensive livestock sector are the largest contributors to GHG emissions and offer the greatest opportunities for avoided emissions. We also identify a range of other opportunities including soil and nutrient management, integrated and diversified farming systems, rangeland management, and biomass-based energy generation. Additional research to replicate and quantify the emissions reduction or carbon sequestration potential of these practices will strengthen the evidence base for California climate policy.

Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

Microbial methanogenesis is a major contributor to global warming, and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still underexplored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with the exchange of syntrophic electron carriers (H₂ or formate) in methanogenic systems presents an additional target for methane control. Here, we show that hypophosphite (H₂PO₂^-), an inorganic formate analogue, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively nontoxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation, and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate the carbon cycle in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive strategy for methane control in syntrophic methanogenic ecosystems.

Extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) and carbapenem-resistant Klebsiella pneumoniae (CRKP) represent a global health risk, with ornamental birds serving as potential reservoirs for their dissemination. This study aimed to isolate and characterize ESBL-KP and CRKP from ornamental birds and their surrounding environments. A total of 112 samples, including equal numbers of feces, cage swab, cage water, cage feed, store feed, handlers hand swab, nasal swab, and air samples, were collected equally from both households and pet bird shops. Overall, 52.68% (59/112, CI₉₅: 0.435-0.6168) isolates were confirmed as positive, where a higher occurrence was observed in pet store samples (32/56, 57.14%) than in household samples (27/56, 48.21%). In the disk diffusion test, 79.67% (47/59, CI₉₅: 0.6773-0.8796) isolates were identified as multidrug-resistant, with high resistance to imipenem and cefotaxime (both 66.10%), meropenem and ceftriaxone (each 59.02%). The occurrence of ESBL-producing isolates was higher in shop samples (26/32, 81.25%) than in household samples (12/27, 44.44%). In the Congo Red assay, 76.28% (45/59, CI₉₅: 0.6403-0.8531) isolates were identified as strong biofilm producers. Resistance genes, bla_CTX-M (92.10%), bla_TEM (84.21%), bla_SHV (78.95%), bla_OXA-51 (51.42%), and bla_NDM (34.29%), conferring resistance to beta-lactams and carbapenems were detected in the K. pneumoniae isolates, along with virulence genes, uge (100%), entB (83.05%), mrkD (81.36%), and kfu (30.51%). As a first report from Bangladesh, this study highlights the widespread occurrence of ESBL-KP, CRKP and biofilm-producing K. pneumoniae in ornamental birds, emphasizing the urgent need for a One Health approach to prevent associated zoonotic and environmental risks.