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Open Access Publications from the University of California

Scholarly Works (20 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2017)
The utilization of dairy wastewater for producing algal biomass is seen as a two-fold opportunity to treat wastewater and produce algae biomass, which can be potentially used for production of biofuels. In animal agriculture system, one of the major waste streams is dairy manure that contains high levels of nitrogen and phosphorus. Furthermore, it is produced abundantly in California's dairy industry, as well as many other parts of the world. We hypothesized that flushed manure, wastewater from a dairy farm, can be used as a potential feedstock after pretreatment to grow Chlorella vulgaris biomass and to reduce nutrients of manure. In this study, we focused on investigating the use of flushed manure, produced in a dairy farm for growing C. vulgaris biomass. A series of batch-mode experiments, fed with manure feedstock and synthetic medium, were conducted and corresponding C. vulgaris production was analyzed. Impacts of varying levels of sterilized manure feedstock (SMF) and synthetic culture medium (SCM) (20-100%) on biomass production, and consequential changes in total nitrogen (TN) and total phosphorus (TP) were determined. C. vulgaris production data (Shi et al., 2016) were fitted into a model (Aslan and Kapdan, 2006) for calculating kinetics of TN and TP removal. Results showed that the highest C. vulgaris biomass production occurs, when SMF and SCM were mixed with ratio of 40%:60%. With this mixture, biomass on Day 9 was increased by 1,740% compared to initial biomass; and on Day 30, it was increased by 2,456.9%. The production was relatively low, when either only SCM or manure feedstock medium (without pretreatment, i.e., no sterilization) was used as a culture medium. On this ratio, TN and TP were reduced by 29.9 and 12.3% on Day 9, and these reductions on Day 30 were 76 and 26.9%, respectively.
    Cover page: Assessing Nutrient Removal Kinetics in Flushed Manure Using Chlorella vulgaris Biomass Production
    • Thesis
    • Peer Reviewed
    UC Davis Electronic Theses and Dissertations (2024)

    Nitrate and bacterial groundwater pollution from dairy farms and surrounding croplands is a large and growing problem not only for surrounding ecosystems, but also for the health of the cattle consuming this untreated water if present at high enough levels. Point-of-use filtration methods could provide a low-cost means of removing such contaminants to within acceptable levels, but experimentation is needed to identify acceptable media and optimal treatment designs.

    This thesis is divided into four main chapters; the first chapter presents an introduction to the issue, pollutant health implications, and existing treatment options within a comprehensive literature review. The second chapter aims to assess the prevalence of nitrate and bacteria levels in dairy cattle water troughs throughout several dairy farms in central California. The purpose of the second chapter is to determine whether contaminant levels are within recommended levels as well as to identify the predominant source of each contamination to inform future design aspects of a treatment system. The third chapter aims to assess different commercially available, natural media for their ability to remove nitrate and bacteria through various column filtration and batch adsorption experiments. The fourth chapter outlines preliminary field-scale experiments conducted to assess removal potential at higher flow rates as well as identifies ways to further optimize for contaminant removal.

    While there are no set regulations for levels of either pollutant for dairy cattle water consumption, the general recommendation of 44 ppm NO3- was exceeded in 47% of the 62 troughs, and 89% of the 44 troughs analyzed for bacterial levels exceeded the recommended 15 CFU/100 mL total coliform count for adult cattle. These results suggest a significant portion of troughs would benefit from nitrate and bacteria reduction, and when alternative water sources are unavailable, column filtration may provide a sufficient treatment option. Of the filter media tested at lab scale, powdered activated carbon (PAC) provided the highest removal efficiency and adsorption capacity for both contaminants, but the high pressure required as well as its susceptibility to reduced long-term efficiency suggests that multi-media column filtration with PAC may improve the viability for a small-scale cattle drinking water filtration treatment system. Granular activated charcoal (GAC), which has larger particle size and lower surface area was found to achieve the second highest removal rate for both contaminants with lower pressure requirements, so column filtration with mixed media including both PAC and GAC is proposed and tested at field scale. While further optimization is required for the proposed treatment system, it offers a low cost and easily implementable treatment option for improving dairy cattle drinking water in troughs.

      • Thesis
      • Peer Reviewed
      UC Davis Electronic Theses and Dissertations (2023)

      Dairy industry is important for milk production and has substantial contribution to the California’s economy, however, dairy farms also produce manure, which impacts the environment. Dairy manure contains carbon, nitrogen and phosphorus, which are beneficial to soil. Manure also contains many bacteria including human pathogen, such as Salmonella and Escherichia coli (E. coli) which poses risk to public health. In this research, an intensive reconnaissance survey of manure stored in dairy lagoon was conducted to determine the prevalence of E. coli and Salmonella. In addition, an attempt was made to develop the ozone and air-based treatment method to reduce pathogen in liquid manure. First a comprehensive review on microbial pollution of manure, and various control method was performed (Chapter 1). Secondly, a field study was undertaken to collect dairy manure from 20 dairy farms to determine the prevalence of indicator E. coli, Shiga toxin producing E. coli (STEC), and E. coli O157:H7 (Chapter 2). Finally, a lab scale experiment was developed to determine the impact of ozone and air injection on E. coli inactivation in liquid manure (Chapter 3). The first chapter addresses the issues of microbial pathogen in manure and associated risk to human, animal and environment and impacts of various treatment methods on bacteria control. Previous studies showed that anaerobic digestion reduces E. coli and Salmonella under prolonged incubation and high temperature conditions, however, many anaerobic pathogens such as Clostridium survive anaerobic environment. In anaerobic incubation, E. coli level is reduced, but these bacteria are not eliminated completely. In the second chapter, several bacteria testing methods were used to determine the prevalence of E. coli, Salmonella, STEC and E. coli O157:H7 which are common pathogens in dairy manure. About 177 manure samples were collected from 20 dairy farms from primary and secondary lagoons to test the bacteria using agar culture-based methods, polymerase chain reaction (PCR) method for detection of E. coli and Salmonella. In addition, a real- time PCR based method was used to determine the presence of E coli O157:H7. Results showed that the prevalence of Salmonella in manure sample is lower than E. coli. The bacteria detection approach presented here could reduce the number of testing required during downstream confirmation process. The presence of Salmonella was found in 2.26 % of the samples, and both the culture-based and PCR methods yielded comparable outcomes in detecting Salmonella. Moreover, approximately 11.30% of the total samples out of the 177 were identified as positive for STEC by qPCR. None of the lagoon samples were positive to E coli O157:H7 by qPCR. The outcomes of this study hold substantial importance to determine the microbial quality of lagoon manure, and aid in the selection of appropriate methodologies for determining the prevalence of pathogenic organisms in dairy manure. In the third chapter, lab scale experiments were conducted to determine the impacts of ozone injection (Ozonation) and air injection (Aeration) in liquid dairy manure on E. coli reduction. Liquid manure was exposed to ozone and air for multiple durations (0 min, 60 min, 120 min, and 240 min) and E. coli levels were determined. Further, manure samples were analyzed for pH, salt content, potassium (K+), sodium (Na+), nitrate (NO3-), calcium (Ca2+), and electrical conductivity (EC, mS/cm). Results showed that Ozonation can be an effective treatment method to reduce E. coli levels in liquid manure. Further nitrate ions were reduced substantially by Ozonation. The analysis of variance (one way and two way) revealed significance difference in E. coli and nitrate reductions in liquid slurry among ozone and air treatments (p <0.05). The study's results carry significance importance in terms of developing a simple field-scale method for reducing microbial and nutrient pollutions from dairy lagoon manure.

        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2024)
        The problem that this study addresses is to understand how microwave radiation is able to degrade genomic DNA of E. coli. In addition, a comparative study was made to evaluate the suitability of a high-throughput automated electrophoresis platform for quantifying the DNA degradation under microwave radiation. Overall, this study investigated the genomic DNA degradation of E. coli under microwave radiation using automated gel electrophoresis. To examine the viable organisms and degradation of genomic DNA under microwave exposure, we used three methods: (1) post-microwave exposure, where E. coli was enumerated using modified mTEC agar method using membrane filtration technique; (2) extracted genomic DNA of microwaved sample was quantified using the Qubit method; and (3) automated gel electrophoresis, the TapeStation 4200, was used to examine the bands of extracted DNA of microwaved samples. In addition, to examine the impacts of microwaves, E. coli colonies were isolated from a fecal sample (dairy cow manure), these colonies were grown overnight to prepare fresh E. coli culture, and this culture was exposed to microwave radiation for three durations: (1) 2 min; (2) 5 min; and (3) 8 min. In general, Qubit values (ng/µL) were proportional to the results of automated gel electrophoresis, TapeStation 4200, DNA integrity numbers (DINs). Samples from exposure studies (2 min, 5 min, and 8 min) showed no viable E. coli. Initial E. coli levels (at 0 min microwave exposure) were 5 × 108 CFU/mL, and the E. coli level was reduced to a non-detectable level within 2 min of microwave exposure. The relationships between Qubit and TapeStation measurements was linear, except for when the DNA level was lower than 2 ng/µL. In 8 min of microwave exposure, E. coli DNA integrity was reduced by 61.7%, and DNA concentration was reduced by 81.6%. The overall conclusion of this study is that microwave radiation had a significant impact on the genomic DNA of E. coli, and prolonged exposure of E. coli to microwaves can thus lead to a loss of genomic DNA integrity and DNA concentrations.
          Cover page: Quantitative Analysis of Genomic DNA Degradation of E. coli Using Automated Gel Electrophoresis under Various Levels of Microwave Exposure.
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2024)
          To determine the evolution of microbial community and microbial shift under anaerobic processes, this study investigates the use of denaturing gradient gel electrophoresis (DGGE). In the DGGE, short- and medium-sized DNA fragments are separated based on their melting characteristics, and this technique is used in this study to understand the dominant bacterial community in mesophilic and thermophilic anaerobic digestion processes. Dairy manure is known for emitting greenhouse gases (GHGs) such as methane, and GHG emissions from manure is a biological process that is largely dependent on the manure conditions, microbial community presence in manure, and their functions. Additional efforts are needed to understand the GHG emissions from manure and develop control strategies to minimize the biological GHG emissions from manure. To study the microbial shift during anaerobic processes responsible for GHG emission, we conducted a series of manure anaerobic digestion experiments, and these experiments were conducted in lab-scale reactors operated under various temperature conditions (28 °C, 36 °C, 44 °C, and 52 °C). We examined the third variable region (V3) of the 16S rRNA gene fingerprints of bacterial presence in anaerobic environment by PCR amplification and DGGE separation. Results showed that bacterial community was affected by the temperature conditions and anaerobic incubation time of manure. The microbial community structure of the original manure changed over time during anaerobic processes, and the community composition changed substantially with the temperature of the anaerobic process. At Day 0, the sequence similarity confirmed that most of the bacteria were similar (>95%) to Acinetobacter sp. (strain: ATCC 31012), a Gram-negative bacteria, regardless of temperature conditions. At day 7, the sequence similarity of DNA fragments of reactors (28 °C) was similar to Acinetobacter sp.; however, the DNA fragments of effluent of reactors at 44 °C and 52 °C were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 97%) and Tepidimicrobium ferriphilum (strain: DSM 16624) (similarity: 100%), respectively. At day 60, the analysis showed that DNA fragments of effluent of 28 °C reactor were similar to Galbibacter mesophilus (strain: NBRC 10162) (similarity: 87%), and DNA fragments of effluent of 36 °C reactors were similar to Syntrophomonas curvata (strain: GB8-1) (similarity: 91%). In reactors with a relatively higher temperature, the DNA fragments of effluent of 44 °C reactor were similar to Dielma fastidiosa (strain: JC13) (similarity: 86%), and the DNA fragments of effluent of 52 °C reactor were similar to Coprothermobacter proteolyticus (strain: DSM 5265) (similarity: 99%). To authors knowledge, this is one of the few studies where DGGE-based approach is utilized to study and compare microbial shifts under mesophilic and thermophilic anaerobic digestions of manure simultaneously. While there were challenges in identifying the bands during gradient gel electrophoresis, the joint use of DGGE and sequencing tool can be potentially useful for illustrating and comparing the change in microbial community structure under complex anaerobic processes and functionality of microbes for understanding the consequential GHG emissions from manure.
            Cover page: Denaturing Gradient Gel Electrophoresis Approach for Microbial Shift Analysis in Thermophilic and Mesophilic Anaerobic Digestions.
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2023)
            An increased understanding of the interaction between manure management and public and environmental health has led to the development of Alternative Dairy Effluent Management Strategies (ADEMS). The efficiency of such ADEMS can be increased using mechanical solid-liquid-separator (SLS) or gravitational Weeping-Wall (WW) solid separation systems. In this research, using pilot study data from 96 samples, the chemical, physical, biological, seasonal, and structural parameters between SLS and WW of ADEM systems were compared. Parameters including sodium, potassium, total salts, volatile solids, pH, and E. coli levels were significantly different between the SLS and WW of ADEMS. The separated solid fraction of the dairy effluents had the lowest E. coli levels, which could have beneficial downstream implications in terms of microbial pollution control. To predict effluent quality and microbial pollution risk, we used Escherichia coli as the indicator organism, and a versatile machine learning, ensemble, stacked, super-learner model called E-C-MAN (Escherichia coli-Manure) was developed. Using pilot data, the E-C-MAN model was trained, and the trained model was validated with the test dataset. These results demonstrate that the heuristic E-C-MAN ensemble model can provide a pilot framework toward predicting Escherichia coli levels in manure treated by SLS or WW systems.
              Cover page: Predicting Escherichia coli levels in manure using machine learning in weeping wall and mechanical liquid solid separation systems
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2021)
              Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins-Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.
                Cover page: Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion.
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2016)
                To identify innovative ways for better utilizing flushed dairy manure wastewater, we have assessed the effect of dairy manure and supplementation with synthetic medium on the growth of Chlorella vulgaris. A series of experiments were carried out to study the impacts of pretreatment of dairy wastewater and the benefits of supplementing dairy manure wastewater with synthetic medium on C. vulgaris growth increment and the ultrastructure (chloroplast, starch, lipid, and cell wall) of C. vulgaris cells. Results showed that the biomass production of C. vulgaris in dairy wastewater can be enhanced by pretreatment and using supplementation with synthetic media. A recipe combining pretreated dairy wastewater (40 %) and synthetic medium (60 %) exhibited an improved growth of C. vulgaris. The effects of dairy wastewater on the ultrastructure of C. vulgaris cells were distinct compared to that of cells grown in synthetic medium. The C. vulgaris growth in both synthetic medium and manure wastewater without supplementing synthetic medium was lower than the growth in dairy manure supplemented with synthetic medium. We anticipate that the results of this study will help in deriving an enhanced method of coupling nutrient-rich dairy manure wastewater for biofuel production.
                  Cover page: Chlorella vulgaris production enhancement with supplementation of synthetic medium in dairy manure wastewater
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2015)
                    Cover page: A neighborhood statistics model for predicting stream pathogen indicator levels
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2014)
                    Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.
                      Cover page: Contamination of water resources by pathogenic bacteria
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