The objective of these studies was to develop near-infrared reflectance spectroscopy calibration equations from diet-fecal pair datasets to predict the diet quality and intake of donkeys. One hundred-forty diet-fecal pair samples were generated from two independent in vivo feeding trials conducted in the United States (N = 100) and Africa (N = 40). At each site, ten female donkeys were fed mixed diets blended from 25 forage and crop residues. The modified partial least square model (MPLS) was used to develop calibration equations for crude protein (CP), digestible organic matter (DOM), dry matter digestibility (DDM) and organic matter digestibility (OMD), for the US, Africa and US/Africa combined datasets, and dry matter (DM) and organic matter (OM) intake calibrations from the US datasets. Crude protein (CP) equations were developed with standard error of calibration (SEC) < 1.0 and coefficient of determination (R2) > 0.90, (SEL = 0.5). The US, US/Africa and Africa CP equations had SEC value of 0.77, 0.97 and 0.88 with corresponding R2 of 0.97, 0.95 and 0.88, respectively. Validation of the US CP equation resulted in a standard error of prediction (SEP) of 1.79 with corresponding coefficient of correlation (r2) of 0.82 and slope of 0.84 indicating high accuracy of prediction. In vivo derived DOM equations were also developed for the US, Africa and US/Africa datasets with SEC values of 2.58, 4.91 and 3.52, and R2 of 0.60, 0.81 and 0.84, respectively. In addition, the SEC and R2 values were 3.25 and 0.72 for US OMD, 3.28 and 0.79 for US DDM, and 4.2 and 0.85 for US/Africa OMD, and 4.3 and 0.87 for US/Africa DDM equation, respectively. Calibration equations for predicting DMI and OMI have resulted in SEC values of 3.45 and 3.21 (g/kgw0.75) and R2 values of 0.89 and 0.84, respectively. The present study explored the relationship between DMI and diet quality attributes. Crude protein and digestible organic matter to crude protein ration (DOM/CP) with r2 values of 0.60 and 0.39, respectively, have shown good correlations with intake. The present studies have confirmed the potential for the fecal NIRS profiling for predicting CP, DOM, DDM, OMD, DMI and OMI of donkeys. Both calibration and validation results have indicated that the present donkey equations were comparable to previously developed equations for ruminants; they have the capability for accurate prediction of diet quality and intake, and can be a useful tool for monitoring the nutritional well-being of donkeys with acceptable accuracy. Research works to further expand the present calibration equations with additional diet-fecal samples particularly from Africa that did not meet the required accuracy level is recommended.

Microbes, including Bacteria, are globally important mediators of elemental transformations in the marine water column, but not until recently has their biomass been suggested to contribute significantly to carbon export flux. Here I characterize lipid and carbon isotopic signatures in marine particulate organic matter (POM) explicitly at microbial size scales, and I quantitatively explore how these signatures are transferred down the water column. In the North Pacific Subtropical Gyre (NPSG) an isotopically-enriched pool of submicron POM appears to dominate export to mesopelagic depths, supporting recent observations that bacterioplankton communities contribute to export flux in proportion to their biological abundance. In the Eastern Tropical North Pacific (ETNP) complex pathways emerge for the flux of POM to the deep ocean. I use the largest data set to date for natural \(^{13}C\) signatures of individual water column lipids to reveal that submicron and larger-size suspended POM size classes are isotopically distinct. Results point to de novo production of lipids above and within the oxygen minimum zone. I develop quantitative models to deconvolve the signatures of sinking and in situ sources of these lipids. Results converge on a best-fit model for downward flux in the ETNP that includes both surface-derived and sub-photic zone lipids. Overall results from the modern ocean suggest that approximately half of total suspended POM is submicron in size, much of it is bacterial in origin, and despite the small size of this material, it participates dynamically in water column export flux. These results also suggest some revised interpretations of organic matter signatures in the geologic record. I formulate a quantitative model of marine microbial production and degradation, and reproduce "inverse" isotopic signatures found in lipids and organic matter preserved in Proterozoic sedimentary rocks. Results suggest that the disappearance of this inverse \(^{13}C\) pattern was a consequence of the shift from Bacteria to Eukarya as dominant producers of marine autotrophic biomass. Together, results of this thesis reveal that heterogeneity in the isotopic signatures of marine suspended POM is associated with particle size, and by extension, must be a function of the composition of the total planktonic community. / Earth and Planetary Sciences

The presence of pharmacologically active and persistent compounds in drinking water sources is an environmental and public health concern. Sources of pharmaceuticals in the aquatic environment include wastewater treatment plant effluents and veterinary use. Antibiotics are of special concern because of their role in the spread of bacterial resistance. Conventional drinking water treatment processes are often ineffective for removing trace organic contaminants. Ozonation processes have demonstrated the ability to remove pharmaceutical compounds from drinking water supplies. During the ozonation of drinking water, the primary oxidants are ozone and hydroxyl radicals formed during the decomposition of ozone. Both oxidants contribute to the removal of pharmaceutical compounds; however, the relative rates of destruction by these two oxidants depends on the treatment operating conditions, the background water chemistry and the structure and reactivity of the target compound. This study investigated the relative impact of natural water characteristics, such as pH, the carbonate system, and natural organic matter, on the removal of the fluoroquinolone antibiotic ciprofloxacin by ozonation processes. Rate constants for k"O3, Cip obtained at pH 7 were approximately one order of magnitude higher than at pH 5 because ciprofloxacin changes from a positively charged cation to a neutral species over this pH range. The results showed that there was very little variation of the rate constants for ciprofloxacin oxidation by O₃ or hydroxyl radicals regardless of the carbonate concentration or the presence of the two organic matters studied in this research. Typical values for k"O3, Cip and k"HO°, Cip obtained at pH 7 ranged between 1.49x10⁴ and 1.64x10⁴ M⁻¹s⁻¹ and 1.29x10¹⁰ to 1.80x10¹⁰ M⁻¹s⁻¹, respectively. However, the presence of carbonate and other hydroxyl radical scavengers did have an impact on O₃ and hydroxyl radical exposure. The relative impact of these two oxidants changed depending on the pH of the system and the presence of carbonate and natural organic matter. / text

Anthropogenically-derived substances, including pharmaceuticals and personal care products, endocrine-disrupting chemicals, and pesticides, are increasingly being detected in drinking water supplies and wastewater effluents. Concerns over the presence of these compounds in water supplies include their ability to impart toxicological activity, their capacity to spread antibiotic resistance, and their potential to affect cell-signaling processes. For these reasons, water treatment processes geared towards removal of these trace organic contaminants are vital. In this work, ozone was used to treat four pharmaceutical contaminants: ciprofloxacin, cyclophosphamide, erythromycin, and ifosfamide. Ciprofloxacin and erythromycin are antibiotic/antimicrobial compounds, and cyclophosphamide and ifosfamide are chemotherapy agents. Ozone effectively transformed all four pharmaceuticals, even in the presence of background natural organic matter, which exerts a considerable ozone demand. The apparent rate constants for the reaction of the pharmaceuticals with ozone at pH 7 were determined: 3.03 M-1s-1 for cyclophosphamide; 7.38 M-1s-1 for ifosfamide; 1.57×104 M-1s-1 for ciprofloxacin; and 7.18×104 M-1s-1 for erythromycin. Cyclophosphamide and ifosfamide, which do not react quickly with ozone, exhibited high rate constants (2.7×109 M-1s-1) for transformation by hydroxyl radicals, which are formed through ozone decomposition. Nevertheless, complete removal of cyclophosphamide and ifosfamide was achievable using a novel continuous aqueous ozone addition reactor and an ozone-based advanced oxidation process (peroxone). In ozone-based processes, pharmaceuticals are systematically transformed via complex oxidative pathways towards CO2, H2O, and the oxidized forms of other elements. Intermediate oxidation products containing oxygen atoms or hydroxyl groups substituted into the chemical structure of the parent pharmaceutical were identified using liquid chromatography-mass spectrometry (LC-MS). Given the structural similarity of intermediate oxidation products to the parent pharmaceuticals, an antimicrobial activity assay was employed to monitor the removal of pharmacological activity associated with ciprofloxacin, erythromycin, and their respective intermediate oxidation products throughout treatment. For solutions containing ciprofloxacin or erythromycin, ozone was able to completely eliminate the corresponding antimicrobial activity. Ciprofloxacin intermediate oxidation products were pharmacologically active; however, erythromycin’s intermediate products did not contribute to the residual antimicrobial activity. These results suggest that the design of conventional and advanced ozone-based processes must incorporate ozone demand from background organic matter and account for destruction of pharmacologically active intermediates. / text

Chitin belongs to the most abundant biopolymers on earth where it has an important role as a structural element in crustaceans, insects, fungi and some phytoplankton. Missing evidence for long-term accumulation of chitin in nature implies fast turnover and as chitin is composed of aminosugar subunits it holds central roles in both carbon and nitrogen cycles. The aim of this thesis was to contribute to a better understanding of organic matter cycling by learning more about the diversity, function and ecology of bacteria that degrade chitin. A metagenome-enabled study of the spatial distribution of chitinolytic bacteria in aquatic ecosystems identified salinity as the major environmental factor for shaping their community composition. To address the role of alternative environmental variables controlling chitinolytic communities, a temporally resolved study was completed in a dimictic freshwater lake. Pronounced seasonal change in the indigenous chitinolytic community was observed and parallel measured environmental parameters pointed to the availability and crystalline form of chitin as significant controlling factors.  The different ecological niches occupied by microbes that utilize chitin for growth were studied in an experimental study. Single-cell quantification of chitinolytic cells and cells incorporating chitin hydrolysis products suggested that commensal use of chitin hydrolysis products without simultaneous chitinase activity could be an important ecological strategy in freshwater bacterioplankton communities. Members of the ubiquitous and often quantitatively dominant group of freshwater Actinobacteria Ac1 were identified as particularly active in this “cheater” lifestyle. Further experiments based on artificially created gradients in bacterial diversity demonstrated the importance of specific bacterial populations and community composition rather than overall community richness in controlling more specific functions such as chitin and cellulose degradation. To conclude, results of this thesis provide insight into the biogeography, niche-separation and species interactions of the functional community of chitin degraders and the influence of general bacterial diversity to the respective system functioning. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 700

Pharmaceuticals, personal care products and dissolved organic matter (OM) are introduced to soil via irrigation with reclaimed wastewater. This thesis examines the basic factors that influence sorption of these components in soil. Sorption of dissolved OM samples of varying composition to clay surfaces was examined. Results indicate that preferential sorption is dependent on clay type but not necessarily OM composition. Analysis of soils revealed aliphatic components, carbohydrates and amino acids are prevalent at the soil-water interface whereas aromatics are inaccessible at the soil-water interface. No clear relationship between sorption affinity of 17β-estradiol, sulfamethoxazole, carbamazepine and phenanthrene and soil OM aromaticity or aliphaticity was observed. A negative relationship between sorption and O-alkyl content may be due to these components blocking contaminant access to high affinity sorption sites. Therefore, application of reclaimed wastewater to soils with O-alkyl-rich OM may result in higher mobility of contaminants.

Pharmaceuticals, personal care products and dissolved organic matter (OM) are introduced to soil via irrigation with reclaimed wastewater. This thesis examines the basic factors that influence sorption of these components in soil. Sorption of dissolved OM samples of varying composition to clay surfaces was examined. Results indicate that preferential sorption is dependent on clay type but not necessarily OM composition. Analysis of soils revealed aliphatic components, carbohydrates and amino acids are prevalent at the soil-water interface whereas aromatics are inaccessible at the soil-water interface. No clear relationship between sorption affinity of 17β-estradiol, sulfamethoxazole, carbamazepine and phenanthrene and soil OM aromaticity or aliphaticity was observed. A negative relationship between sorption and O-alkyl content may be due to these components blocking contaminant access to high affinity sorption sites. Therefore, application of reclaimed wastewater to soils with O-alkyl-rich OM may result in higher mobility of contaminants.

Monitoring data for potable water in the R.M. of Macdonald regional water system indicates elevated levels of chlorine disinfection by-products (DBPs), trihalomethanes (THMs). Dissolved Organic Carbon (DOC) and chlorine dose are the key precursors for the formation of THMs. Currently, the DOC is not removed efficiently at the Sanford water treatment plant, which supplies the R.M.’s potable water distribution system. The raw water DOC concentration incoming to the plant varied from 8.9mg/L to 31.8mg/L during this study. Sanford treated water effluent contained an average DOC of 6.5mg/L and the THM levels ranged from 86.6ppb to 175.7ppb. One of the objectives of this study was to conduct jar tests to optimize Sanford’s water treatment process to improve removal of DOC. Optimization of the coagulation process successfully reduced the DOC level in the plant effluent by 51% during the summer and 34% in the winter. The DOC reduction resulted in a THM reduction of 73.5ppb in the summer and 59.9ppb during the winter. Results showed that removal of 1mg/L of DOC eliminates 26.8ppb of THMs in summer and 11.9ppb during the winter. Another goal of this project was to investigate the relationship between THMs and their precursors, which includes: water DOC, free chlorine residual, and the chlorine contact time. Water samples were strategically collected throughout the Sanford regional water distribution system; the samples were tested for DOC, UV254, SUVA, chlorine residual, and contact time. A linear relationship between THM formation and chlorine contact time (R2 of 0.92) was found. This indicates that the content of THMs can be decreased by reducing the amount of time the water stays in the distribution system.

Mercury (Hg) is a known neurotoxin that is often found in concentrations exceeding safe consumption guidelines in aquatic biota. This is evident in northern Canada, where northerners consume significant amounts of animals such as beluga, seals and burbot. In the Mackenzie River Basin, recent increases in Hg concentration in many of these animals over the past 25 years have been observed. The warming climate, and with it, the changing carbon cycle, are hypothesised in this thesis to play a role in the increases. Within the context of the two major zones (mountainous and peatland), with distinct geomorphology, hydrology and geology, traditional fossil fuel exploration methods (Rock-Eval pyrolysis, organic petrography) have been employed in a novel manner on recent sediments to qualify and quantify the OM and several geochemical analyses have been used to determine the geochemical sources of Hg. The mountainous zone is composed mostly of refractory OM, from forest fire char and heavily reworked OM. It also contains, and fluxes, most of the Hg, which derives from oxidative weathering and erosion of widespread sulfide minerals. However, Hg from this zone is in chemical forms of limited bioavailability. The peatland zone has a greater proportion of labile OM, with higher concentrations of DOC and algal-derived OM. Lake-fed tributaries in this zone contain even higher proportions of labile OM. At one of these sites, the sediment core record shows that Hg has been increasingly associated with labile OM over time, due to increasing primary productivity accelerated by climate change, and is resulting in an increase in scavenged Hg. The temporal trend in algal-bound Hg in the sediment record matches very well with the temporal trend of Hg in burbot sampled from the area, providing one of the first and strongest lines of evidence for the climatic impact on Hg bioaccumulation in Arctic ecosystems.

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