Occurrence and fate of organic contaminants in wastes

This thesis deals with the determination of organic contaminants in wastes and is part of the multidisciplinary faculty programme 'Biological waste in circulation between urban and rural areas - biology and flow of energy and material' which started at SLU in 1994. To ensure long-term sustainability of food production it is important to recycle resources such as the nutrients and organic material in organic waste. The biodegradable fraction of source separated household waste is attractive as raw material for composting and anaerobic digestion, because the products can be used in agriculture and horticulture. Quality is an important aspect on compost and anaerobically digested organic household waste, and it is important to ensure that the products are not contaminated. As the available information on organic contaminants in the biodegradable fraction of household waste and the products thereof is limited, an important goal with this work was to increase the knowledge of organic contaminants in these material as a foundation for future studies to reduce the environmental risk from these materials. Chlorinated paraffins (CPs) were found in fresh household waste. CPs are a complex mixture of chlorinated alkanes with varying (10-30) carbon chain lengts and varying (30- 70%) unspecific chlorination. The high numbers of isomers and homologues complicates the determination of CPs. We found that multivariate analysis can be used to interpret chromatographic data of CPs and this was used to characterise the CP contamination of houshold waste. It is presently impossible to pin-point the source of CP contamination using the data available, but most probably the contamination occurs during the collection of the waste. To further improve the determination of CPs an extraction method using high diffusion liquids, pressurised liquid extraction (PLE) was developed. PLE was shown to be a suitable technique for extracting CPs from complex matrices such as fresh household waste. A source close to the collection chain is also indicated for polychlorinated biphenyls (PCB). The PCB-profile found in the fresh household waste resembles that of a low chlorinated technical product. The PCB-profile expected in this type of material would originate from waste of animal origin in which the low chlorinated congeners have been degraded and the more highly chlorinated and persistent congeners dominate. Differences in the degradation rate of PCBs between composting and anaerbically degestion of the waste were also observed. A third indication of a contamination source in the collection chain is the presence of the n-alkanes in the fresh and anaerobically digested household waste, which suggest a petrogenic rather than a biogenic origin. Since the major part of the organic fraction of household waste is of plant origin, much of which is treated with pesticides, it was expected to find pesticides in the waste. Many of the pesticides were not degraded during composting or anaerobic digestion, and two that were not found in the waste were found in compost or anaerobically sludge. In these cases the organic bulk material is mineralized more rapidly than the pesticides. The anaerobic biotransformation of nonylphenol mono- and diethoxylates (NPEOI-2) was studied in sludge, landfilled sludge and landfilled municipal solid waste. The NPEO1-2 are degradation products of nonylphenol ethoxylates (heavy duty surfactants) and are further degraded to nonylphenol (NP) which is far more persistent and ecotoxic than its parental compo

Invisible Spheres of Urban Nature - The Role of Microbial Ecology for Landscape Architecture

This thesis explores the role of microbial ecology for landscape architecture. The first chapter contains the theoretical framework of this thesis with an introduction to the world of microorganisms and the state of knowledge in microbial ecology on human health. Afterwards, approaches from the perspective of microbial ecology to promote microbial diversity in an urban context are discussed as well as developments in landscape architecture that overlap with them. Then I formulate my research question based on this scientific framework: Does urban spontaneous vegetation promote microbial activity in the soil and what conclusions can be drawn from this for landscape architectural planning?In the second chapter, I explore Pfeiffer‘s circular chromatography soil test (PCC), an experimental method to visualise the components of a soil sample that also allows conclusions about microbial activity. PCC is not used as a substitute for more complex scientific analysis, but as a visual approach to engage with soil and its biology from a new perspective and with relatively basic resources.The third chapter describes the learning curve during the conduction of the PCC experiments as well as the soil sampling in places with different vegetation during my field trip to Berlin and Munich. The results of the PCC tests are then analysed and interpreted.In the fourth chapter, I discuss the results of the interpretation, addressing findings on microbial activity of the different sampling sites and the suitability of the PCC method for landscape architecture. Finally, I conclude what the results of my literature review and experiments mean for landscape architectural planning and the further research questions that arise from this thesis

The effect of sterilization on biological, organic geochemical and morphological information in natural samples

The loss of biological, organic geochemical, and morphological science information that may occur should a Mars surface sample be sterilized prior to return to earth is examined. Results of experimental studies are summarized

Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress

Past studies of water stress in Eucalyptus spp. generally highlighted the role of fewer than five “important” metabolites, whereas recent metabolomic studies on other genera have shown tens of compounds are affected. There are currently no metabolite profiling data for responses of stress-tolerant species to water stress. We used GC–MS metabolite profiling to examine the response of leaf metabolites to a long (2 month) and severe (Ψpredawn < −2 MPa) water stress in two species of the perennial tree genus Eucalyptus (the mesic Eucalyptus pauciflora and the semi-arid Eucalyptus dumosa). Polar metabolites in leaves were analysed by GC–MS and inorganic ions by capillary electrophoresis. Pressure–volume curves and metabolite measurements showed that water stress led to more negative osmotic potential and increased total osmotically active solutes in leaves of both species. Water stress affected around 30–40% of measured metabolites in E. dumosa and 10–15% in E. pauciflora. There were many metabolites that were affected in E. dumosa but not E. pauciflora, and some that had opposite responses in the two species. For example, in E. dumosa there were increases in five acyclic sugar alcohols and four low-abundance carbohydrates that were unaffected by water stress in E. pauciflora. Re-watering increased osmotic potential and decreased total osmotically active solutes in E. pauciflora, whereas in E. dumosa re-watering led to further decreases in osmotic potential and increases in total osmotically active solutes. This experiment has added several extra dimensions to previous targeted analyses of water stress responses in Eucalyptus, and highlights that even species that are closely related (e.g. congeners) may respond differently to water stress and re-waterin

A statistical evaluation of six classes of hydrocarbons: which classes are promising for future biodegraded ignitable liquid research?

The current methods for identifying ignitable liquid residues in fire debris are heavily based on the holistic, qualitative interpretation of chromatographic patterns with the mass spectral identification of selected peaks. The identification of neat, unweathered ignitable liquids according to ASTM 1618 using these methods is relatively straightforward for the trained analyst. The challenges in fire debris analysis arise with phenomena such as evaporation, substrate interference, and biodegradation. These phenomena result in alterations of chromatographic patterns which can lead to misclassifications or false negatives. The biodegradation of ignitable liquids is generally known to be more complex than evaporation [20], and proceeds in a manner that is dependent on numerous factors such as: composition of the petroleum product/ignitable liquid, structure of the hydrocarbon compound, soil type, bacterial community, the type of microbial metabolism that is occurring, and the environmental conditions surrounding in the sample. While nothing can be done to prevent the biodegradation, continued research on biodegraded ignitable liquids and the characterization of the trends observed may be able to provide insight into how an analyst can identify a biodegraded ignitable liquid residue. This research utilized normalized abundance values of select ions from pre-existing gas chromatography-mass spectrometry (GC-MS) data on samples from three different gasoline and diesel biodegradation studies. A total of 18 ions were selected to indicate the presence of six hydrocarbon classes (three each for alkanes, aromatics, cycloalkanes, naphthalenes, indanes, and adamantanes) based on them being either base peaks or high abundance peaks within the electron impact mass spectra of compounds within that hydrocarbon class. The loss of ion abundance over the degradation periods was assessed by creating scatter plots and performing simple linear regression analyses. Coefficient of determination values, the standard error of the estimate, the slope, and the slope error of the best fit line were assessed to draw conclusions regarding which classes exhibited desirable characteristics, relative to the other classes, such as a linear degradation, low variation in abundance within the sampling days, and a slow rate of abundance loss over the degradation period. Additional analyses included two-way analysis of the variance (ANOVA), to assess the effects of time as well as different soil type on the degradation of the hydrocarbons, stepwise multinomial logistic regressions to identify which classes were the best predictors of the type of ignitable liquid, and one-way ANOVAs to determine where the differences in the ratios of hydrocarbon classes existed within each of the ignitable liquids, as well as between the two liquids. Hydrocarbon classes identified as exhibiting characteristics such as slow and/or reliable rates of abundance loss during biodegradation are thought of as desirable for future validation studies, where specific ranges of hydrocarbon class abundance(s) may be used to identify the presence of a biodegraded ignitable liquid. Classes of hydrocarbons that have experienced biodegradation that maintain an abundance close to that of a neat, non degraded counterpart, or that reliably degrade and have predictable abundance levels given a particular period of degradation, would be instrumental in determining whether or not an unknown sample contains an ignitable liquid residue. It is the hope that these assessments will not only provide helpful information to future researchers in the field of fire debris analysis, but that they will create interest in the quantitative, statistical assessment of ignitable liquid data for detection and identification purposes

Antibiotic residues and antibiotic-resistant bacteria in pig slurry used to fertilize agricultural fields

Pig manure may contain antibiotic residues, antibiotic-resistant bacteria or pathogens, which may reach the environment upon fertilization. During this study, 69 antibiotic residues belonging to 12 classes were quantified in 89 pig slurry samples. These samples were also studied for the presence of Salmonella and for E. coli resistant to meropenem, colistin, ciprofloxacin, or cefotaxim. The obtained isolates were further tested for antibacterial susceptibility. No antibiotic residues were detected in four samples, whereas in the other samples, up to 12 antibiotics were found. The most frequently detected antibiotic residues were doxycycline, sulfadiazine, and lincomycin. Doxycycline was found in the highest concentration with a mean of 1476 mu g/kg manure (range: 18-13632 mu g/kg). Tylosin and oxytetracycline were found with mean concentrations of 784 mu g/kg (range: 17-5599 mu g/kg) and 482 mu g/kg (range: 11-3865 mu g/kg), respectively. Lincomycin, had a mean concentration of 177 mu g/kg manure (range: 9-3154 mu g/kg). All other 18 antibiotic residues were found with mean concentrations of less than 100 mu g/kg manure. Fifty-one slurry samples harbored Salmonella; 35% of the Salmonella isolates were sensitive to a panel of 14 antibiotics, whereas the other 65% were resistant up to five antibiotics. For E. coli, 52 manure samples contained E. coli isolates which were resistant to ciprofloxacin and 22 resistant to cefotaxime. All ciprofloxacin and cefotaxime-resistant isolates were multi-resistant, with resistance up to nine and eight antibiotics, respectively. This research indicates that pig slurry used for fertilization often contains antibiotic residues and antibiotic-resistant bacteria, including pathogens

Mass spectrometric studies of ether lipids in Archaea and sediments

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been implemented as a means to separate and detect tetraether lipid cores derived from the complex lipids of Archaea. Distinct dissociation pathways during tandem mass spectrometry were noted for the lipid cores, providing information regarding their structure on-line. Analysis of cellular material from species of Methanothermobacter and Sulfolobus revealed tetraether lipid cores which contain up to four cyclopentyl rings per etherified alkyl chain, including structures identified previously in each genera. Identical structures were similarly identified in novel isolates from New Zealand hot springs. Product ions in the MS/MS spectra of the lipid cores include those formed from individual losses of both ring-containing C40 alkyl chains, allowing the reported structures to be verified with respect to the distribution of the rings within the two chains. A number of additional, hitherto unreported isomers and higher homologues of the ring-containing structures were resolved, both chromatographically and/or by characteristic product ions in MS/MS. Structures in which the two chains appear to be conjoined by a covalent link were also identified in Ignisphaera aggregans, the first such identifications in a Euryarchaeote. The array of structures revealed highlights both the complexity of the archaeal lipidome, which is more extensive than has been attributed previously, and the potential of LC-MS/MS as a powerful tool for probing tetraether lipid core structure. Ether lipid cores extracted from ancient aquatic sediments and contemporary soil were used to investigate the scope of LC-MS/MS for profiling of extremely complex distributions sourced from ecological communities as opposed to single organisms. Over 100 ether lipid components in total were identified during the studies, the vast majority of which represent novel structures. These include isoprenoid lipid cores of known archaeal origin and structures which may represent their transformation products; triolic structures in which one of the two capping glycerol moieties has been lost and chain or glycerol methylated higher homologues. A wealth of non-isoprenoid lipid cores were similarly identified, with inferred structures suggestive of a eubacterial or mixed eubacterial/archaeal origin. The components, once constrained to more specific origins, may be of chemotaxonomic value for use in modern environmental profiling or in palaeoecological reconstructions made using fossilised lipid cores

Structure analysis of biologically important prokaryotic glycopolymers

Of the many post-translational modifications organisms can undertake, glycosylation is the most prevalent and the most diverse. The research in this thesis focuses on the structural characterisation of glycosylation in two classes of glycopolymer (lipopolysaccharide (LPS) and glycoprotein) in two domains of life (bacteria and archaea). The common theme linking these subprojects is the development and application of high sensitivity analytical techniques, primarily mass spectrometry (MS), for studying prokaryotic glycosylation. Many prokaryotes produce glycan arrangements with extraordinary variety in composition and structure. A further challenge is posed by additional functionalities such as lipids whose characterisation is not always straightforward. Glycosylation in prokaryotes has a variety of different biological functions, including their important roles in the mediation of interactions between pathogens and hosts. Thus enhanced knowledge of bacterial glycosylation may be of therapeutic value, whilst a better understanding of archaeal protein glycosylation will provide further targets for industrial applications, as well as insight into this post- translational modification across evolution and protein processing under extreme conditions. The first sub-project focused on the S-layer glycoprotein of the halophilic archeaon Haloferax volcanii, which has been reported to be modified by both glycans and lipids. Glycoproteomic and associated MS technologies were employed to characterise the N- and O-linked glycosylation and to explore putative lipid modifications. Approximately 90% of the S-layer was mapped and N-glycans were identified at all the mapped consensus sites, decorated with a pentasaccharide consisting of two hexoses, two hexuronic acids and a methylated hexuronic acid. The O-glycans are homogeneously identified as a disaccharide consisting of galactose and glucose. Unexpectedly it was found that membrane-derived lipids were present in the S- layer samples despite extensive purification, calling into question the predicted presence of covalently linked lipid. The H. volcanii N-glycosylation is mediated by the products of the agl gene cluster and the functional characterisation of members of the agl gene cluster was investigated by MS analysis of agl-mutant strains of the S-layer. Burkholderia pseudomallei is the causative agent of melioidosis, a serious and often fatal disease in humans which is endemic in South-East Asia and other equatorial regions. Its LPS is vital for serum resistance and the O-antigen repeat structures are of interest as vaccine targets. B. pseudomallei is reported to produce several polysaccharides, amongst which the already characterised ‘typical’ O-antigen of K96243 represents 97% of the strains. The serologically distinct ‘atypical’ strain 576 produces a different LPS, whose characterisation is the subject of this research project. MS strategies coupled with various hydrolytic and chemical derivatisation methodologies were employed to define the composition and potential sequences of the O-antigen repeat unit. These MS strategies were complemented by a novel NMR technique involving embedding of the LPS into micelles. Taken together the MS and NMR data have revealed a highly unusual O-antigen structure for atypical LPS which is remarkably different from the typical O-antigen. The development of structural analysis tools in MS and NMR applicable to the illustrated types of glycosylation in these prokaryotes will give a more consistent approach to sugar characterisation and their modifications thus providing more informative results for pathogenicity and immunological studies as well as pathway comparisons.Open Acces

Evaluation of Tiered Environmental Forensic Methods for Petroleum Derived Light and Middle Range Distillates

Environmental forensics of crude oil releases to the environment has been a topic of considerable research in recent years. However, less study has been conducted to develop and employ environmental forensic strategies for light and middle range distillates released to the environment. Complex molecular structures allow certain petroleum biomarkers to be quite recalcitrant to changes in their molecular structure from environmental processes such as weathering, making these biomarkers common target analytes for crude oil environmental forensics studies. However, refining and weathering processes remove a significant amount of commonly analyzed biomarkers from light and middle range distillates, presenting challenges for environmental forensic studies. A tiered environmental forensics strategy was developed to attempt to identify diagnostic compounds and ratios that are most beneficial for application in light and middle distillate chemical fingerprinting. Samples were collected from a Study Site that was evidently contaminated by multiple sources. Contaminated groundwater and light non-aqueous phase liquid (LNAPL) samples were collected for laboratory analysis from various areas of the Study Site. Additionally, fresh gasoline and diesel samples were collected directly from the on-site fuel dispensers and analyzed as reference samples. Distribution patterns of C3-alkylbenzene compounds proved valuable for linking the light distillate contaminant plume at the Study Site to the reference sample. C3-alkylbenzenes were found to be a beneficial target analyte compound group for environmental forensics studies on sites contaminated by light distillates due to the recalcitrant nature of this compound group. Further, analysis of diagnostic ratios of certain analyte pairs with similar solubility and chemical properties was sufficient to confirm the source of light distillate contamination across the Study Site, supporting the defensibility of the light distillate study methodology. The distinct distribution and diagnostic ratios of the biomarker sesquiterpanes compound group and alkylated PAHs were used to differentiate LNAPL collected from a contaminated portion of the Study Site to the fresh diesel reference sample. The LNAPL collected at the Study Site was determined to have originated from a different crude oil feedstock source and/or refining process than the fresh diesel reference sample