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published_or_final_version / abstract / toc / Medicine / Master / Doctor of Medicine

published_or_final_version / abstract / toc / Microbiology / Master / Master of Philosophy

Denna rapport är en sammanställning av de 100 undersökta enskilda brunnarna i Landskrona kommun vid årsskiftet 05/06. Det utfördes analyser på mikrobiologisk-, nitrat-, nitrit- och även kemiska bekämpningsmedelspåverkan. Syftet med denna rapport är att bearbeta och presentera analysresultaten av de 100 enskilda brunnarna i Landskrona kommun och försöka dra slutsatser kring dessa. Alla analysresultaten sammanställdes i tabeller och så småningom kundes vissa slutsatser dras kring varför resultatet såg ut som det gjorde. Resultatet visade att endast åtta av de 100 brunnarna var otjänliga gällande mikrobiologisk påverkan. Denna parameter är väldigt varierande beroende mycket på yttre omständigheter men det kan ge en indikation på att brunnen inte är tillräckligt tät och därför kan ytvatten tränga in i brunnen. När det gäller nitritpåverkan blev bara en brunn otjänlig. Men när det gällde nitrat var det istället 17 % av brunnarna som visade sig vara otjänliga. Detta är ändå ett relativt bra resultat beroende på hur landskapet ser ut i Skåne med stor påverkan från enskilda avlopp, jordbruk och gödsling. Sist men inte minst analyserades kemiska bekämpningsmedel och gav ett oroande resultat. Hela 35 % av brunnarna var otjänliga pga. kemiska bekämpningsmedel. Detta resultat är inget ovanligt utan kan genom danska undersökningar bara bekräftas. Kemiska bekämpningsmedel kan sprida sig långa sträckor och inte bara vid den plats där ämnena använts eller spillts. De slutsatser som kan dras genom denna undersökning är att grävda brunnar i ytliga jordlager löper störst risk att i framtiden bli otjänliga då dessa utsetts för störst påverkan av föroreningar och ytvatten. Brunnar placerade på gårdsplan är speciellt utsatta och är starkt påverkade av både mikroorganismer och kemiska bekämpningsmedel. När det gäller kemiska bekämpningsmedel är resultaten från Landskrona liknande de från både Danmark och övriga Skåne. / The problem with bad drinking water in wells are a wide problem in an landscape such as Skåne. The purpose of this report is to work up all the data from the different analysis regarding drinking water quality from wells in Landskrona municipality. The parameters that were analysed were microorganisms, the content of nitrate and nitrite and also the concentration of pesticides. Many reports in the field of the subject were collected to get a good picture and a better knowledge of the different problems that lie ahead. This resulted in various conclusions but some of the conclusions was confirmed from other examinations. That wells in the ground are more exposed than wells in mountain. The concentration of pesticides were very high in many of the wells wich shows that this will be a great problem for us to deal with in the future. Examinations in both Denmark and remaining parts of Sweden also show high concentration of pesticides. This only confirm that the problem isn’t just a local here in the municipality.

Research aim – to determine the spreading, dynamics and activity of microorganisms, witch participate in soil nitrogen transformation processes, in different by pH and fertilisation level Dystric Albeluvisol (Abd).

Bioremediacija suprantama kaip aplinką valanti technologija, kuri teršalų šalinimui naudoja biologinį potencialą. Apžvalgoje nagrinėjami įvairių polimerinių ir natūralios kilmės junginių biodegradacijos procesų ypatumai, mikrobiologinės grunto bioremediacijos efektyvumo priklausomybė nuo įvairių abiotinių ir biotinių veiksnių. Pateikta analizė apie žemiausios trofinės grandies-mikroorganizmų asociacijų formavimąsi ir funkcionavimą užterštame grunte, aptariamas bioaugmentacijos, biostimuliacijos, biopreparatų efektyvumas naftos produktais užteršto grunto bioremediacijai. Aptariamas naujas ištirtas termofilinių bakterijų naftaleno skaidymo kelias. Gautų duomenų pagrindu apžvalgoje daromos išvados, kad mikroorganizmai gali būti sėkmingai naudojami valant stipriai užterštą gruntą ex-situ sąlygomis. Bioremediacijos technologijos suteikia galimybes pagausinti vietines mikroorganizmų populiacijas, sustiprinti mikroorganizmų veiklą, naudojant papildomas maisto medžiagas, stimuliuoti aktyvių metabolitų sintezę. / Bioremediation is the application of biological processes for the clean up of pollutants present in the environment. The scope of the review encompasses the following subjects: biodegradation of various polymeric and natural origin compounds; the applications of microorganisms to laboratory scale and field scale soil bioremediation, with a focus on petroleum hydrocarbons; bioaugmentation and characterization of microbial communities; the factors affecting soil bioremediation processes including: availability of microbes, accessibility of contaminants, and a heterogeneous environment; the use of microbial metabolites, such as surfactants to improve availability of contaminants. From this review it can be concluded that microorganisms are an effective ex situ technology that can be used for bioremediation of problematic soils. Bioremediation technology allows for the convenient manipulation and control of several environmental parameters that could lead to enhanced and faster treatment of polluted soils: nutrient source (biostimulation), inocula (bioaugmentation), increased availability of pollutants by inducing biosurfactant production inside the microorganisms, etc. Bioremediation also encompasses ex situ methods like enzyme catalyzed pollutant breakdown. The data on the degradation of naphthalene by thermophilic bacteria via a novel pathway, through protocatechuate are presented.

Agriculture management including tillage and crop residues impact the functioning of soil microbiota. Soil microbiota cycle nutrients, with greenhouse gases being a byproduct within the cycle. The main objectives of this thesis were to 1) assess tillage and corn residue impact on N-cycling soil microorganisms and N2O emissions in situ (Chapter 3); and 2) evaluate N-cycling soil microorganisms in situ relative to N2O flux during a spring thaw cycle (Chapter 4). In situ sampling addresses how changing field conditions influence soil bacterial processes. Results indicated tillage and removal of corn residue declined soil microbial abundance and increased N2O emissions. These responses were dependent on local environmental conditions; moisture, carbon and nitrogen availability. The spring thaw study highlighted N-cycling microorganisms were present and active over the spring thaw event, and delayed nosZ denitrifier activity was related to the timing of significant N2O emission events, suggesting new evidence of de novo denitrification. / Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) and Natural Science and Engineering Research Council (NSERC)

Soil nitrogen availability to plants is a fundamental control on the structure and functioning of arctic tundra ecosystems. Despite recent evidence that biogeochemical and microbial dynamics during the non-growing season impact nitrogen availability to plants in tundra ecosystems, very little is known about soil microbial patterns and mechanisms for nutrient mobilization in the winter, spring and fall. In this dissertation I have examined the environmental and microbial controls on seasonal nitrogen mobilization in a widespread Canadian low arctic birch hummock tundra ecosystem. In particular, I have investigated the potential for increased winter snow depth and different above-ground vegetation-types to alter soil microbial community patterns and nutrient mobilization from organic matter into plant-available pools. First, I demonstrated that experimentally deepened winter snow altered soil microbial physiology during winter, defined as increased microbial carbon limitation to growth and activity. Second, I established that deepened snow enhanced spring nutrient mobilization during distinct environmental phases, producing large peaks in the soil microbial biomass and soil solution carbon, nitrogen and phosphorus during snow thaw. Third, I showed that laboratory predictions of early-spring air temperature freeze-thaw cycles promoting tundra soil nitrogen loss are not relevant, as the soil environment and soil biogeochemistry were relatively stable after snow melt and before plant growth began. Fourth, I demonstrated that microbial functional groups did not differ strongly under different tundra vegetation types, but higher quality shrub litter induced positive feedbacks on soil carbon availability and soil nitrogen mineralization in the late summer. Finally, I illustrated that annual patterns of tundra soil microbial community structure and composition were strongly linked to soil biogeochemistry and that significant shifts in fungal/bacterial ratios occur during snowmelt. This research suggests two broad conclusions: a) that soil microbial activity is responsive to changes in above-ground vegetation; and b) that seasonal changes in microbial community structure and microbial biochemistry are strongly correlated. Therefore, the synchronicity of microbial seasonal succession and plant species-specific timing of nitrogen uptake is a critical factor restricting the potential for ecosystem N losses at spring thaw and ultimately in supplying growth-limiting nutrients to plants in the following summer. / Thesis (Ph.D, Biology) -- Queen's University, 2009-09-25 23:29:53.103

In the N2 fixing legume symbiosis, mineral nitrogen (N) not only decreases N2 fixation, but also delays and inhibits the formation and development of nodules. The purposes of this thesis were to elucidate the role of signaling in the mineral N effects on nodulation and nitrogen fixation in soybean [Glycine max (L.) Merr.] and to attempt to find ways to overcome this inhibition. The responses of soybean plants, in terms of daidzein and genistein synthesis and exudation, to different mineral N levels were studied. Daidzein and genistein distribution patterns varied with plant organs, mineral N levels, and plant development stages. Mineral N inhibited daidzein and genistein contents and concentrations in soybean root and shoot extracts, but did not affect root daidzein and genistein excretion in the same way. In both synthesis and excretion, daidzein and genistein were not affected equally by mineral N treatments. Variability existed among soybean cultivars in the responses of root daidzein and genistein contents and concentrations to mineral N levels. The amount of daidzein and genistein excreted by soybean roots did not always correspond to the daidzein and genistein contents and concentrations inside the roots. On the Bradyrhizobium japonicum side, nod gene expression was inhibited by mineral nitrogen. Genistein was used to pre-incubate B. japonicum cells or was applied directly into the plant growing medium. The results showed that genistein manipulation increased nodule weight and nodule nitrogen fixation under greenhouse conditions, but interactions existed among soybean cultivars, genistein concentrations and nitrate levels. Similar results were found under field conditions. Soybean yield was increased on sandy-loam soil by preincubation of B. japonicum cells with genistein. Addition of genistein beginning at the onset of nitrogen fixation also improved soybean nodulation and nitrogen fixation. Soybean cultivars had different sensitivities to genistein additi / Other studies also show that temperature affected genistein and daidzein content and concentration in soybean roots. The effect of temperature varied among soybean cultivars. Some PGPR strains can mitigate the negative effects of nitrate on soybean nodulation and nitrogen fixation, however, this is influenced by soybean genotype. Applying PGPR together with genistein preincubation of B. japonicum cells improved soybean nodulation and increased yield. The level of improvement varied among soybean cultivars and PGPR strains. Preincubation of B. japonicum cells with genistein improved strain competitiveness under greenhouse, but not field conditions. / Overall, these findings suggested that both plant-to-Bradyrhizobium and Bradyrhizobium-to-plant signals play important roles in the effects of mineral N on nodulation and N fixation. Signal manipulation could partially overcome the inhibitory effects of mineral N on soybean- B. japonicum N fixation symbiosis.

As South Africa begins its National HIV-1 treatment program, it is urgent that we collect data that will help define the phylogenetic relationships, transmissibility and drug responsiveness of C viruses. In this thesis, data is presented on the genetic diversity of locally circulating drug naive subtype C strains, as an indication of their natural susceptibility to antiretroviral drugs, prior to the national roll-out of antiretroviral therapy. At the time this thesis was initiated, antiretroviral therapy was only available in South Africa in a few clinical trials and in the private sector, and it was therefore difficult to obtain large numbers of samples from treatment-experienced patients. Nevertheless, valuable information on the prevalence and patterns of resistance mutations in subtype C infected patients was obtained from small studies on patients receiving HAART, concomitant HAART and TB treatment, HAART and treatment for Kaposi Sarcoma, and single dose nevirapine for the prevention of mother-to-child transmission of HIV-1 infection. The results show that the general antiretroviral drug naive population do not harbour any major resistance-associated mutations to the currently available protease and reverse transcriptase inhibitors, with no differences in genetic variation between the different ethnic groups infected with subtype C. Phenotyping of some of these isolates showed that they were susceptible to the available protease and reverse transcriptase inhibitors, and hyper-susceptible to the protease inhibitor, Lopinavir. Phylogenetic analysis of recent and retrospective subtype C isolates showed that there are multiple lineages of subtype C viruses circulating in South Africa, indicative of multiple introductions of subtype C across its many borders. Polymorphisms in the protease, reverse transcriptase and C2-V5 region of envelope in these drug naive samples lead to significant variation in the number, type and location of potential phosphorylation sites. There was also variation in the cleavage sites controlling the initiation and rate of Gag and Gag-Pol processing (p2/NC) and the activation of protease (TFP/p6gag) suggesting that there may be important differences in the way that B and C viruses regulate polyprocessing and virion assembly. Similar to studies on subtype B, 10 to 18% of the patients on HAART developed drug resistance. However, those on concomitant HAART and TB treatment developed resistance as early as one month after starting treatment. Generally, the resistance mutations that were seen were consistent with those seen in treatment experienced subtype B isolates. Of note was the high level of resistance to the entire class of NNRTIs. This could be reflective of the predominant use of NNRTI-based regimens, as well as the low genetic barrier in this class of drugs. The NNRTI mutations included the V106M mutation that is considered a signature mutation of EFV experienced subtype C isolates. Resistance was high (40%) in mothers and infants 6 weeks after each received a single dose of NVP. K103N was most common mutation in the mothers, while Y181C was most common in the infants. Of note were the changes in functional properties caused by these mutations, by the introduction or alteration of putative myristoylation and phosphorylation sites in the RT. Taken together, these data suggests that the pattern of resistance in African patients will be similar to that observed for the treatment of subtype B infection. However, patients should be closely monitored for viral rebound very early on in treatment. Also, given the high rate of resistance in mothers and infants after single dose NVP, the search for safer regimens to prevent MTCT should be intensified. Although the mechanisms are unknown, our results indicate that several of the phosphorylation-related substitutions in the pol and env genes of KZN and other C viruses are highly conserved and positively selected. It will be important to determine whether these sites play an important role in the replicative capacity and proteolytic processing of C viruses, and in viral entry. These data provide important benefits for public health policy and planning and for future patient treatment management. / Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2004.