Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Il polietilene (PE) rappresenta più del 60% di tutte le plastiche derivate dal petrolio a livello mondiale, e si sta accumulando ad un tasso di diversi milioni di tonnellate per anno a causa della sua riluttanza alla degradazione biotica e abiotica. La degradazione microbica è stata proposta come possibile strada alternativa nella riduzione dei rifiuti plastici. Lo scopo generale di questo lavoro è stata l'identificazione di ceppi batterici in grado di metabolizzare il PE e di identificare le vie metaboliche coinvolte in tale processo di biodegradazione. Abbiamo analizzato mediante approccio metagenomico diversi campioni di plastica raccolti in una discarica abbandonata, ed è stata scoperta una forte relazione tra le proprietà della plastica (inclusa la presenza di coloranti) e la comunità microbica Analizzando la comunità microbica esposta al PE nell’ ambiente, abbiamo isolato 10 ceppi batterici in grado di crescere utilizzando il PE come unica fonte di energia e di carbonio. Uno di questi ceppi, Pseudomonas aeruginosa UC4003, ha mostrato la più alta capacità di crescere in terreno minimo e polietilene. Quando cresce su PE, questo ceppo produce un enzima extracellulare, proteina-attivatore per l’ossidazione degli n-alcani (PA), coinvolto nelle prime fasi di degradazione di polietilene. / Plastics production, use and degradation are hot topics that have come to the forefront over recent years. Polyethylene (PE) represents more than 60% of all petroleum-derived plastics worldwide and is accumulating at rates of several millions of tons per year because of its strong recalcitrance to biotic and abiotic degradation. Microbial degradation has been proposed as a possible alternative way to reduce plastic wastes. The general aim of this work was the identification of bacterial strains able to metabolize PE and to identify the biochemical pathways of this biodegradation process. In an abandoned landfill we collected different plastic samples; using a metagenomic approach, we found a strong relationship between the plastic properties (including the presence of colorants) and the microbial community By screening the natural microbial community exposed to PE in environment, we isolated 10 bacteria which revealed the ability to grow on PE as only energy and carbon source. A bacterium, Pseudomonas aeruginosa UC4003, showed the highest growth rate in minimal salt medium and polyethylene. When grown on PE, this strain produced an extracellular enzyme, protein-like activator for n-alkane oxidation (PA), involved in the first step of polyethylene degradation.

Climate change is likely to alter plant species composition and interactions between plants and soil microbes that together dictate the quantity and quality of forage produced in pastures, the base of animal production in central Kentucky. This study assessed the seasonal dynamics of soil microbes and their response to increased temperature (+3oC) and growing season precipitation (+30% of the mean annual). Total soil microbial biomass, community composition, enzyme activities, potential carbon mineralization, and catabolic responses to selected substrates were measured seasonally in the different climate treatments. In this system, seasonal variability was a dominant driving factor for all the soil microbial characteristics that I investigated. Summer maxima and winter minima were identified in the active microbial biomass, while soil microbial community structure differed between each season. Extracellular enzyme activities were generally highest in either the spring or summer, while seasonal patterns for each substrate were unique across catabolic response profiles. Climate treatments produced few significant main or interactive effects on the soil microbial biomass and function. This resiliency, coupled with evidence of functional redundancy, suggests that central Kentucky pasture ecosystems may be well-equipped to handle future environmental stress associated with climate change and to maintain critical ecosystem services.

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The relationship between biodiversity and ecosystem functioning is important in maintaining agroecosystem sustainability. Plant-microbe symbioses, such as exists between the grass tall fescue (Schedonorus arundinaceum) and the asexual fungal endophyte Epichloë coenophiala, can be utilized to enhance agroecosystem functions, such as herbivore resistance. “Novel” E. coenophiala strains that vary in the production of mammal- and insect-toxic compounds have been identified, inserted into tall fescue cultivars, and are planted in pastures globally. Novel fungal endophyte-tall fescue associations may have divergent ecosystem function effects. This study assessed effects of different fescue-endophyte symbiotic combinations on pasture ecosystem function, including aboveground (fescue biomass, plant species richness, alkaloid synthesis, arthropod abundance) and belowground (soil microbial biomass, soil enzyme activity, trace gas fluxes) parameters. Results showed no significant effects of increasing symbiotic diversity within a fescue stand on aboveground measurements, bar arthropod abundance and alkaloid synthesis. Most soil parameters quantified had significant symbiotic diversity effects. For example, soil microbial biomass decreased whereas soil enzyme activity increased with increasing symbiotic diversity. Overall, our results suggested that increasing symbiotic diversity had weak to moderate effects on aboveground processes and stronger effects on certain belowground processes, indicating that symbiotic diversity can impact ecosystem functions and warrants further research.

Abstract Grazing by reindeer (Rangifer tarandus L.) affects vegetation and soil microbial processes in tundra ecosystems. It is considered that grazing can induce two alternative vegetation states that differ in plant species composition and the rate of nutrient cycling. I hypothesised that these alternative vegetation states differ in ecosystem responses to climate warming. I tested the hypothesis using a factorial warming and fertilisation experiment on long-term lightly grazed (LG) and heavily grazed (HG) tundra. The reindeer grazing induced vegetation shift from dwarf shrubs to graminoids increased microbial activities for SOM decomposition. The grazer-induced shifts in vegetation and microbial activities in combination with the fertilisation via urine and faeces had important consequences on soil N availability and soil C quality that determined the ecosystem-level consequences of climate warming. Due to higher soil N availability, warming increased plant productivity (GEP) on HG but not on LG tundra, where N limitation prevented the warming-increased plant production. The varying effects of warming on GEP at different grazing intensities determined the effects of warming on ecosystem net C sink, which was unaffected by warming on HG but decreased on LG tundra. Reindeer grazing reduced the soil C quality, as soils under LG stored a higher proportion of carbohydrates vulnerable to microbial decomposition than soils under HG. According to laboratory soil incubations, the grazer-induced reduction in soil C quality mitigated the responses of soil microbial activity to prolonged warming. Warming caused a stronger decrease in concentrations of phenolics, an important means of plant defence against biotic and abiotic stresses, in Empetrum nigrum ssp. hermaphroditum under HG than LG. Grazing history by reindeer, with the associated vegetation shift from dwarf shrubs to graminoids, can significantly alter the ecosystem-level consequences of climate warming. Overall, this thesis highlights that the effects of reindeer grazing on soil properties, soil N availability and C quality, are important determinants of the ecosystem responses to climate warming. Therefore, future research on climate warming should take into account herbivores and aim towards a more holistic approach that includes both aboveground and belowground components of the ecosystem. / Tiivistelmä Tundralla porolaidunnus vaikuttaa kasvillisuuteen ja maaperän mikrobien toimintaan. Porolaidunnus voi aikaansaada kaksi vaihtoehtoista kasvillisuuden tilaa, jotka eroavat toisistaan paitsi kasvilajiston myös ravinnekierron suhteen. Esitin hypoteesin, jonka mukaan ilmaston lämpenemisen vaikutukset eroavat tundratyypeillä, jotka edustavat vaihtoehtoisia kasvillisuustiloja. Testasin hypoteesia faktoriaalisen lämmitys- ja lannoituskokeen avulla tundra-alueilla, joilla poron laidunnuspaine on ollut pitkäaikaisesti joko kevyttä tai voimakasta. Poron aiheuttama kasvillisuusmuutos varpuvaltaisesta heinävaltaiseksi lisäsi maaperän mikrobien hajotusaktiivisuutta. Poron aiheuttamat erot kasvillisuudessa ja mikrobiaktiivisuuksissa yhdessä virtsan ja papanoiden lannoittavan vaikutuksen kanssa muuttivat maaperän typen saatavuutta sekä hiilen laatua. Erot maaperän ominaisuuksissa puolestaan ohjasivat ilmaston lämpenemisen ekosysteemitason vaikutuksia. Lämmitys kasvatti ekosysteemituotantoa ravinteikkaalla voimakkaasti laidunnetulla tundralla mutta ei kevyesti laidunnetulla tundralla, joka oli typpirajoitteinen. Lämmityksen erilaiset vaikutukset ekosysteemituotantoon eri laidunpaineissa määrittivät lämmityksen vaikutuksen ekosysteemin hiilinieluun, joka pysyi muuttumattomana voimakkaasti laidunnetulla tundralla mutta pieneni kevyesti laidunnetulla tundralla. Porolaidunnus alensi maaperän hiilen laatua, ja kevyesti laidunnetulla tundralla maaperässä oli enemmän mikrobien hajotukselle alttiita hiilihydraatteja kuin voimakkaasti laidunnetulla tundralla. Laboratoriossa suoritetun inkubaatiokokeen perusteella maaperän hiilen alhaisempi laatu lievensi mikrobien hajotusaktiivisuuden vastetta pitkäaikaiseen lämmitykseen. Lämmitys vähensi pohjanvariksenmarjan fenoliyhdisteiden, jotka ovat tärkeä osa kasvien puolustusta bioottisia ja abioottisia stressitekijöitä vastaan, pitoisuuksia enemmän voimakkaasti kuin kevyesti laidunnetulla tundralla. Poron laidunnushistoria yhdessä kasvillisuusmuutoksen kanssa voi merkittävästi vaikuttaa ilmaston lämpenemisen ekosysteemitason seurauksiin. Tämän väitöstyön tulokset osoittavat, että poron vaikutukset maaperän typpeen ja hiileen määrittävät lämpenemisen vaikutukset ekosysteemissä. Tulevaisuudessa ilmastonmuutostutkimuksen pitäisikin kokonaisvaltaisemmin huomioida sekä herbivorian että ekosysteemin eri osien merkitys.

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