Terrestrial inputs of organic matter contribute greatly to the functioning of aquatic ecosystems, subsidizing between 30-70% of secondary production. This contribution of terrestrial resources is especially important in boreal lakes that are largely nutrient-poor and thus more responsive to these additions. Yet the mechanisms underlying initial processing of terrestrial resources by microbial communities at the base of lake food webs remain poorly understood. With this in mind, this thesis aims to advance our understanding of lake sediment microbial community assembly and functioning along abiotic gradients, primarily reflecting variation in terrestrial organic matter inputs that are predicted to increase with future environmental change. Chapter 1 reviews current knowledge on the terrestrial support of lake food webs and highlights gaps in understanding the factors influencing the microbial processing of terrestrial resources. It also provides an overview of metagenomics methods for microbial community analysis and their development over the course of the thesis. Chapter 2 tests how much of ecosystem functioning is explained by microbial community structure relative to other ecosystem properties such as the present-day and past environment. Theory predicts that ecosystem functioning, here measured as CO2 production, should increase with diversity, but the individual and interactive effects of other ecosystem properties on ecosystem functioning remain unresolved. Chapter 3 further questions the importance of microbial diversity for ecosystem functioning by asking whether more diverse microbial communities stabilize ubiquitous functions like CO2 production and microbial abundances through time. It also aims to identify the biotic and abiotic mechanisms underlying positive diversity-stability relationships. Chapter 4 then explores how microbial communities assemble and colonize sediments with varying types and amounts of terrestrial organic matter in three different lakes over a two-month period. Understanding how microbial communities change in relation to sediment and lake conditions can help predict downstream ecosystem functions. Finally, Chapter 5 discusses the main findings of the thesis and ends with proposed avenues for future research.

Atribacteria (OP9), candidate phylum with no representatives in pure culture, is found in various anaerobic environments worldwide. “Caldatribacterium”, a lineage within Atribacteria that is predicted to be a strictly anaerobic sugar fermenter based on cultivation-independent genomic analyses, is currently being maintained in lab enrichment cultures with fucose as its sole growth substrate. Metagenomics and 16S rRNA gene tag sequencing indicated that the fucose culture was a co-culture of “Caldatribacterium” and an uncultivated member of the genus Thermodesulfobacterium. Due to failed attempts to isolate “Caldatribacterium” by dilution-to-extinction and plating, it was hypothesized that “Caldatribacterium” is dependent in some way on the Thermodesulfobacterium. To better understand the possible interaction, multiple isolates of the sulfate reducer were obtained under sulfate-reducing conditions with H2 as an electron donor, and one of the isolates was characterized. Whole genome and 16S rRNA gene sequence comparisons of the isolate and other related members of the genus Thermodesulfobacterium suggested the isolate represents a distinct species in this genus, for which the name T. auxiliatoris is proposed. T. auxiliatoris was capable of using H2, formate, and lactate as sole electron donors, but not fucose or other sugars, suggesting that its growth in the co-culture might be dependent on one or more fermentation substrates produced by “Caldatribacterium”. Addition of T. auxiliatoris to highly diluted samples of the co-culture that likely contained only “Caldatribacterium”, which did not exhibit growth on their own, demonstrated that T. auxiliatoris was sufficient to support growth of “Caldatribacterium” on fucose. When this dilution experiment was repeated with various other organisms and substrates, it was found that several other thermophilic sulfate reducers (T. commune, T. hveragerdense, or Thermodesulfovibrio yellowstonii) could also support growth, as well as supernatant from the T. auxiliatoris pure culture or yeast extract. This last finding allowed for isolation of “Caldatribacterium”, which could form colonies on solid media when yeast extract and casamino acids were present. Fluorescent in situ hybridization and nanometer-scale secondary ion mass spectrometry demonstrated that “Caldatribacterium” took up a variety of sugars and amino acids in mixed culture, and that addition of acetate or bicarbonate, substrates of T. auxiliatoris, stimulated sugar uptake in “Caldatribacterium”. These results support a model where T. auxiliatoris and “Caldateribacterium” are dependent on each other in co-culture on fucose, where “Caldatribacterium” provides growth substrates for T. auxiliatoris, which in turn provides “Caldatribacterium” with some sort of soluble, essential compound(s) that can be produced by other sulfate reducers and are present in yeast extract. Further characterization of the “Caldatribacterium” isolate, the first representative of the phylum Atribacteria, will allow for detailed study of its metabolic capabilities that can be extended to other members of this phylum. Further analysis of responses of T. auxiliatoris and “Caldatribacteirum” when grow in co-culture and the specific metabolite(s) that are exchanged between the two organisms could allow for testing whether these interactions occur in more complex, natural systems.

Thesis (M.Sc. (Soil Science)) --University of Limpopo, 2013 / The study was conducted to assess the impact of mining activities on selected soil physical, chemical and microbial properties on farmlands around three selected mining sites. Nine soil samples were collected from each of the following farms : Hans Merensky, Mogoboya and Leon Tom, Foskor Mine and JCI mining sites, respectively. Additional nine soil samples were collected from non-polluted Waterbok farm that serves as a control for the purpose of comparison. The samples were taken at 0–15, 15–30, 30–45 cm depths at three sampling points on each farm for physical, chemical and biological studies. However, soil samples collected for microbial (fungi, bacteria and actinomycetes) counts were surface (0–15 cm) soil samples. Soil chemical properties determined include pHw, electrical conductivity (ECe), exchangeable acidity (EA), organic carbon, available phosphorous, exchangeable cations as well as heavy metal (i.e. Mn, Zn, Cu, Pb, Cd, As and Sb) concentrations. The physical parameters determined include texture (sand, silt and clay) as well as bulk density. Soil pHw and ECe values decreased with depth; and ranged from 6.94 to 6.50 and from 12.24 to 10.76 mS cm-1, respectively. Exchangeable acidity showed a gradual increase with depth and ranged from 0.72 to 0.80 cmol(+)(kg), while percent organic carbon decreased with depth ranging from 1.41 to 2.19 %. Exchangeable cations, particularly K and Mg increased with depth while Ca decreased marginally with soil depth. Available phosphorous content decreased following increases in distance from the pollution source while heavy met.al contamination decreased with soil depth but increased further away from the pollution source. Significantly high loads of Pb, As and Sb were recorded at all depths on the three farms around the mining sites, which were largely responsible for the pollution but worse on the Leon Tom farm; with Pb constituting the greatest pollutant. The concentration of extractable heavy metals in the studied areas was in the order: As >Sb>Pb>Zn>Cu >Mn >Cd. Cadmium level appeared generally very low in all samples while elevated levels of Mn, Cu and Zn were detected at all depths in the polluted soils.Significant differences in microbial levels were detected at the various sampling points. The highest count of 3.82 and 6.20 CFU g-1 for fungi and actinomycete, respectively were both from the Leon Tom farm, while 6.46 CFU g-1 counts for bacteria was obtained from Mogoboya farm. Interestingly, fungal and actinomycetes activities were more sensitive to heavy metal contamination than bacteria that were significantly increased following soil pollution. / National Research Foundation (NRF)

Intercropping, defined as two or more crops grown on the same land area at the same time, is a sustainable alternative to sole crops. Intercropping has been associated with multiple benefits, such as increased nutrient and soil organic carbon (SOC) cycling, decreased soil erosion and increased carbon (C) sequestration. A common intercropping practice is to integrate cereal and legume crops such as maize (Zea mays L.), and soybean (Glycine max (L.) Merr.). Most studies on intercropping have focused on yield, weed control, and land use efficiency in the tropics. Few studies have researched C and nitrogen (N) dynamics in temperate intercrops, with respect to soybean and maize residue stabilization. Soil from Balcarce, Argentina, was incubated for 140 days with soybean, maize, or no residue. Throughout the incubation, results illustrated the effect of residue application upon the soil, specifically through significantly higher amounts of light fraction (LF) C and LFN concentrations, soil microbial biomass (SMB) C and SMBN concentrations, higher microbial diversity, lower N2O production rates, in addition to distinct isotopic values in soil fractions and CO2 (p<0.05). Furthermore, it was observed from δ15N-TN and δ15N-LF that treatments with soybean residues included had higher N cycling (p<0.05), emphasizing the importance of including N-fixing legumes in complex agroecosystems. Significant changes over time in SMB and SMCS characteristics, and isotope values (p<0.05) indicated the preferential utilization of relatively young and easily accessible litter. Furthermore, the loss of labile material over the incubation resulted in more recalcitrant forms (such as older C and lignin) to be utilized. Slightly higher SOC, TN, LFC and LFN concentrations, as well as lower CO2 production rates suggested 2:3 (rows of maize:rows of soybean) as a more desirable intercrop design for C sequestration. The 1:2 intercrop design was observed to be more beneficial for microbial community structure, furthering the idea that intercropping is a beneficial alternative to sole cropping. This study improves knowledge in residue stabilization and C sequestration in complex agroecosystems, providing encouragement for the implementation of more sustainable management practices.

This thesis presents the first randomised controlled trial (RCT) to investigate whether supplemented probiotic bacteria-"live microorganisms that, when administered in adequate amounts, confer a health benefit on the host" (Sanders, 2008)-affect mood and other psychological outcomes in people presenting with low mood. Seventy-nine participants with at least moderate symptoms of depression were randomised in a double-blind manner to receive either a probiotic preparation containing Lactobacillus helveticus and Bifidobacterium longum or a matched placebo for eight weeks. The RCT phase was followed by an open label extension in which all participants were offered the active study product for a further 8 weeks. Participants were followed up at 6 months post-study. Based on the existing evidence from gut-brain axis research, and on models linking depression with inflammation, immune activation, low vitamin D levels, and the gut microbiota (outlined in Chapters 1 and 2), it was hypothesised that: the overall sample would have elevated levels of inflammatory biomarkers and low levels of vitamin D at baseline, and that this would be associated with scores on psychological and irritable bowel syndrome (IBS) outcome measures; that group differences (active treatment versus placebo) would be observed in scores on psychological outcome measures after eight weeks of probiotic intervention; that group differences would also be observed in blood levels of proinflammatory cytokines, hsCRP, vitamin D and BDNF, and scores on a measure of gut function/IBS, and that levels of these variables may predict or impact on treatment response; and that group differences would be observed on outcome measures at the point of the 6-month follow-up between those who continued to take the probiotic and those who discontinued probiotic use. In total, 58 of the 77 participants who provided baseline blood samples (75%) had at least one marker of inflammation elevated outside the normal reference range at baseline. Baseline vitamin D was approaching the deficient level, displayed a seasonal pattern, and was associated with severity on one measure of cognition. No significant differences were found between the active treatment and placebo groups on any psychological outcome measure, the measure of gut function or in the level of any blood-based biomarker in the randomised phase. Baseline vitamin D level was found to moderate treatment effect on several outcome measures. The results of the open label extension supported the lack of efficacy observed in the randomised phase, and also allowed for the comparison of efficacy over intervention periods of varying durations. The results of the follow-up at 6 months post-trial indicated that, while mean scores on psychological outcome measures remained lower than baseline, there was regression on some outcome measures after the study. When the participants who replied to the 6 month follow-up questionnaire were divided into groups based on their self-reported dominant treatment since the trial (probiotics/nutrition, standard treatment or no treatment) there was no difference in mood or other psychological outcomes among the groups at 6 months. The current trial found no evidence that this probiotic formulation is effective in treating the symptoms of depression or IBS, or in moderating the levels of inflammatory and other biomarkers in a sample recruited with moderate depression. This finding does not support the theory proposed in several narrative reviews which suggests probiotics as a possible intervention for depression and other mental health outcomes, but is supported by the systematic review of human probiotics studies presented in Chapter 3 which found overall limited evidence of probiotic efficacy for psychological outcomes. Future studies in the area should attempt to further broaden this field, in particular by recruiting samples with mild and/or non-chronic depression for interventional studies, or by approaching probiotics as a preventative or adjuvant treatment strategy for depression.

The objective of this thesis was to investigate the effects of mammalian grazers, such as microtine rodents and reindeer, (top-down effects) and nutrient availability (bottom- up effects) on the plant community of a tundra heath. I conducted a large-scale fertilization experiment and studied the impact of grazers using exclosures. I measured the effects of fertilization and grazing on soil microbial activity and nutrient cycling. I investigated the responses to fertilization of the invertebrate community, I studied the effects on the quality of bilberry as food for mammalian herbivores, and I looked at how concentrations of nutrients and carbon-based secondary defences against herbivory fluctuated between seasons in unfertilized and fertilized treatments. The results of my thesis show that the plant community investigated is exposed to a strong top-down control by mammalian herbivores. On the fertilized and grazed areas the aboveground biomass of the vascular plant community did not increase compared to unfertilized areas. However, the productivity of the plant community was clearly nutrient- limited. During the eight years of the experiment, on the fertilized areas plant biomass was significantly increased inside the herbivore exclosures In my study mammalian herbivores at comparatively low densities and grazing outside the growing season were sufficient to control the biomass of a heterogeneous plant community. Microtine rodents (Norwegian lemmings and grey-sided voles) preferred the fertilized areas for overwintering. The food plant quality of bilberry for grey-sided voles was improved on the fertilized areas throughout the year. Grazing decreased the nitrogen storage in the aboveground plant biomass. Reindeer and rodents had also important indirect effects on the plant community by decelerating soil nutrient cycling and soil microbial activity. This effect may be accelerated by the impact of herbivore on plant species composition. Graminoids, which contained the highest nitrogen concentrations in their tissues, increased rapidly on the fertilized areas, but their abundance was significantly lower on grazed fertilized areas. The invertebrate community was detritus-based and received their energy indirectly from the litter via soil microbes and detritivores. Fertilization increased the biomass of invertebrate carnivores, but had no effect on the biomass of invertebrate herbivores. Apparent competition between detritivores and invertebrate herbivores, mediated by carnivorous invertebrates predating on both of them, is supposed to keep the densities and grazing pressure of invertebrate herbivores low. Grazing damage by invertebrates was very low and only 0.021 % of the total vascular plant biomass was removed. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 2001, härtill 6 uppsstser.</p> / digitalisering@umu

Intercropping, defined as two or more crops grown on the same land area at the same time, is a sustainable alternative to sole crops. Intercropping has been associated with multiple benefits, such as increased nutrient and soil organic carbon (SOC) cycling, decreased soil erosion and increased carbon (C) sequestration. A common intercropping practice is to integrate cereal and legume crops such as maize (Zea mays L.), and soybean (Glycine max (L.) Merr.). Most studies on intercropping have focused on yield, weed control, and land use efficiency in the tropics. Few studies have researched C and nitrogen (N) dynamics in temperate intercrops, with respect to soybean and maize residue stabilization. Soil from Balcarce, Argentina, was incubated for 140 days with soybean, maize, or no residue. Throughout the incubation, results illustrated the effect of residue application upon the soil, specifically through significantly higher amounts of light fraction (LF) C and LFN concentrations, soil microbial biomass (SMB) C and SMBN concentrations, higher microbial diversity, lower N2O production rates, in addition to distinct isotopic values in soil fractions and CO2 (p<0.05). Furthermore, it was observed from δ15N-TN and δ15N-LF that treatments with soybean residues included had higher N cycling (p<0.05), emphasizing the importance of including N-fixing legumes in complex agroecosystems. Significant changes over time in SMB and SMCS characteristics, and isotope values (p<0.05) indicated the preferential utilization of relatively young and easily accessible litter. Furthermore, the loss of labile material over the incubation resulted in more recalcitrant forms (such as older C and lignin) to be utilized. Slightly higher SOC, TN, LFC and LFN concentrations, as well as lower CO2 production rates suggested 2:3 (rows of maize:rows of soybean) as a more desirable intercrop design for C sequestration. The 1:2 intercrop design was observed to be more beneficial for microbial community structure, furthering the idea that intercropping is a beneficial alternative to sole cropping. This study improves knowledge in residue stabilization and C sequestration in complex agroecosystems, providing encouragement for the implementation of more sustainable management practices.

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2009. / Grape juice is transformed into wine through the complex processes of alcoholic and malolactic fermentation that is performed by yeasts, lactic acid bacteria and acetic acid bacteria. However, the microbes involved in these processes do not only take part in ensuring the successful production of wine, but also cause spoilage of the wine if their growth is not controlled. Conventional, culture-dependent methods of microbiology have been used as the main technique in detecting and identifying these spoilage microbes. Cultureindependent techniques of molecular biology have recently become more popular in detecting possible spoilage microbes present in must and wine, since it allows the detection and identification of viable, but non-culturable microbes and are not as timeconsuming as conventional microbiological methods. The aim of this study was to investigate the sustainability of polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) analysis in detecting wine spoilage microbes inoculated into sterile saline solution (SSS) (0.85% (m/v) NaCl) and sterile white wine and red wine as single microbial species and as part of mixed microbial populations. Three methods of DNA isolation from SSS, sterile white wine and sterile red wine inoculated with reference microbial strains were compared in terms of DNA concentration and purity, as well as simplicity of the technique. These three DNA isolation methods were the TZ-method, the proteinase K-method and the phenol extraction method. DNA could not successfully be isolated from red wine using any of the three DNA isolation methods. The TZ-method was the method of choice for the isolation of DNA from inoculated SSS and sterile white wine as this technique gave the best results in terms of simplicity, DNA concentration and purity. PCR and DGGE conditions were optimised for the universal primer pair, HDA1-GC and HDA2, the wine-bacteria specific primer pair, WBAC1-GC and WBAC2, and the yeast specific primer pair, NL1-GC and LS2. DNA from Acetobacter pasteurianus, Lactobacillus plantarum, Pediococcus pentosaceus, Oenococcus oeni, Brettanomyces bruxellensis and Saccharomyces cerevisiae were amplified with the appropriate primers and successfully resolved with DGGE analysis. PCR and DGGE detection limits were successfully determined when 106 cfu.ml-1 of the reference microbes, A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis were separately inoculated into SSS and sterile white wine. It was possible to detect low concentrations (101 cfu.ml-1) with PCR for A. pasteurianus, Lb. plantarum, Grape juice is transformed into wine through the complex processes of alcoholic and malolactic fermentation that is performed by yeasts, lactic acid bacteria and acetic acid bacteria. However, the microbes involved in these processes do not only take part in ensuring the successful production of wine, but also cause spoilage of the wine if their growth is not controlled. Conventional, culture-dependent methods of microbiology have been used as the main technique in detecting and identifying these spoilage microbes. Cultureindependent techniques of molecular biology have recently become more popular in detecting possible spoilage microbes present in must and wine, since it allows the detection and identification of viable, but non-culturable microbes and are not as timeconsuming as conventional microbiological methods. The aim of this study was to investigate the sustainability of polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) analysis in detecting wine spoilage microbes inoculated into sterile saline solution (SSS) (0.85% (m/v) NaCl) and sterile white wine and red wine as single microbial species and as part of mixed microbial populations. Three methods of DNA isolation from SSS, sterile white wine and sterile red wine inoculated with reference microbial strains were compared in terms of DNA concentration and purity, as well as simplicity of the technique. These three DNA isolation methods were the TZ-method, the proteinase K-method and the phenol extraction method. DNA could not successfully be isolated from red wine using any of the three DNA isolation methods. The TZ-method was the method of choice for the isolation of DNA from inoculated SSS and sterile white wine as this technique gave the best results in terms of simplicity, DNA concentration and purity. PCR and DGGE conditions were optimised for the universal primer pair, HDA1-GC and HDA2, the wine-bacteria specific primer pair, WBAC1-GC and WBAC2, and the yeast specific primer pair, NL1-GC and LS2. DNA from Acetobacter pasteurianus, Lactobacillus plantarum, Pediococcus pentosaceus, Oenococcus oeni, Brettanomyces bruxellensis and Saccharomyces cerevisiae were amplified with the appropriate primers and successfully resolved with DGGE analysis. PCR and DGGE detection limits were successfully determined when 106 cfu.ml-1 of the reference microbes, A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis were separately inoculated into SSS and sterile white wine. It was possible to detect low concentrations (101 cfu.ml-1) with PCR for A. pasteurianus, Lb. plantarum, iv Pd. pentosaceus, and B. bruxellensis in SSS when amplified with the HDA1-GC and HDA2 primer pair. A PCR detection limit of 102 cfu.ml-1 was determined in sterile white wine for Pd. pentosaceus and 103 cfu.ml-1 for B. bruxellensis using this primer pair. The results obtained from the PCR amplification with the WBAC1-GC and WBAC2 primer pair compared well with the results of the HDA1-GC and HDA2 primer pair. The results from the DGGE detection limits indicated that it was possible to detect lower concentrations (101 – 102 cfu.ml-1) of A. pasteurianus, Lb. plantarum and Pd. pentosaceus with the HDA1-GC and HDA2 primer pair than the WBAC-GC and WBAC2 primer pair (102 – 104 cfu.ml-1). Lower detection limits were also determined for B. bruxellensis amplified with the HDA1-GC and HDA2 primer pair (103 – 104 cfu.ml-1) than with the NL1-GC and LS2 primer pair (105 cfu.ml-1). PCR and DGGE detection limits for the inoculation of A. pasteurianus, Lb. plantarum and B. bruxellensis at an inoculum of 108 cfu.ml-1 as part of mixed populations in SSS and sterile white wine compared well with the results obtained from the reference microbes inoculated as single microbial species. PCR detection limits of 101 cfu.ml-1 were determined for all three reference microbes inoculated as part of mixed populations when amplified with the HDA1-GC and HDA2 and the WBAC1-GC and WBAC2 primer pairs. It was observed that similar or higher DGGE detection limits were obtained for the reference microbes inoculated in sterile white wine (101 – 107 cfu.ml-1) than when inoculated into SSS (101 – 105 cfu.ml-1). PCR-based DGGE analysis proved to be a technique that could be used successfully with the universal, wine-bacteria and yeast specific primer pairs for the detection of A. pasteurianus, Lb. plantarum, Pd. pentosaceus and B. bruxellensis. The culture-independent technique makes the early detection of possible spoilage microbes at low concentrations in wine possible.

Bacterioplankton provide important ecosystem functions by carrying out biogeochemical cycling of organic matter. Playing an important role in the microbial loop they help remineralize carbon and nutrients. Bacteria also interact with phytoplankton during phytoplankton blooms. However, fundamental understanding on the underlying molecular mechanisms involved in the degradation of phytoplankton-derived organic matter is still in its infancy. Therefore, we analysed data from a mesocosm experiment following a natural phytoplankton-bloom from an upwelling system in the North- East Atlantic Ocean. The purpose was to contribute a mechanistic understanding based on functional gene expression analysis of natural microbial assemblages. Our results show the difference in functional gene expression within a bacterial metacommunity and how this functional response drastically switches between bloom build up and senescence. Transcripts showed a broad change in gene expression involving major SEED categories, with the bloom senescence phase exhibiting a higher relative abundance in major categories such as Carbohydrates, Protein Metabolism and Amino Acids and Derivatives. Within these categories genes connected to carbon utilization and transport systems (Ton and Tol) as well as chemotaxis showed a higher abundance during bloom senescence. The change in functionality based on transcripts showed a different bacterial community composition appearing over a very short time. We thus conclude that the bacterial functional gene expression response between build-up and degradation bloom phases is remarkably different and associated with a change in the identity of bacteria with active expression. Our findings highlight the importance of bacterial substrate specialists with different functional roles during different time points of phytoplankton blooms.

No description available.