No description available.

Increasing socio-economic growth and development of South Africa’s freshwater systems require continuous augmentation of water sources to meet the growing water requirements of communities and industries. Anthropogenic disturbances have caused the water quality of many freshwater systems to drastically deteriorate due to constant disposal of domestic, industrial, and agricultural waste into surface waters. Government agencies make use of biomonitoring programmes to effectively manage the countries’ freshwater resources. These programmes use a variety of biological indicators (e.g., macroinvertebrates, fish, diatoms and algal species) and physico-chemical variables to determine the state of the environment. However, attempts to use microbial community structures as bioindicators of anthropogenic perturbations are greatly neglected. This study used molecular techniques (PCR-DGGE and 454-pyrosequencing) and multivariate analysis to develop a robust monitoring technique to determine the impacts of environmental disturbances on bacterial community compositions in river systems in the North West Province. Significant contributions made by this project included the establishment of a bacterial diversity framework for South African freshwater systems that are impacted by a variety of anthropogenic activities (e.g., urban and informal settlements, agriculture and mining). Furthermore, case studies demonstrated the prevalence of specific taxa at polluted sites, as well as positive and negative associations between taxa and environmental variables and pollutants. Finally, biogeochemical cycles could be partially matched to bacterial community structures in river systems. The first part of the project included a pilot study that investigated bacterial structures in a segment of the Vaal River in response to environmental parameters using molecular techniques and multivariate analysis. The most important observations made during this study included the generation of a larger bacterial diversity dataset by pyrosequencing compared to PCR-DGGE. In addition, metagenomic and multivariate analyses provided clues about potential biogeochemical roles of different taxa. The second and third part of the project included two case studies that investigated bacterial communities in the Mooi River and Wonderfonteinspruit in response to environmental activities. Both these systems are impacted by a variety of external sources such as urban and informal settlements, agriculture, and mining. The results demonstrated that perturbations nearby the Mooi River and Wonderfonteinspruit caused the overall water quality to deteriorate which in turn had a profound impact on bacterial community composition. Bacterial community structures at reference/control sites (Muiskraal and Turffontein dolomitic eye) had overall high species diversity (richness and evenness), whereas polluted sites showed lower species diversity and were dominated by the Beta- and Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia. In addition, various potential pathogens (e.g. Eschirichia/Shigella, Legionella, Staphylococcus, Streptococcus etc.) were identified at impacted sites. Multivariate analysis suggested that bacterial communities and certain taxa (Malikia, Algoriphagus, Rhodobacter, Brevundimonas and Sphingopyxis) at polluted sites were mainly impacted by temperature, pH, nutrient levels, and heavy metals. Finally, the proportion of nitrogen and sulphur bacteria corresponded well with the nitrogen and sulphur levels measured in the Wonderfonteinspruit. Based on these results, it was concluded that bacterial community structures might provide a good indicator of anthropogenic disturbances in freshwater systems and may be incorporated into biomonitoring programs. / PhD (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Increasing socio-economic growth and development of South Africa’s freshwater systems require continuous augmentation of water sources to meet the growing water requirements of communities and industries. Anthropogenic disturbances have caused the water quality of many freshwater systems to drastically deteriorate due to constant disposal of domestic, industrial, and agricultural waste into surface waters. Government agencies make use of biomonitoring programmes to effectively manage the countries’ freshwater resources. These programmes use a variety of biological indicators (e.g., macroinvertebrates, fish, diatoms and algal species) and physico-chemical variables to determine the state of the environment. However, attempts to use microbial community structures as bioindicators of anthropogenic perturbations are greatly neglected. This study used molecular techniques (PCR-DGGE and 454-pyrosequencing) and multivariate analysis to develop a robust monitoring technique to determine the impacts of environmental disturbances on bacterial community compositions in river systems in the North West Province. Significant contributions made by this project included the establishment of a bacterial diversity framework for South African freshwater systems that are impacted by a variety of anthropogenic activities (e.g., urban and informal settlements, agriculture and mining). Furthermore, case studies demonstrated the prevalence of specific taxa at polluted sites, as well as positive and negative associations between taxa and environmental variables and pollutants. Finally, biogeochemical cycles could be partially matched to bacterial community structures in river systems. The first part of the project included a pilot study that investigated bacterial structures in a segment of the Vaal River in response to environmental parameters using molecular techniques and multivariate analysis. The most important observations made during this study included the generation of a larger bacterial diversity dataset by pyrosequencing compared to PCR-DGGE. In addition, metagenomic and multivariate analyses provided clues about potential biogeochemical roles of different taxa. The second and third part of the project included two case studies that investigated bacterial communities in the Mooi River and Wonderfonteinspruit in response to environmental activities. Both these systems are impacted by a variety of external sources such as urban and informal settlements, agriculture, and mining. The results demonstrated that perturbations nearby the Mooi River and Wonderfonteinspruit caused the overall water quality to deteriorate which in turn had a profound impact on bacterial community composition. Bacterial community structures at reference/control sites (Muiskraal and Turffontein dolomitic eye) had overall high species diversity (richness and evenness), whereas polluted sites showed lower species diversity and were dominated by the Beta- and Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia. In addition, various potential pathogens (e.g. Eschirichia/Shigella, Legionella, Staphylococcus, Streptococcus etc.) were identified at impacted sites. Multivariate analysis suggested that bacterial communities and certain taxa (Malikia, Algoriphagus, Rhodobacter, Brevundimonas and Sphingopyxis) at polluted sites were mainly impacted by temperature, pH, nutrient levels, and heavy metals. Finally, the proportion of nitrogen and sulphur bacteria corresponded well with the nitrogen and sulphur levels measured in the Wonderfonteinspruit. Based on these results, it was concluded that bacterial community structures might provide a good indicator of anthropogenic disturbances in freshwater systems and may be incorporated into biomonitoring programs. / PhD (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Le lien entre la macrofaune et les communautés bactériennes benthiques a été déterminé selon deux approches : (1) une approche expérimentale à l’échelle de l’individu ciblée sur les effets de l’activité et de la bioturbation du polychète déposivore de surface Melinna palmata sur la distribution des communautés bactériennes des premiers millimètres de l’interface eau-sédiment ; (2) une approche in situ à l’échelle de la communauté de mise en corrélation des patrons spatiaux de distribution des communautés de macrofaune et de bactéries.Melinna palmata appartient à un nouveau groupe fonctionnel de bioturbation décrit pour la première fois, convoyeur de surface. L’utilisation de ce nouveau modèle biologique a permis de mettre en évidence que les activités de prospection et d’égestions modifient significativement la distribution des communautés bactériennes de la couche oxique de l’interface eau-sédiment. Ce lien est à la fois influencé par l’apport de matière organique de différentes qualités, et impacte la consommation et la minéralisation de cette matière organique.Le lien entre les patrons spatiaux de distribution des communautés de macrofaune et de bactéries a été étudié in situ, dans la vasière Ouest-Gironde. Les deux compartiments ont évolué le long d’un gradient avéré de teneur en matière organique et de taille des particules dans cette vasière.La corrélation des matrices biologiques n’a cependant pas été statistiquement significative et nécessite d’être approfondi. / The link between benthic macrofauna and bacterial communities was assessed with two different approaches: (1) an experimental approach at the individual scale, focused on the effects of behaviour and bioturbation of the deposit feeder polychaete Melinna palmata on the bacteria lcommunity distribution on the very sediment-water interface; (2) an in situ approach at the scale of the community, focused on the correlation between spatial distribution patterns of the two biological compartments. Melinna palmata belongs to a new functional group of bioturbation described for the first time: surface conveyor. Its use allowed determining that prospection and egestion induced a significant change of bacterial communities on the sediment-water interface. This link was influenced by organic matter enrichment while influencing its fate. In a second part, the link between spatial distribution patterns of the communities was assessed in situ in the West-Gironde mud patch. Both macrofauna and bacteria changed along a gradient of organic matter quantity and quality and of particles size described in this system. However, the correlation between matrices was not statistically significant and needs to be more developed.

Bacteria play important roles in the transformation of nutrients in wetlands, but few studies have examined parameters affecting variation in bacterial community composition between wetlands. We compared the composition of eubacterial and denitrifying bacterial biofilm communities in 32 agricultural constructed wetlands in southern Sweden, and the extent to which wetland environmental parameters could explain the observed variation. Structure and richness of the eubacterial 16S rRNA gene and three denitrifying bacterial enzyme genes (nirK, nirS and nosZ), analysed by molecular fingerprinting methods, varied among the constructed wetlands, which could be partly explained by different environmental parameters. Results from the enzyme gene analyses were also compared to determine whether the practice of using a single denitrifying bacterial gene could characterize the overall community composition of denitrifying bacteria. We found that nirK was more diverse than both nirS and the nosZ, and the band structure and richness of the three genes were not related to the sam environmental parameters. This suggests that using a single enzyme gene may not suffice to characterize the community composition of denitrifying bacteria in constructed agricultural wetlands. / <p>Included in doctoral thesis: Milenkovski, Susann. Structure and Function of Microbial Communities in Constructed Wetlands - Influence of environmental parameters and pesticides on denitrifying bacteria. Lund University 2009.</p>

In the Boreal region, the length of day and night varies extremely over the year and organisms are exposed to different diel (24 h) fluctuations of light and temperature. Among them are pelagic populations of bacteria that are ubiquitous in freshwater ecosystems. The structure of prokaryotic assemblages in lakes is regulated by both abiotic and biotic parameters known to have diel patterns; yet, knowledge on changes of the active bacterial community composition (aBCC) over diel cycles is limited, especially at short temporal scales. Here, measurements of physicochemical parameters, nutrient levels and chlorophyll a concentrations, characterization of the carbon pool and 16S rRNA sequencing were used to elucidate the aBCC in a peat bog and the oligotrophic lake Klocka in Jämtland county, Sweden. I show that the activity of bacterioplankton communities remained relatively stable at 6-h intervals and did not follow any diel patterns during an uneven light regime period in June. However, the activity of peat bog communities changed in a cyclic pattern over three diel cycles during an even light period in September, whereas diel changes did not substantially differentiate between sampling periods and among depths in Klocka. The results of the thesis provide valuable insights into the importance of diel cycles in bacterial diversity and community dynamics in lentic habitats.

No description available.

Mikrobielle Gemeinschaften werden direkt und indirekt von einem komplexen System verschiedenster Interaktionen zwischen biotischen und abiotischen Faktoren beeinflusst. So zum Beispiel von verschiedenen Pflanzenarten und ihren jeweiligen Eigenschaften, dem Nährstoffgehalt des Bodens, sowie dem pH-Wert. Im Gegenzug gestalten Mikroorganismen als wichtige Treiber der C- und N-Kreisläufe ihre Umwelt. Im Rahmen der vorliegenden Arbeit wurden mehrere Studien unter kontrollierten Feld- und Laborbedingungen, sowie unter natürlichen Bedingungen im Freiland durchgeführt, um verschiedene Einflussfaktoren zu bestimmen und den Grad ihres Einflusses zu ermitteln. Die Zusammensetzung der prokaryotischen Gemeinschaften in den verschiedenen Bodenproben wurden mit Hilfe phylogenetischer Marker, der 16S-rRNA Gene und der 16S-rRNA, analysiert. Die erhaltenen Amplikon-basierten Daten wurden dann prozessiert und die Indices für Artenvielfalt und Artenreichtum berechnet. Zusätzlich wurden Betadiversitätsanalysen durchgeführt, um Unterschiede in der Zusammensetzung der bakteriellen Gemeinschaft zwischen den verschiedenen Behandlungen sichtbar zu machen. Des Weiteren wurden die erhaltenen DGGE Profile für Clusteranalysen verwendet, um Ähnlichkeiten oder Unterschiede in der Struktur der Bakteriengemeinschaft zwischen den verschiedenen Behandlungen aufzuzeigen. Die vorliegende Arbeit gibt einen Einblick über den Einfluss der Baumarten, Baumartendiversität, des Laubes und des Probennahmezeitpunktes auf die Zusammensetzung und Diversität von Bakteriengemeinschaften in Böden. Die erhaltenen Daten zeigten, dass die Laubschicht der Haupteinflussfaktor auf die Zusammensetzung der bakteriellen Gemeinschaft in der Rhizosphäre von jungen Buchen und Eschen ist. Des Weiteren zeigte sich, das verschiedene Baumarten, deren Diversität, sowie saisonale Unterschiede nur einen geringen Einfluss auf die Struktur der bakteriellen Gemeinschaft haben. Zusätzlich konnte gezeigt werden, dass die mikrobielle Gemeinschaftsstruktur nicht signifikant von Buchen- und Eschensetzlingen beeinflusst wird, vermutlich aufgrund des frühen Entwicklungsstadiums der verwendeten Baumsetzlinge. Weiterhin konnte gezeigt werden, dass die Buchensetzlinge das Wachstum von Bakterien inhibierten, während das Pilzwachstum gefördert wurde. Dies wurde vermutlich hervorgerufen durch eine Verschiebung des pH-Wertes im Boden verursacht durch buchenspezifische Wurzelausscheidungen. Morphologisch unterschiedliche Baumarten beeinflussen die Struktur und Diversität mikrobieller Gemeinschaften auf verschiedenen Wegen. Die Analyse der Bakterien- und Pilzgemeinschaften in natürlichen Waldböden unter erwachsenen Buchen und Fichten zeigte einen signifikanten Einfluss der untersuchten Baumarten auf deren Zusammensetzung. Es konnte ein Einfluss des pH-Werts auf die Bakterien- und Pilzvielfalt unter den analysierten Fichtenbeständen gezeigt werden. Des Weiteren wurden die Auswirkungen hoher NO3- Depositionen auf die CH4 und N2O Gasflüsse und die aktiven Bakterien- und Archeengemeinschaften in gemäßigten Laubwaldböden mit Hilfe von Mesokosmen untersucht. Es konnte ein starker Effekt der NO3- Düngung auf die CH4 Aufnahmeraten und N2O Emissionen des gedüngten Laubwaldbodens gezeigt werden. Die N-Düngung hemmte die CH4 Aufnahme des Bodens, während die N2O Emission stieg. Die Bakteriengemeinschaft in den gedüngten Mikrokosmen verschob sich im Verlauf des Versuches in Richtung einer denitrifizierenden Gemeinschaft, dominiert durch die Gattung Rhodanobacter. Darüber hinaus konnte eine Reduzierung der bakteriellen Vielfalt und der CO2 Emission innerhalb der N-gedüngten Mikrokosmen gezeigt werden. Des Weiteren sanken die CO2 Emissionsraten in beiden Behandlungen im Verlauf des Experiments. Dies deutet auf eine reduzierte Aktivität der vorhandenen Bodenmikroorganismen hin, möglicherweise hervorgerufen durch eine C Limitierung des verwendeten Waldbodens. Obwohl eine Verschiebung in der relativen Häufigkeit der auftretenden nitrifizierenden Archeen der Gattung Nitrosotalea nachgewiesen wurde, konnte eine signifikante Veränderung in der Zusammensetzung der gesamten Archeengemeinschaft nicht beobachtet werden. Die Ergebnisse zeigten jedoch einen erheblichen Beitrag methylotropher, methanotropher und nitrifizierender Bakterien, welche in geringer Zahl auftraten, in Bezug auf die gemessene CH4 Aufnahme. Des Weiteren wurden die Auswirkungen der Anwesenheit von Ameisen und ihrer Aktivitäten auf die Aktivität und Vielfalt der mikrobiellen Gemeinschaften im Boden und Ameisennest untersucht. Ameisen transportierten den von Läusen gewonnenen Honigtau in den Boden und verursachten damit eine Abnahme der mikrobiellen Biomasse in der Streuschicht, während die δ15N-Signatur, die basale Atmung und die mikrobielle Biomasse im Boden erhöht wurden. Im Gegensatz dazu konnten mittels Cluster-Analyse der erstellten DGGE Profile keine deutlichen Unterschiede der mikrobiellen Gemeinschaftsstruktur in den untersuchten Mikrokosmen gezeigt werden. Im Gegensatz dazu beeinflusste die Nestbauaktivität und der Eintrag von organischen Substanzen in den Boden durch die Ameisen jedoch die Struktur der Bakteriengemeinschaften im Freiland. Die Cluster-Analyse der erhaltenen DGGE Profile zeigte Unterschiede in der Zusammensetzung der bakteriellen Gemeinschaft in Abhängigkeit vom Probenentnahmeort und der Ameisenaktivität. Außerdem konnte gezeigt werden, dass sich die Struktur der Bakteriengemeinschaft in den Ameisennestern von der im Umgebungsboden unterschied. Ein sekundäres Projekt dieser Arbeit war die Erfassung und der Vergleich der mikrobiellen Gemeinschaften in biologischen Bodenkrusten zweier unterschiedlicher Standorte in extrazonalen, trockenen Bergsteppen der nördlichen Mongolei. Die Studie zeigte deutliche Unterschiede in der mikrobiellen Gemeinschaftsstruktur der beiden Standorte, welche sich im Grad der Störung unterschieden.

No description available.

Biocrusts and the ecosystem services they provide are becoming more susceptible to fire as exotic annual grass invasions facilitate the spread of desert wildfires. Further, precipitation patterns across the western United States are predicted to change over the next century, and have the potential to dramatically influence fire regimes and the recovery of burned biocrusts. Despite these changes to desert fire and precipitation cycles, our understanding of post-fire biocrust recovery is limited, especially regarding the first two years after fire. To investigate biocrust recovery, we created burn manipulations (i.e., unburned and burned) and tracked crust form and function over two years in one cold and one hot desert ecosystem (UT, USA). We evaluated the entire bacterial community, but focused on Cyanobacteria species that confer soil stability and N fixation capabilities to biocrusts. Specifically, we quantified shifts in biocrust bacterial community composition using target metagenomics of 16S rDNA; monitored biocrust moss and lichen cover; measured N fixation potential; and assessed soil infiltration rates and soil stability. We found little evidence that biocrust form or function recovered from fire within two years. Based on pyrosequencing results, fire altered biocrust community composition in interspace and shrub biocrusts. Cyanobacteria species were almost completely eliminated by fire, constituting 9-21% of unburned plots and less than 0.01% of burned interspace and shrub biocrust communities. Based on cover estimates, no lichen or moss species survived the fire or recovered within two years. N fixation potentials decreased by at least six-fold in burned interspace biocrusts, representing a reduction in soil N inputs into already N-limited desert soils. Soil infiltration rates also drastically declined in burned biocrusts and remained depressed, but only remained depressed for one year. To investigate the interactions between biocrust recovery, fire, and precipitation, we nested precipitation treatments manipulating the amount of monthly rainfall (i.e., ambient, plus 30% and minus 30%) within burn treatments during the second year. Soil NH4+ was the only parameter to be affected by precipitation, and exhibited a positive relationship with precipitation magnitude at the end of one year. Our results demonstrate that fire is a strong destabilizer of the bacterial components of biocrust communities and that the ecosystem services provided by crusts recover at different rates, with N dynamics recovering more slowly than soil ecohydrology.