Thesis (Ph. D.)--Montana State University--Bozeman, 2005. / Typescript. Chairperson, Graduate Committee: John C. Priscu. Includes bibliographical references (leaves 181-201).

Made available in DSpace on 2016-05-17T16:51:22Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-08-14. Added 1 bitstream(s) on 2016-05-17T16:54:58Z : No. of bitstreams: 1 000864109.pdf: 2175142 bytes, checksum: fff8a8ccb57c55f7ae5759469cbc46dd (MD5) / Para que um subsolo exposto tenha restabelecido, mesmo que parcialmente, a dinâmica de seus atributos na camada superficial e, com isto, apresente condições para receber e dar suporte à vegetação de cerrado é necessário a utilização de técnicas específicas. Para acelerem esta etapa uma alternativa seria a introdução de resíduos, como as macrófitas aquáticas removidas das águas de represas de usinas hidrelétricas, como resíduo orgânico e cinza de bagaço de cana-de-açúcar produzida em usinas sucroalcooleiras, como resíduo agroindustrial. Desta forma, o objetivo do trabalho foi o condicionamento de um subsolo exposto no Cerrado por meio de resíduos e da revegetação. A área foco tem extensão de 10,66 km 2, em área contínua, localizada à margem direita do Rio Paraná e degradada na década de 60 durante construção da Usina Hidrelétrica de Ilha Solteira-SP. Realizou-se a caracterização inicial da área e as demais avaliações foram feitas após 12 e 24 meses da implantação do experimento. A área foi gradeada (grade pesada), para rompimento do encrostamento superficial e escarificada, à profundidade média de 0,37 m. A área foi novamente gradeada para desmanchar os torrões produzidos durante a subsolagem e para a incorporação dos resíduos (macrófitas aquáticas e cinza de cana-de-açúcar) distribuídos a lanço. Após seis meses, mudas de dez espécies arbóreas de Cerrado foram introduzidas aleatoriamente, no espaçamento de plantio 4,0 x 5,0 m, totalizando 1.080 mudas. O delineamento experimental foi o de blocos ao acaso, em esquema fatorial 3 x 4, sendo os tratamentos composto de 3 doses de macrófitas (0, 16 e 32 t ha -1 ) e 4 doses de cinza (0, 15, 30 e 45 t ha -1 ), totalizando 12 tratamentos, com 03 repetições, estabelecidos em parcelas de 20 x 30 m (600 m 2 ), separadas por faixas de 5 m de largura. Após 24 meses da instalação do experimento... / To restore in an exposed subsoil, even partially, the dynamics of their attributes in the surface layer and, thus, presents conditions to receive and support the Cerrado vegetation, the use of specific techniques is required. To accelerate this step, an alternative could be the introduction of waste, such as aquatic weeds removed from water reservoirs of hydro power plants, as an organic waste, and ash sugarcane bagasse produced in sugarcane mills, as an agroindustrial waste. Thus, the objective was the conditioning of exposed subsoil in the Cerrado, through organic and inorganic waste addition and revegetation. The focus area has an extension of 10.66 km 2, in continuous area, located on the right bank of the Paraná River and degraded in the 60s during construction of the Ilha Solteira hydroelectric power. It conducted the initial characterization of the area and other evaluations were done after 12 and 24 months of implementation of the experiment. The area was fenced (heavy grade), to break the surface crusting, and scarified, at the average depth of 0.37 m. The area was again barred to break up the clods produced during the subsoil and the incorporation of waste (aquatic weeds and sugarcane ash) happened after them being spread on the subsoil surface. After six months, seedlings of ten Cerrado tree species were introduced randomly, in planting spacing of 4.0 x 5.0 m, totaling 1,080 seedlings. The experimental was a randomized block in a 3 x 4 factorial design, consisting of 3 doses of macrophytes (0, 16 and 32 t ha -1 ) and 4 ash levels (0, 15, 30 and 45 t ha -1 ), a total of 12 treatments, with 03 repetitions, established in plots 20 x 30 m (600 m 2 ), separated by 5 m wide ranges. After 24 months of experiment installation were evaluated: density, macro and microporosity, fertility, height and diameter of the plants, released CO 2 -carbon (CO 2 -C) and number of spores of arbuscular ...

This study aimed to investigate the feeding behaviour of the calanoid copepod, Pseudodiaptomus hessei, particularly whether it prefers to feed on a planktonic or benthic food source. The effect of different microalgae species on the feeding preference, ingestion, and gut evacuation rate were investigated. Two microalgae species (Isochrysis galbana and Tetraselmis suecica) were used, to test gut fullness and gut evacuation of P. hessei. The copepods were starved for 6 h and allowed to feed on monalgae diets, I .galbana and T. suecica, and a 1:1 binary diet mixture of T. suecica and I. galbana. The gut fullness and gut evacuation rates were determined by observing under the dissecting microscope and gut content percentage was recorded (as 0, 25, 50, 75 or 100 percent) along with copepod sex. Copepods that feed on T. suecica fill their gut after 30 min, while those that feed on I. galbana do so after 40 min. There was a significant difference (p= 0.02) between sexes with males filling their gut faster than females. However, copepods that fed on I. galbana evacuated their gut content completely after 30 min, while those fed on T suecica evacuated theirs after 40 min. There was no difference between males and females for gut evacuation. Even though there was high gut fullness rate when P. hessei was feeding on T. suecica, I. galbana is recommended as the best mono-algae diet to culture P. hessei. The feeding behaviour of P. hessei was investigated, as to whether it prefers to feed on a planktonic or benthic food source. Copepods were starved for 3 h and then allowed to feed on two microalgae species (I. galbana and T. suecica), one presented as a benthic and other as planktonic. Controls included swapping the modes of presentation for each algae species. Ingested microalgae species were quantified using real-time PCR, with threshold cycles interpreted as relative abundance ratio (planktonic microalgae divided by benthic microalgae species). Pseudodiaptomus hessei preferred to feed on planktonic food sources initially as there was a difference between planktonic and benthic ingested food (p=0.026). Copepods shifted from planktonic to benthic food sources after 80 min of feeding planktonically. Planktonic food sources were the preferred choice for P. hessei regardless of microalgae species offered. The results from this study also confirm that P. hessei feed on a benthic food source during the day under culture conditions. This information can be used as baseline information for aquaculturists to rear the species as live feed for marine fish larvae.

Orientador: Ana Maria Rodrigues Cassiolato / Co-orientador: Kátia Luciene Maltoni / Banca: Renato Alberto Momesso Franco / Banca: Carolina dos Santos Batista Bonini / Resumo: Para que um subsolo exposto tenha restabelecido, mesmo que parcialmente, a dinâmica de seus atributos na camada superficial e, com isto, apresente condições para receber e dar suporte à vegetação de cerrado é necessário a utilização de técnicas específicas. Para acelerem esta etapa uma alternativa seria a introdução de resíduos, como as macrófitas aquáticas removidas das águas de represas de usinas hidrelétricas, como resíduo orgânico e cinza de bagaço de cana-de-açúcar produzida em usinas sucroalcooleiras, como resíduo agroindustrial. Desta forma, o objetivo do trabalho foi o condicionamento de um subsolo exposto no Cerrado por meio de resíduos e da revegetação. A área foco tem extensão de 10,66 km 2, em área contínua, localizada à margem direita do Rio Paraná e degradada na década de 60 durante construção da Usina Hidrelétrica de Ilha Solteira-SP. Realizou-se a caracterização inicial da área e as demais avaliações foram feitas após 12 e 24 meses da implantação do experimento. A área foi gradeada (grade pesada), para rompimento do encrostamento superficial e escarificada, à profundidade média de 0,37 m. A área foi novamente gradeada para desmanchar os torrões produzidos durante a subsolagem e para a incorporação dos resíduos (macrófitas aquáticas e cinza de cana-de-açúcar) distribuídos a lanço. Após seis meses, mudas de dez espécies arbóreas de Cerrado foram introduzidas aleatoriamente, no espaçamento de plantio 4,0 x 5,0 m, totalizando 1.080 mudas. O delineamento experimental foi o de blocos ao acaso, em esquema fatorial 3 x 4, sendo os tratamentos composto de 3 doses de macrófitas (0, 16 e 32 t ha -1 ) e 4 doses de cinza (0, 15, 30 e 45 t ha -1 ), totalizando 12 tratamentos, com 03 repetições, estabelecidos em parcelas de 20 x 30 m (600 m 2 ), separadas por faixas de 5 m de largura. Após 24 meses da instalação do experimento... / Abstract: To restore in an exposed subsoil, even partially, the dynamics of their attributes in the surface layer and, thus, presents conditions to receive and support the Cerrado vegetation, the use of specific techniques is required. To accelerate this step, an alternative could be the introduction of waste, such as aquatic weeds removed from water reservoirs of hydro power plants, as an organic waste, and ash sugarcane bagasse produced in sugarcane mills, as an agroindustrial waste. Thus, the objective was the conditioning of exposed subsoil in the Cerrado, through organic and inorganic waste addition and revegetation. The focus area has an extension of 10.66 km 2, in continuous area, located on the right bank of the Paraná River and degraded in the 60s during construction of the Ilha Solteira hydroelectric power. It conducted the initial characterization of the area and other evaluations were done after 12 and 24 months of implementation of the experiment. The area was fenced (heavy grade), to break the surface crusting, and scarified, at the average depth of 0.37 m. The area was again barred to break up the clods produced during the subsoil and the incorporation of waste (aquatic weeds and sugarcane ash) happened after them being spread on the subsoil surface. After six months, seedlings of ten Cerrado tree species were introduced randomly, in planting spacing of 4.0 x 5.0 m, totaling 1,080 seedlings. The experimental was a randomized block in a 3 x 4 factorial design, consisting of 3 doses of macrophytes (0, 16 and 32 t ha -1 ) and 4 ash levels (0, 15, 30 and 45 t ha -1 ), a total of 12 treatments, with 03 repetitions, established in plots 20 x 30 m (600 m 2 ), separated by 5 m wide ranges. After 24 months of experiment installation were evaluated: density, macro and microporosity, fertility, height and diameter of the plants, released CO 2 -carbon (CO 2 -C) and number of spores of arbuscular ... / Mestre

It is acknowledged that some microbes have interrupted distributions, yet these distributions have rarely been correlated with environmental variables. The wild biogeography of the fermenting yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus are explored in this study, considering multiple environmental variables as potential effectors of each species' geographical distributions. I demonstrate that summer temperatures predict maximum species distribution limits for both S. paradoxus and S. cerevisiae on oak bark, and that S. paradoxus is more likely to be isolated from larger, older trees. Modelling these data predicts a generally denser southern European population of S. paradoxus, with S. cerevisiae being scarce on oak bark throughout Europe. It was not possible to recover ancient Saccharomyces DNA sequences from samples of sub-fossilized oaks, from Greco-Roman and North African amphora residues, or from North African 6th-14th Century pottery residues, which may be a consequence of the low concentration of these species in comparable modern environmental samples. Even from air dried breads and recent wines, Saccharomyces aDNA was not recovered as part of this study, although ancient DNA sequences from plants and other yeasts were identified in other samples via the same methods. Any future recovery of ancient Saccharomyces sequences may therefore be challenging. Novel plant sequences possibly belonging to the Musaceae family and Pinus genus were identified from 6th-14th century AD North African pottery; as well as a Vicia-like DNA sequence from a 13th-12th century BC North African amphora.

Philosophiae Doctor - PhD / Soil communities are regarded as among the most complex and diverse assemblages of microorganisms with estimated bacterial numbers in the order of 109-1 cells.g. Studies on extreme soils however, have reported lower cell densities, supporting the perception that the so-called extreme environments exhibit low species diversity. To assess the extent of microbial diversity within an extreme environment, the mineral soils of the Dry Valleys, Ross Dependency, Eastern Antarctica were investigated using 16S rDNA analysis. Three mineral soils designated MVG, PENP and BIS were analysed, each differing with respect to altitude, protein, lipid, water and DNA content. The mid-altitude sample, MVG, yielded the highest levels of DNA and the low altitude BIS soil contained the highest levels of protein, lipid and water. 16S clone libraries were constructed and 60 unique clones were identified and sequenced. BLASTn analysis revealed eight phylogenetic groups with Cyanobacteria, Actinobacteria and Acidobacteria representing the majority. The Cyanobacterial phylotypes were unique to the desiccated high-altitude soils of the PENP sample, suggesting a soil-borne Cyanobacterial population. 21% of the phylotypes identified were assigned as ‘uncultured’. DNA isolated from the Antarctic mineral soils was also used to construct a metagenomic clone library consisting of 90700 clones with an average insert size of 3.5 kb, representing an estimated 3.4% of the available metagenome. Activity-based screening of the library for genes conferring lipolytic activity yielded no positive clones. It is suggested that the failure to produce positive clones might be a result of insufficient nucleotide coverage of the metagenomic DNA. The metagenomic DNA extracted from the Dry Valley mineral soils was further analyzed using PCR. Two sets of degenerate primers based on conserved regions within lipolytic genes were used to target lipase and esterase genes. One set of primers was selected from a previous study. A second primer set was designed manually from amino acid alignments of true lipase genes from family I, sub-families I-VI. PCR analysis resulted in nine partial gene fragments varying between 240 bp and 300 bp. Bioinformatic analysis revealed that all nine partial gene fragments harboured α/β-hydrolase motifs, putatively identifying two esterases and three lipases from both bacterial and fungal origin. / South Africa

Philosophiae Doctor - PhD / This thesis presents significant advances into the microbial ecology of hypolithic communities in two hyperarid deserts. Deserts account for one fifth of the Earths total surface area. These zones differ substantially in terms of climate, geomorphology, hydrology and vegetation. Desert biomes are, however, generally depauperate with particularly with respect to macroorganisms. Hypoliths, photosynthetic microbial assemblages associated with quartz rocks, are widely distributed in hot and cold desert environs where they may represent a large fraction of the standing biomass and mediate key ecosystem processes, including nutrient cycling. However, important questions regarding their (i) development (ii) community structure and assembly patterns and (iii) functional structure remain unaddressed. Here, molecular tools (T-RFLP, clone libraries and pyrosequencing) and multivariate data analyses were used to address these questions. This study presents evidence of species recruitment in the development of hypolithic communities in the Namib Desert. Hypolithic bacterial communities were compared at a fine scale (10 m radius). Multivariate analysis of T-RFLP-derived data showed that hypolithic and open soil communities were structurally distinct. Applying the ecological concept of ‘indicator species’, 6 and 9 indicator lineages were identified for hypoliths and soil, respectively. Hypolithic communities were dominated by cyanobacteria affiliated to Pleurocapsales, whereas actinobacteria were prevalent in the open soil. These results are consistent with the concept of species sorting and suggest that the underside of the quartz rocks provide conditions suitable for the development of discrete and demonstrably different microbial assemblages.However, strong evidence for neutral assembly processes was found, as almost 90% of the taxa present in the hypoliths were also detected in the open soil. All together, these results suggest that hypolithons do not develop independently from microbial communities found in the surrounding soil, but selectively recruit from local populations.The bacterial community structure and assembly patterns in hypolithons from Miers Valley (Antarctica) were investigated. Previous studies in this valley have identified three morphologically distinct hypolithic community types: cyanobacteria dominated(Type I), fungus dominated (Type II) and moss dominated (Type III). The bacterial composition of surface soils and hypolithic communities were shown to be clearly and robustly distinct, using T-RFLP analysis. Moreover, the bacterial assemblages were similar in Type II and Type III hypolithons and clearly distinct from those foundin Type I. Using16S ribosomal RNA gene (rRNA) 454 pyrosequencing,Proteobacteria were shown to be the most important bacterial component of all three types of hypolithic communities. As expected, Cyanobacteria dominated Type I hypolithons, whereas Actinobacteria dominated Types II and III hypolithons. Using a probabilistic dissimilarity metric and random sampling, deterministic processes were demonstrated to be relatively more important in shaping the structure of the bacterial community found in Type II and Type III hypolithons. Taken together, these results suggest that hypolithic development favors a sequential pathway with Type II hypolithons serving as an intermediate development state between Type I and Type In a more in depth analysis of the diversity patterns of key nutrient cycling genes in Antarctic Miers Valley edaphic communities, genes coding for carbon fixation (greenand red-like cbbL), nitrogen fixation (nifH), nitrification (amoA) and denitrification(nirK and nirS), were targeted. Multivariate analysis (PERMANOVA) showed that hypolithic and open soil communities were functionally distinct. Type I hypoliths were functionally more diverse than soils, suggesting higher potential for enzymatic activities. Taxonomic structure (derived from 16S rRNA data) showed congruence with functional traits (genes involved in C and N cycling). Redundancy analysis suggested that chemical variables (S, F, and NO3) were important structuring forces in the different communities. Taken together, the results suggest that stochastic processes such as dispersion cannot override the influence of environmental factors on functional diversity patterns.

Magister Scientiae (Biodiversity and Conservation Biology) - MSc (Biodiv and Cons Biol) / The Bokkeveld Plateau, a region hosting high plant endemism, is home to two arid mountain centre renosterveld types. One, Nieuwoudtville Shale Renosterveld, has partially been transformed into croplands and pastures, with about 40 % remaining as non-contiguous fragments on privately owned land, and is used as natural rangelands for sheep grazing. The vegetation, soil chemical parameters, and rhizosphere soil microbial ecology of a dominant plant, Eriocephalus purpureus, were assessed. A combination of field sampling and recording, laboratory analyses of soil samples, and interviews were used to glean data. Data were statistically analysed using multivariate techniques. Overall plant species richness did not differ among the study sites, though plant species richness and cover of the different plant growth form categories varied among the sites. Soil chemical parameters varied among sites. Soil chemical and rhizosphere soil microbial parameters co-varied, and showed different profiles among the study sites. High cover of E. purpureus was associated with high microbial enzyme activity, while high cover of (other, non-dominant) non-succulent shrubs was associated with high bacterial functional diversity. Cover of geophytes, Asparagus capensis and perennial grass was associated with high microbial biomass. The findings indicate that E. purpureus-dominated Niewoudtville Shale Renosterveld is heterogeneous not only in terms of vegetation, but also in terms of soil chemical and microbial parameters. The results support the conservation of all fragments of remaining renosterveld, as they may serve as valuable resources of not only plant genetic material but also of soil microbial communities.

Soil microbial communities can be characterized by community structure and function (community composition) across a spectrum of spatial scales, and variation in soil microbial composition has been associated with a number of environmental gradients. This study investigates the structure and function of soil microbial communities under mature, undisturbed forested sites across a range of regional climates in British Columbia and Alberta, and also examines the variation in community composition within sites. Phospholipid fatty acid analysis was used to investigate the structure of soil microbial communities and total soil microbial biomass at each site. Extra-cellular enzyme assays established the functional potential of the soil microbial community at each site. Multivariate analysis of the data showed that the soil microbial communities under different forest types did significantly separate along the regional climate gradient by both community structure and function, despite high local variation in the communities. Soil moisture content and soil organic matter concentration consistently exhibited the strongest relationship with microbial community characteristics, although the functional and structural responses to the external drivers were different. Microbial community function and structure also changed with soil depth but not with time of sampling. Microbial community function was related to the regional annual average precipitation gradient. Most of the locations exhibited unique microbial community functional profiles in their soil layers; however the enzyme activities in the samples from the driest (Ponderosa Pine) and wettest (Mountain Hemlock) locations were notably different from each other and from those of the other locations, especially in the organic layers. The moist maritime-influenced Coastal Western Hemlock (CWH) forest exhibited microbial community structural characteristics which were unique from those of the other forest locations. The higher abundance of bacteria relative to fungi in the CWH forest soils may be related to the significantly higher available nitrogen concentrations at this site. / Forestry, Faculty of / Graduate

Virulence (parasite- induced host fitness reduction) is thought to correlate positively with pathogen reproduction rates, but its relationship with pathogen transmission is likely to be determined by a trade- off between the costs and benefits of harming hosts. This project aims to investigate factors which affect host-parasite interactions and particularly those which may play a role in virulence evolution. In doing so, it describes experiments carried out using a monogenean ectoparasitic flatworm (Gyrodactylus arcuatus) and its three-spined stickleback (Gasterosteus aculeatus) host. Populations of this fish species experience a range of both environmental and ecological conditions. Such environmental heterogeneity has been found to drive changes in fish phenotypic traits such as morphology, behaviour, life history and physiology which may consequently affect parasite fitness. I demonstrate that under these conditions, parasite strains from different host populations evolve variation in virulence levels. I also reveal that coevolution in this host parasite system is likely to lead to local adaptation of G. arcuatus at the host population level. I show that competition between parasite species sharing a single host leads to increased parasite reproduction rates, but it shortens the infection time which may be due to earlier stimulation of host immune responses. I show that virulence is neither influenced by the population density, immunity (epidermal mucus), social behaviour of fish hosts nor the natural parasite life expectancy. Lastly, I find that virulence in this system is negatively influenced by the density of stickleback predators and positively associated with loch water pH. Taken together, these results suggest that in this host parasite system, both ecological and environmental factors which drive phenotypic changes in fish hosts may evolutionarily feedback to affect parasite virulence.