Please read the section 05chapter5 (General summary and conclusions, especially p168-170) of this document / Thesis (DSc (Agriculture))--University of Pretoria, 2007. / Agricultural Economics, Extension and Rural Development / unrestricted

The astounding complexity of microbial communities limits the ability to study the role of genomic diversity in shaping the community composition at the species level. With the advancement and increased affordability of high-throughput sequencing methods, it is increasingly recognized that genomic diversity at the sub-species level plays an important role in selection during microbial community succession. Recent studies using the cpn60 universal target (UT) have shown that it is a high-resolution tool that provides superior resolution in comparison to 16S rRNA based tools and can predict genome relatedness. However, studies to characterize the nature and degree of genome content differences predicted by cpn60 UT sequence relationships have not been conducted. In this work, we focused on the Enterococcus community obtained from feces of healthy pigs. Enterococci are both accessible with selective culture, and interesting since the genus includes members that are significant human pathogens and others that are used as probiotics. Previous work has shown that cpn60 UT sequences can resolve pig fecal Enterococcus faecalis and E. hirae into phylogenetically and phenotypically distinct ecotypes. The utility of cpn60 UT sequences for resolution of Enterococcus species was first established in the year 2000, and this demonstration included 17 Enterococcus species. We have expanded the analysis to include all currently recognized Enterococcus species and confirmed that cpn60 UT sequences provide higher resolution than 16S rRNA sequences for identification of Enterococcus species. In addition, we showed that cpn60 UT sequences could resolve sub-groups in E. faecium consistent with results obtained from comparison of whole genome sequences. GTG rep PCR based clusters for E. faecalis and E. hirae isolates were generally consistent with the cpn60 defined Enterococcus ecotypes observed in our previous study, suggesting that cpn60 UT sequences predict overall genomic relationships. Results from analysis of CRISPR sequences provided insights into the extensive networking and transfer of genetic material that takes place within the intestinal Enterococcus community. We conducted whole genome sequencing of representative isolates to characterize further the genomic diversity in cpn60 defined E. hirae ecotypes to determine the nature and degree of genome content differences predicted by cpn60 UT sequences. Differences in phosphotransferase systems, amino acid metabolism pathways for glutamine, proline and selenocystiene, potassium-transporting ATPases, copper homeostasis systems and putative prophage associated sequences, CRISPRs and antibiotic resistance genes were observed. Results from in vitro growth competition assays showed that isolates from E. hirae-1 and E. hirae-2 were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig fecal microbiome, and with observed gene content differences between the ecotypes. Results presented in this thesis provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high resolution profiling of complex microbial communities.

The restoration of degraded tallgrass prairies can mitigate climate change due to the carbon accrued during the development of grasslands. The focal species, dominant grass Andropogon gerardii, can assist the recovery of grassland ecosystem functioning. Climate, local adaptation, and biodiversity have been found to impact the accrual of carbon in grasslands. This study examined the difference in ecosystem functioning between ecotypes along a dry to mesic precipitation scale. The study site for this project was at the Southern Illinois University Agriculture Research Center in Carbondale, Illinois. The field site was planted with seeds originating from dry to mesic ecotypes, and the resulting ecosystem functioning was analyzed. It was found that the Kansas non-local ecotypes had significantly higher biodiversity, while the local Illinois sites demonstrated local adaptation with A. gerardii. Aboveground plant biomass was higher in the local sites, but there was no difference in carbon accrual between any of the ecotypes. While ecotypic variation in a dominant species will usually differentially influence ecosystem functioning, in this case, high biodiversity and local adaptation result in similar carbon inputs in grassland soil. It is necessary to analyze the carbon content of the soil in the drier field sites in order to determine if major differences in rainfall leads to differences in carbon accrual. If the goal of restoring a tallgrass prairie in southern Illinois is to assist with climate change mitigation, then it does not make a significant difference if the dominant species is sourced locally or non-locally.

The freshwater isopod Asellus aquaticus has been shown to exist in two different ecotypes, stonewort ecotypes and reed ecotypes. The differentiation is likely due to adaptation towards different predator regimes and possibly also other selective forces. It is unknown if the ecotypes have different adaptations when it comes to food preferences and roles in the ecosystems. In the present study, isopods of each ecotype were collected from two lakes where the differentiation of pigmentation was especially pronounced to examine whether this had a connection with other physiological adaptations. Growth rate, competitiveness, exposing behaviour and grazing efficiency were tested in two experiments with periphyton or coarse detritus as food sources. None of the results indicated a specialization towards their regular food. Instead, the stonewort ecotype had significantly faster growth rate for both food sources. Presence of snails caused a slight, but statistically insignificant increase in growth rate when periphyton was the food source. Individuals of the reed ecotype were more exposed on the substrate than the stonewort ecotype, but the difference was not statistically significant. Grazing efficiency of both detritus and periphyton was similar and not significantly different between ecotypes. The results thus show no indication to phenotypical differences between ecotypes in the ability to graze or process different types of food. However, currently known adaptations, e.g. in behaviour and pigmentation may be important for the ecological role of the species. / Sötvattengråsuggan Asellus aquaticus har visats kunna förekomma i två ekotyper, kransalgsekotyper och vassekotyper. Differentieringen beror troligen på en anpassning till olika predatorregimer och möjligen även andra selektiva krafter. Det är okänt om ekotyperna har olika anpassningar till födoval och roller i ekosystemen. I denna studie samlades vattengråsuggor av vardera ekotyp in från två sjöar där differentieringen av pigmentering var speciellt markant för att undersöka om detta hade något samband med anpassningar till lokala födoresurser. Tillväxthastighet, konkurrenskraft, exponerat beteende och beteseffektivitet testades i två experiment med perifyton eller detritus som matkällor. Inga av resultaten visade på en specialisering till den normalt förekommande matkällan. Istället visade sig kransalgsekotypen ha signifikant högre tillväxthastighet för båda matkällorna. Närvaro av snäckor orsakade en liten, men icke signifikant ökning av tillväxthastigheten hos vattengråsuggor med perifyton. Individer av vassekotypen var exponerade på substratet oftare än kransalgsekotypen, men skillnaden var inte statistiskt signifikant. Beteseffektiviteten av både detritus och perifyton var jämbördig och inte signifikant olika mellan ekotyperna. Resultaten visar inga indikationer på fenotypiska skillnader mellan ekotyperna i förmåga att beta eller omsätta olika födotyper. Däremot kan fler ekologiska effekter beroende på de i nuläget kända anpassningarna, exempelvis beteende och pigmentering inte uteslutas, och kan ha betydelse för artens funktion i ekosystemet.

Native plant materials are often seeded to restore biodiversity and ecosystem function in areas overtaken by exotic weeds. Plant materials are evaluated on intraspecific differences in productivity and expression of traits advantageous to establishment (e.g., phenology, seed mass, and growth rate); some investigations also consider population-level adaptation to exotic species. However, there is a lack of studies that broadly evaluate response to competition from exotic species at multiple scales within a species. In a greenhouse experiment, we used analysis of variance to assess the growth response of a perennial grass native to the Intermountain West, (Elymus elymoides), to competition from a common invasive species, (Bromus tectorum), at three levels of intraspecific differentiation: subspecies, lineage (wild vs. domestic germplasm), and population. We used regression analysis to assess whether E. elymoides populations from highly invaded areas were less affected by B. tectorum competition. Finally, we explored the relationship between growth traits and competitive response using random forest regression. We found significant differences among E. elymoides subspecies in their response to B. tectorum competition, no difference between wild and domestic lineages, and no population-level differentiation within subspecies. Field abundance of B. tectorum had a significant positive relationship with E. elymoides biomass, but not competitive response, suggesting that E. elymoides has not adapted to the invader. Elymus elymoides plants which were less affected by competition were smaller, allocated more biomass to leaves, and had fewer fine roots, suggesting that light interception and tissue retention were prioritized by seedlings in this competitive greenhouse environment.

Salt stress is one of the major problems in the present world’s agriculture. Plants encounter drought stress even in the availability of water because of osmotic imbalance in the cell due to excess salts. Plants avoid water uptake, which in turn decreases the photosynthetic activity. In this work, we measured the effect of salt stress on three accessions of Arabidopsis thaliana (Columbia (Col-0), Landsberg erecta (Ler-0), Wassilewskija (Ws-4)) by subjecting the plants to stress with 0-150 mM NaCl followed by recovery. The impact of the stress was clearly observed in all three accessions during stress and recovery period. Chlorophyll content in leaves decreased with increasing salt concentration. Proline levels increased during salt stress conditions. Non-photochemical quenching and PSII activity slightly decreased under stress conditions. Salt treated plants showed slow acidification of lumen with delayed Non-photochemical quenching in recovery phase. Ler-0 was the most sensitive ecotype to salt stress followed by Ws-4 and Col-0.

Primula elatior represents a promising model for addressing the role of phenotypic plasticity vs. genetic basis of traits in populations differentiated along altitudinal gradients. Phenotypic plasticity is mainly exhibited by the extensive variability of the leaves. Genetic structure of P. elatior populations has been poorly studied so far, the first insights suggested potentially large intraspecific genetic variation. Therefore, the first aim of this study was to reveal the genetic structure as well as morphological and cytological variation of P. elatior populations in the central Europe and compare those to another two intraspecific taxa from the southeastern Europe. Further, I selected three target mountain regions to address the role of altitudinal differentiation for structuring genetic diversity. Finally, I evaluated the status of the putative endemic species Primula elatior subsp. corcontica from the Krkonoše Mts. Microsatellite analyses, multivariate morphometrics and flow cytometry were employed to evaluate variation of P. elatior populations. I identified six major genetic groups by genotyping 12 nuclear microsatellite loci in the study area of central and southeastern Europe with the clear separation of subp. intricata. Focused on the central Europe, three well-defined genetic groups...

Dissertation (MSc)--University of Pretoria, 2010. / Plant Science / Unrestricted

The purpose of this study was to find out if ecological races with different growth rates existed in douglas fir. Seeds were collected from six areas by the Forest Service and the author. A study was made of stem and tap root growth utilizing three photoperiods of varying length. Rate of tap root growth was significant for ecotype suggesting selection for tap root length in the plants from utah and Arizona. Each geographical area represents a growth rate ecotype with a wide break in the data on stem growth.

I have studied the genetic variation of single species using morphological variation and enzyme electrophoresis. I have striven to understand the interaction between the breeding structure and the ecology of the species in relation to the community, in which it lives. The work was done in the county of Västerbotten, northern Sweden. In the Skeppsvik archipelago I have studied the population structure of Silene dioica: ecotypic variation in other populations. I have also studied the genetic diversity of Angelica archangelica, Bistorta vivipara, Viscaria alpina and the earthworm Eiseniella tetraedra along the free-flowing Vindel and Sävar Rivers and the regulated Urne River. The island populations of S. dioica are subdivided into several breeding units and levels of differentiation among subpopulations within islands were about twice as high as among islands. Restricted seed and pollen dispersal creates patches made up of related individuals that may diverge as a result of drift. Frequent seed and pollen dispersal occurs among islands and they will receive the same alleles. This may explain the pattern of differentiation observed. In contrast, the patches within islands may be founded by only a few individuals. * S. dioica exhibits morphological differentiation in vegetative and floral characters between serpentine, cold spring, rich forest and coastal habitats. There was no association between  genetic and geographical distance or between genetic distance and habitat. Serpentine and cold spring, which represented the most extreme habitats were also most differentiated. Populations of S. dioica are subject to herbivory; predation may exert a selective pressure on vegetative characters. A number of selective forces such as pollinators and fungal parasites act on reproductive characters. Assuming that water dispersal is important I tested several hypotheses to explain patterns of genetic diversity expected to be exhibited by riparian organisms along free-flowing and regulated rivers. I show that dispersal, distribution and breeding structure are important determinants of the evolution of the riparian flora. Patterns of genetic diversity may be exhibited at many spatial scales, e.g. among entire rivers, and between types of riverbanks within a river reach. Populations must be sampled at a spatial scale relevant to the hypothesis to be tested. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 2002, härtill 5 uppsatser.</p> / digitalisering@umu