Gastrotricha are small aquatic invertebrates with approximately 770 known species. The group has a cosmopolitan distribution and is currently classified into two orders, Chaetonotida and Macrodasyida. The gastrotrich fauna of Sweden is poorly known: a couple of years ago only 29 species had been reported. In Paper I, III, and IV, 5 freshwater species new to science are described. In total 56 species have been recorded for the first time in Sweden during the course of this thesis. Common species with a cosmopolitan distribution, e. g. Chaetonotus hystrix and Lepidodermella squamata, as well as rarer species, e. g. Haltidytes crassus, Ichthydium diacanthum and Stylochaeta scirtetica, are reported. In Paper II molecular data is used to infer phylogenetic relationships within the morphologically very diverse marine family Thaumastodermatidae (Macrodasyida). Results give high support for monophyly of Thaumastodermatidae and also the subfamilies Diplodasyinae and Thaumastodermatinae. In Paper III the hypothesis of cryptic speciation is tested in widely distributed freshwater gastrotrichs. Heterolepidoderma ocellatum f. sphagnophilum is raised to species under the name H. acidophilum n. sp. The results indicate that L. squamata may be a complex of at least two species. In Paper III and V the phylogeny of Chaetonotidae (Chaetonotida), the largest family within Gastrotricha, is inferred. The group suffers from a troubled taxonomy and is hypothesized to be nonmonophyletic. Results show that members of Dasydytidae are nested within the group. Since only 3 of 17 sampled genera are monophyletic, it is hypothesized that the cuticular structures used in current classification do not reflect phylogenetic relationships. The phylogenetic hypothesis generated in Paper V indicates a marine origin of the predominantly limnic Chaetonotidae with a subsequent secondary invasion to marine environments of some taxa. / Gastrotricha of Sweden - Biodiversity and Phylogeny

Dissertation (Ph.D.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references.

Background : Old fields are abandoned agricultural areas that are undergoing secondary succession. A variety of factors influence the assembly, invasibility, and species turnover during secondary succession in old fields. Old fields are important ecological research locations as an increasing amount of agricultural land is abandoned worldwide. Objectives : 1) To determine if exotic and native "invaders" display differences in invasion success in an old field, and 2) To observe how native and exotic species abundances change over the course of secondary succession under predictable disturbance regimes and resource levels with regards to the Core-Satellite Species (CSS) hypothesis. Methods : An old field located in southern Illinois subject to three levels of fertilization (control, annually fertilized, and fertilized every 5 years) crossed with three levels of mowing treatments (control, spring mowed, and spring/fall mowed) established in 1996 was used to test objectives Seedlings of C3 grasses (native and exotic) were planted within one fertilizer treatment to compare invasion success. Species composition data (species occurrence and abundance at three heights) in all blocks were previously collected from 1996 to 2002 and the sample plots were resampled in 2013. Species sampled in 2013 were assigned to core or satellite categories per the CSS hypothesis. Results : Invading exotic seedlings had higher survivorship than invading native seedlings from the same functional group within the same fertilizer level, and added fertilizer increased seedling survivorship. The number of core and satellite species varied early after experiment establishment in 1996 but has since leveled off, and the ratio of exotic to native species cover at heights <1m ratio was affected by an interaction between mowing treatment and time. The species occupancy distribution of all species in 2013 was not bimodally distributed, but the occupancy distribution of exotic species in 2013 was bimodally distributed.The community composition of the plots varied among blocks, but was affected by an interaction between fertilizer treatment and mowing. Conclusions : Exotic invading grass seedlings in a successional community were relatively more successful than native invading grass seedlings. However, overall survivorship of all invading grass seedlings was low, a typical finding in grasslands. The identity of core and satellite species continued to fluctuate through time following 17 years of secondary succession. Resource availability and disturbance regime affects on community composition throughout secondary succession, and may result in many alternative stable states. This research supports the `CSS' and `parallel dynamics' hypotheses and indicates that presence of exotic species within a community does not necessarily facilitate invasion by new exotic species.

Biodiversity is a complex concept incorporating genes, species, ecosystems, composition, structure and function. The global scientific and political community has recognized the importance of biodiversity for human well-being, and has set goals and targets for its conservation, sustainable use, and benefit sharing. Monitoring biodiversity will help meet conservation goals and targets, yet observations collected in-situ are limited in space and time, which may bias interpretations and hinder conservation. Remote sensing can provide complementary datasets for monitoring biodiversity that are spatially comprehensive and repeatable. However, further research is needed to demonstrate, for various spatial scales and regions, how remotely sensed datasets represent different aspects of biodiversity. The overall goal of this dissertation is to advance the mapping and monitoring of biodiversity indicators, globally and within Canada, through the use of remote sensing. This research produced maps that were rich with spatially explicit, spatially continuous data, filling gaps in the availability and spatial resolution or scalability of information regarding ecosystem function (primary productivity) at global scales, tree species composition at regional scales (Saskatchewan, Canada), and ecosystem structure at local scales (coastal British Columbia, Canada). Further, the remotely sensed indicator datasets proposed and tested in each of the research chapters are repeatable, ecologically meaningful, translate to specific biodiversity targets globally and within Canada, and are calculable at multiple spatial scales. Challenges and opportunities for fully implementing these or similar remotely sensed biodiversity indicators and indicator datasets at a national level in Canada are discussed, contributing to the advancement of biodiversity monitoring science. / Graduate

Engineering design considerations of artificial coastal structures were tested to resemble as far as possible the nearest natural equivalent habitat, ecologically valuable rocky shores, as a potential management option. Coastal areas around the world attract urbanisation but these transitional areas between sea and land are inherently vulnerable to risk of flooding and erosion. Thus hard structures are often built in sensitive coastal environments to defend assets such as property and infrastructure (roads, railways, ports) against rising and stormy seas. The design, construction and maintenance of hard defences should wherever possible incorporate ecological considerations to enhance biodiversity, including maintaining or restoring natural habitats and wild species to ensure favourable conservation status. Artificial habitats are less topographically complex than natural rocky shores, at millimetre scales in terms of surface roughness, centimetre to meter scales for crevices and pools to tens, hundreds and occasionally thousands of meters for variation in tidal height and wave action gradients. The habitat value of design features of an existing seawall and breakwater, such as areas of different slope and orientation, and the presence of crevices and pools, that are analogous to habitat created by topographical features on a natural shore, were demonstrated by their ability to support distinct assemblages of species. X Furthermore, evidence is provided that a greater variation in the type of design features led to a higher species diversity occupying the structure, and included species that would otherwise not be present on the structure. The long term succession on artificial structures and the biodiversity reached on intertidal coastal defence structures is described to inform understanding of timescales over which successional processes operate. As a consequence of succession, artificial structures of large extent eventually resemble natural rocky shores of the same exposure. Increased surface heterogeneity of concrete armour units on Plymouth Breakwater by drilling holes was effective in adding habitat and increasing local species diversity. These can be added at the construction stage or post construction. In a real case study, added recessed pools, holes and surface texture during the construction of a tidal defence sea wall at Shaldon made heterogeneous surfaces to add habitat and influence species diversity, without compromising the engineering function or aesthetics of the structure. This study provides coastal engineers and decision makers with well researched practical design options to inform future construction and maintenance of coastal defence structures that will encourage specific outcomes to mitigate the negative environmental impact of artificial structures and contribute to conservation priorities.

Studies presented in this thesis, highlight the complexity and importance of Mycosphaerella leaf disease (MLD) on Eucalyptus spp., especially in South Africa. In Chapter I, a review of the literature dealing with Mycosphaerella and MLD of Eucalyptus spp. is presented. It is clear from this review that the disease is prevalent in most countries where Eucalyptus spp. are commercially grown, including Australia where they are native. The number of Mycosphaerella species known from Eucalyptus spp. is increasing and this suggests that their economic effect on commercial Eucalyptus forestry, will probably Increase. It will thus become important to effectively identifY species responsible for MLD. To do this, the existing complex taxonomy of this group of fungi, will undoubtedly prove to be an obstacle. However, DNA based identification methods are proving useful in identifying species and delimiting lineages within Mycosphaerella. Future commercial propagation of Eucalyptus spp. will need to seriously consider the use of hybrids resistant to infection by Mycosphaerella spp. Furthermore, there will be a serious need for effective quarantine measures to prevent the introduction of new, perhaps more pathogenic, Mycosphaerella spp. into areas where they do not already occur. Three species of Mycosphaerella, M. molleriana, M. M. nubilosa and M. juvenis have traditionally been regarded as the most important Mycosphaerella spp. in South Africa. At various times, each species has been considered to be the only pathogen causing MLD in the country. Results from Chapter 2 and Chapter 3 have shown that M. nubilosa is the main pathogen responsible for MLD, especially, on E. nitens in the KwaZulu-Natal province of South Africa. This is interesting as M. molleriana, which was originally thought to be the only species in South Africa, was not isolated. Moreover, the susceptibility of E. nitens to M. nubilosa appears to be high, resulting in severe defoliation. Considering that E. nitens is a popular species grown at higher altitudes of South Africa, the recognition of M. nubilosa is important. This fungus is well recognized in Australia as an important pathogen and comparisons of data from that country will be useful in the future. Several Mycosphaerella spp. have, in the past been found to occur within single stands of commercial Eucalyptus spp. As part of the research presented in Chapter 3, surveys conducted in South Africa showed that there are seven species of Mycosphaerella occurring in plantations. These include: M. ellipsoidea, M. irregulariramosa, M. juvenis, M. lateralis, M. marksii, M. nubilosa and one newly described species M. fori. All of these species, apart from M. fori, were previously known to occur in South Africa. It is interesting that M. juvenis, previously thought to be one of the main species causing MLD, was found only to occur in a low numbers. This suggests that species causing epidemics may change over time. The identification of M. fori from a previously well surveyed area was unexpected. This new species was dominant in Tzaneen and future surveys will be conducted to determine its distribution and host range within South Afiica. The identification of a new species also highlights the need for additional surveys in South Africa to identify new species and to recognize possible new introductions of exotic Mycosphaerella spp. The presence of M. ellipsoidea, M. irregulariramosa, M. lateralis and M. marksii in this survey was not unusual, as they were previously known in South Africa. However, they were found only to occur at low levels and, as such, do not seem to contribute significantly to outbreaks of MLD.Various taxonomic and DNA-based methods have been used for the identification of Mycosphaerella spp. However, some taxonomic characters are of little value at the species level. In Chapter 4, RFLP's were considered as an option to differentiate between species of Mycosphaerella on Eucalyptus. Results of this study showed that the restriction enzyme HaeIII may be used for RFLP identification of Mycosphaerella spp. From a total of twenty-one Mycosphaerella spp. tested, RFLP digestion with HaeIII could resolve six of these species to species level. However, other species formed groups that had similar restriction profiles. They could be further separated based on ascospore germination patterns. This study forms a foundation for future studies in which other enzymes may be used together with HaeIIi to elucidate groups of species. It is suggested though, that this technique be combined with existing methods such as ascospore germination patterns and anamorph associations to identify species of Mycosphaerella occurring on Eucalyptus spp. with confidence. This should negate the use of expensive sequencing techniques, which are currently necessary. In virtually every country where Eucalyptus is grown commercially, MLD is prevalent. However, the specific Mycosphaerella spp. in countries are generally not the same. In Chapter 5, I used DNA sequence data from the ITS region of the rDNA operon as well as morphological data to identify M. heimii from Brazil and Hawaii, U.S.A. This represents the first report of the species from these countries. M heimii was previously thought to occur only in Madagascar and Indonesia, where it is recognized as a primary pathogen of several Eucalyptus spp, including E. urophylla. This is one of the main Eucalyptusspp. in Brazil. It has thus been suggested that this species may have been introduced into these countries via infected seed lots. This highlights the need for effective quarantine measures within these and other South American countries to inhibit the further spread of this pathogen through South America. Copyright / Dissertation (MSc)--University of Pretoria, 2011. / Microbiology and Plant Pathology / Unrestricted

No description available.

Salmonella enterica serovar Typhimurium is responsible for a variety of diseases in domestic animals and humans. The infection of mice causes similar disease progression to human typhoid fever, thus representing a model for this systemic disease. The ability of S. Typhimurium to reside in a macrophage phagosome is important for their survival and spread to different organs. The antimicrobial mechanisms in this compartment include reactive oxygen species, reactive nitrogen species and elevated copper levels. S. Typhimurium possesses two copper-exporting P1B-type ATPases, CopA and GolT, both of which contribute to copper resistance. A previous study has shown that copper export by CopA and GolT confers a survival advantage in resting macrophage phagosomes. In this study the role of copper resistance systems has been examined further. The reduced survival of ΔcopA/ΔgolT in macrophages is detected beyond 8 hours post infection and coincides with increased nitrite production by macrophages. We have established that ΔcopA/ΔgolT display some increased sensitivity to reactive nitrogen species. However, whilst treatment of macrophages with the iNOS inhibitor L-NMMA reduced macrophage bactericidal activity against wildtype S. Typhimurium, this was not the case for ΔcopA/ΔgolT. In contrast, survival of ΔcopA/ΔgolT was not impaired in macrophages treated with the copper-chelator BCS. Furthermore real-time PCR confirmed the expression of copA and golT is elevated during infection of macrophages treated with IFN-γ or L-NMMA, but is reduced during infection of BCS treated macrophages. This indicates that bactericidal activity in macrophages is associated with copper availability and this is unaffected by reactive nitrogen species released due to iNOS activity. In contrast to Escherichia coli Salmonella lacks a cus system associated with export across the outer membrane and hence the mechanism of copper export from the periplasm is not known. TolC was investigated as a potential outer membrane copper exporter based on clustering of TolC dependent systems to genes with sequence similarity to the S. typhimurium periplasmic copper chaperone CueP, across several bacteria. Mutation of tolC gave reduced copper tolerance and over-accumulation of copper at non-lethal concentrations under aerobic conditions. However TolC does not provide a role in copper tolerance or homeostasis under anaerobic conditions. TolC also does not provide tolerance or homeostasis to other divalent cations: Zn, Ni and Co. TolC therefore provides specific transport of copper under aerobic conditions in S. Typhimurium.

This thesis concerns the study of selected Ceratocystis species and Ophiostoma species infecting wounds on broad-leaved trees, particularly those occurring in Africa. However, two chapters also deal with these fungi from Australia, Norway, Sweden and Austria. The dissertation is comprised of a literature review, followed by four research chapters, addressing the occurrence of Ceratocystis spp. and Ophiostoma spp. in Africa, Australia and Norway. The first chapter of the dissertation is a review of Ceratocystis spp. and Ophiostoma spp. with particular reference to Africa, hardwood tree species and wound infections. The review highlights the importance of wood and trees, especially on the African continent, and discusses the threat of deforestation. This is despite efforts by many African countries to establish forests of non-native tree species to address the demand for wood and wood products on the continent. Reforestation is associated with increased risks of the introduction of pests and pathogens, including species of Ceratocystis and Ophiostoma. The taxonomic history of these two fungal genera is summarized, and the review further focuses on the economically important species in these genera, particularly those infecting hardwood tree species on the African continent. The lack of information regarding Ceratocystis spp. and Ophiostoma spp. on hardwood trees in Africa is thus highlighted. Furthermore, the review summarised the dispersal mechanisms of these pathogens, highlighting dispersal too and infection of wounds. Ceratocystis pirilliformis was described in 2003 and it is the only species in the Ceratocystis fimbriata species complex that has pear-shaped ascomatal bases. This fungus was first described from Australia where Eucalyptus spp. are endemic. It was later reported from South Africa on Eucalyptus grandis trees. Chapter two of this dissertation attempts to address questions regarding the geographic distribution, impact and origin of C. pirilliformis in South Africa. This was in line with the fact that it has been suggested that the fungus is likely native to Australia. To address this question, surveys were conducted in many Eucalyptus planting areas in South Africa and the genetic diversity of the fungus in the country was investigated using microsatellite markers previously developed for C. fimbriata. C. pirilliformis was found in three Eucalyptus-growing areas of South Africa, which has considerably increased the known geographic range of the fungus in South Africa. The gene diversity as well as the genotypic diversity for the fungus was found to be very low in the country and the population is apparently clonal. Results thus support the view that C. pirilliformis was accidentally introduced into South Africa. In chapter three of this dissertation, O. quercus is reported for the first time from wounds on non-native Acacia mearnsii in Uganda. In addition a new Pesotum sp., P. australi prov. nom. is described from wounds on native A. mearnsii in Australia. This fungus resembles other Pesotum anamorphs of Ophiostoma in many ways, especially species of the O. piceae complex. However, it can be distinguished from these species by many morphological traits and also based on phylogenetic inference. The closest phylogenetic neighbor of P. australi prov. nom. is O. quercus. The fact that it was isolated from A. mearnsii in Australia indicates that it is probably a native fungus in that area. In chapter four, two Ceratocystis spp. and one Ophiostoma sp. are described as new to science, from wounds on native broad-leaved tree in South Africa. Three other Ophiostomaspp. are also reported in this study. Until recently, very little research has been done with regard to Ceratocystis spp. and Ophiostoma spp. occurring on native tree species in Africa. However, results presented in this chapter strongly suggest that these fungi are common on native trees in Africa and many other species, including potential pathogens await discovery. Chapter five of the dissertation reports, for the first time, Ophiostoma catonianum, O. pluriannulatum and O. quercus from native broad-leaved trees in Norway. It also reports O. catonianum for the first time from Austria and O. quercus for the first time from Sweden. In the past, very little research has been undertaken to explore the diversity of these fungi on hardwood trees in the Nordic countries or other parts of Europe, where most research has been focused on Ceratocystis spp. and Ophiostoma spp. associated with conifer-infesting bark beetles. This chapter represents a preliminary study with important discoveries. It indicates that these fungi are common on wounds on hardwood trees in Europe and emphasizes the importance of expanding these studies in the Nordic countries, to include more hosts and geographic areas. Such studies will almost certainly reveal more species and possibly new species of Ceratocystis and Ophiostoma. / Dissertation (MSc)--University of Pretoria, 2010. / Microbiology and Plant Pathology / Unrestricted

Spontaneous mutagenesis can be divided into three main steps: the introduction of DNA damage and lesions, damage recognition and DNA repair. All sources of spontaneous mutagenesis originate from within the cell itself, e.g., polymerase errors cause DNA mismatches and reactive oxygen species alter the chemical composition of DNA bases. The combined effects of all these processes influence spontaneous genomic mutation rates, which are thought to be a characteristic of individual species and/or groups of species. Although much is known about different mutagens and how they cause mutations the sequence context of these mutations are less well understood. The results of this MSc study on mutation in the filamentous fungus Fusarium circinatum showed that the 5ʹ and 3ʹ neighbouring bases of a single nucleotide polymorphism can significantly influence the type of substitution that occurred leading to the formation of mutational motifs. This was the case for both sets of genes examined (core housekeeping and non-ribosomal protein synthetase genes), whose evolution is known to differ. The fact that none of the identified motifs are shared between the two sets of genes could indicate that the cellular mutagens and/or repair machinery function differently for the two gene groups. Furthermore, none of the mutable motifs that have been identified for the well-known mutagens in model organisms could be detected in the fungus, which suggests that mutagens and/or DNA repair mechanisms of this fungus are unique. Although limited information is available for non-model eukaryotes, an estimate for the rate at which mutations arise across the genome of F. circinatum could be a good starting point for comparisons of its evolutionary rate to those of its close relatives. This was accomplished using a fluctuation analysis involving nitrate non-utilizing mutation reversion. Although mutation rate determined in this study is probably not precisely accurate, it represents a good starting point for future comparative studies on the evolutionary rate of Fusarium species. As a whole this study laid the foundation for a better understanding of spontaneous mutagenesis at specific sites in certain groups of genes as well as across the genome of the economically important plant pathogen F. circinatum. Restricted until August 2017 / Dissertation (MSc)--University of Pretoria, 2013. / gm2013 / Microbiology and Plant Pathology / Unrestricted