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The rhizosphere and rhizoplane environments of higher plant roots are specialised microhabitats for soil organisms. These organisms include nematodes which are capable of responding to attractants from roots over several centimetres (Rode, 1962, 1969). The aim of this project was to investigate the various aspects of chemotaxis in host finding by nematodes, and the relative importance of electrotaxis in this process. This involved experimentation on root diffusate as a whole, on various ions etc which may be attractive components of root diffusate, on interference by lectins on the host finding process and finally into nematode response to applied electrical fields with comparison to field strengths measured at root surfaces. The working hypothesis used throughout this project was the occurrence of long distance attraction via a non-specific factor which is replaced by a more specific factor as the distance between host and parasite is reduced. Examination of the diffusate as a whole clearly demonstrated that nematode attraction is a directed response. It also gave some support to the theory of successive attractive factors, with each successive factor being of higher molecular weight and lower diffusibility. The response to H+, OH-, Na+, five amino acids and cAMP was tested. The two pH extremes were equally attractive, the Na+ and amino acids were neither attractive nor repulsive and the cAMP was repulsive at the higher concentration used. These results suggested that the ions might have a secondary involvement in attraction by stimulating the initial movement of the nematodes but would be non-specific. Any attraction to amino acids noted by other workers e.g. Bird (1959) might be due to the acidic nature of the amino acids tested. Experiments were carried out using concanavalin A to interfere with host finding as suggested by Marban-Mendoza et al. (1987) through its effects on surface carbohydrates. The experiments produced some evidence to support this theory, and further experiments were made to try to elucidate the mechanism. The results from this further work indicate the effect in pH dependent via changes in aggregate size, but also that there may be a dilution involvement as well. Application of electrical fields to the nematodes produced directional movement, but at voltages approximately 1,000 times that measured at the root surfaces with the vibrating probe. It is therfore concluded that chemotaxis is the primary means by which nematodes locate their host plants, but the possibility of electrotaxis being used to locate specific feeding sites is discussed.

Previous research has documented shifts in microbial hindgut populations resulting from dietary starch inclusion, and recent evidence indicates only 30% of equine cecal contents has been cultured successfully. Next generation sequencing (NGS) techniques allows detection of new species previously undetected. Therefore, the objective of this study was to determine community profiles equine cecal microbiota in response to abrupt dietary starch inclusion. Seven cecally cannulated Quarter horse geldings (497 to 580 kg) were utilized in a crossover design with two 28 d periods and a 28 d washout between each. Horses were randomly assigned to dietary treatments consisting of commercial concentrate offered individually at either 0.6% (LS) or 1.2% BW (HS; as fed) daily divided into 2 meals at 12 h intervals. Prior to start of each period horses were allowed ad libitum access to coastal bermudagrass (Cynodon dactylon) hay and concentrate was fed on d 1 with no adaptation. Samples of cecal fluid were collected on d 1 prior to 0 h and 3, 6, 9, and 12 h post morning meal and on d 1, 2, 3, and 7 at 6 h post morning meal. Cecal pH was determined immediately and a samples of cecal fluid were stored. Genomic DNA was extracted and the V4-V6 segment of 16s rRNA gene was PCR amplified using universal Eubacterial primers 530Fand 1100R and sequenced on the Roche 454 FLX platform. The reads were denoised, chimera checked, and Operational Taxonomic Units (OTUs) were identified using the reference Ribosomal Database Project 16S rRNA dataset. Data were analyzed using PROC MIXED procedure of SAS. Bacterial phyla were largely unaffected by dietary treatment for the first 12 h after the initial concentrate meal except for Verrucomicrobia which was greater in LS horses (P ≤ 0.04). Regardless of treatment, Bacteriodetes increased (P ≤ 0.02) over the first 12 h following initial addition of dietary starch. Adaptation to dietary treatments over 7 d resulted in decreased numbers of Tenericutes (P ≤ 0.07) in HS horses compared to LS. Cecal environment and microbial populations were altered after abrupt and long term exposure to dietary starch.

“Exotic-type” Cu silicate-oxide deposits hosted by Miocene pediment gravels represent an unusual, but characteristic, by-product of the supergene enrichment of Cenozoic porphyry Cu deposits in northern Chile. Carbon stable isotopic analysis is employed herein to clarify the environment of exotic ore formation and to provide guidelines for the exploration for non-outcropping mineralisation. Two main sample suites were examined: chrysocolla-rich ores from the Huinquintipa and Mina Sur deposits; and soils overlying a paleochannel in the Huinquintipa area known to be mineralised. The samples were processed using four different analytical techniques to determine their 13C values: (1) Elemental Analysis Isotope Ratio Mass Spectrometry (EA/IRMS) of the whole sample; (2) crushing in vacuo followed by IRMS to analyse fluid inclusions; (3) thermal extraction at 100˚C, followed by IRMS to analyse weakly bound carbon dioxide; and (4) ethylenediaminetetraacetic acid (EDTA) extraction followed by IRMS. EDTA-partial extraction favours the dissolution of minerals with divalent cations, releasing as carbon dioxide the carbon trapped within the crystal structure. All four of these analytical techniques have been used before, but this is the first time that they have all been used together on exotic copper silicate and oxide mineralisation. Three major carbon sources are identified: (1) atmosphere-derived carbon dioxide with a 13C value of around 0 ‰; (2) plant-derived carbon dioxide with a 13C of about -25 ‰; and (3) microbe-derived carbon dioxide with a 13C of approximately -50 ‰. The bulk of the carbon liberated by EA/IRMS was plant-derived. The thermally- and crushing-released carbon dioxide has the highest proportion of atmosphere-derived carbon, whereas EDTA-extraction preferentially liberated the lightest of carbon. On the conclusion that EDTA preferentially dissolved Cu-rich silicate mineraloids, it is concluded that microbial consortia, including methanogenic microbes, were hosted specifically by the high-grade Cu assemblages and plausibly played a critical role in their precipitation. The same microbial-carbon signature was obtained through the EDTA-extraction of soil samples above the paleochannel. Carbon isotopic analysis of CO2 sequestered through EDTA-extraction could therefore be used as an exploration tool for buried exotic mineralisation. Future exploration should exploit the presence of microbes in niche-specific environments. / Thesis (Master, Geological Sciences & Geological Engineering) -- Queen's University, 2007-12-19 15:43:17.198 / Anglo American plc

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Human intestinal microbiomes exhibit a large degree of interindividual compositional variation. Animal models, such as the zebrafish, facilitate the design of controlled and highly replicated studies that allow us to understand the normal variation in vertebrate intestinal composition and to study the rules guiding normal assembly of these complex communities. The smaller intestinal size and high fecundity of the zebrafish allow us to fully sample the intestinal contents of many animals, while the optical transparency allows direct in vivo observation of fluorescently labeled bacterial species within the intestine. The studies in this dissertation utilize these advantages to investigate the composition, colonization dynamics and functional requirements for colonization in the vertebrate intestine. We first describe the taxonomic composition and diversity of the zebrafish intestinal microbiota from wild-caught and domesticated zebrafish. In the process, we identify a set of core bacterial genera that are consistently present in zebrafish intestines. We then use species from two of these genera in subsequent studies to gain a detailed understanding of the colonization dynamics and genetic requirements of the two species. We initially describe the application of light sheet microscopy to imaging the zebrafish intestine and associated colonizing bacteria. We find that a single species, Aeromonas veronii, does not occupy the entire intestinal space and that competition within the same species appears to prevent further colonization. These results are extended to a zebrafish isolated Vibrio species as well as A. veronii by tagging bacteria with transposon insertions and tracking the changes in colonizing population sizes. These insertion libraries also identify genes in each bacterial species that are important in the process of colonization, highlighting the key role for motility and chemotaxis in this process. The descriptions and methods discussed in this dissertation advance the use of this important model organism towards the understanding of vertebrate host-microbial interactions. This dissertation includes previously published co-authored material as well as unpublished co-authored material. / 10000-01-01

There is a growing body of evidence that normal nervous system activity requires signals from resident microbes. We have yet to discover the mechanisms by which the microbiota influence brain function. However, we know that the enteric nervous system (ENS) serves as an important interface between the developing host and its microbiota. In this dissertation I will introduce a novel computer-assisted method for ENS characterization and a novel, incredibly specific mechanism of host-microbe interactions. With new ENS characterization method I developed, it will be possible to better understand the role of the ENS during development, by more rapidly and algorithmically assessing ENS phenotypes. Furthermore, my discovery of a single microbially-sourced protein that influences vertebrate host prey capture behavior and visual system development, will provide a new appreciation for the role resident microbes, both in model organisms and in ourselves. By both establishing a new, less biased, approach to image analysis and describing a surprising new regulatory host-microbe interaction, the work I describe in this dissertation should provide the foundation for an explosion of exciting discoveries in the near future.

Secondary salinisation has affected large areas of inland southwestern Australia, and in particular, low lying aquatic areas; causing the loss of freshwater submerged macrophyte communities and their replacement by salt-tolerant species. At high salinities, the salt-tolerant macrophyte-dominated ecological regime may be replaced by a regime dominated by benthic microbial communities, further reducing the structural and functional diversity of salinised wetland ecosystems. There is little prospect of restoring salinised systems to a freshwater state, meaning that saline macrophyte dominated wetlands have a heightened structural and functional importance in this landscape. Prior to this study, little was known about the drivers for change from one ecological regime to another in salinising wetlands or about rates of ecosystem response to these drivers. This study used experimental and observational data from seven saline wetlands in order to identify some of the potential mechanisms for the transition between the salt tolerant submerged macrophyte-dominated regime and the benthic microbial community-dominated regime. The applicability of existing conceptual models for ecological regime shifts was then tested against these data. Some of the mechanisms responsible for the formation and maintenance of the macrophyte-dominated regime were explored by examining the effects of salinity on germination and flowering in a series of salt-tolerant submerged macrophytes. The initiation and dominance of benthic microbial communities over a range of salinity and wetting regimes was also examined. The results suggested that macrophyte communities are unlikely to develop in seasonally-drying wetlands at high salinities (>45 ppt), but will usually germinate and establish well at lower salinities. It was also predicted that although benthic microbial communities can survive and grow across a wide range of salinities, they are likely to be outcompeted at low salinities by macrophytes or by phytoplankton blooms if water column nutrient levels are high. However, water permanence may facilitate benthic microbial community dominance. Existing conceptual models of ecological regime transitions, such as the alternative regimes model, did not account for the effect of water regime on the dynamics of seasonally-drying systems. Therefore, a new conceptual model incorporating the interaction between hydrology and salinity in seasonally-drying wetlands was proposed.

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