Bacterial biofilms form on liquid/air and liquid/solid surfaces and consist of cells combined with an extracellular matrix such as exopolysaccharides, extracellular DNA, and glycoproteins. Bacteria have up to a 1000-fold increase of antibiotic resistance in biofilms compared to planktonic cells. Furthermore, biofilm cells show better tolerance to adverse environmental conditions such as nutrition limitations, temperature changes, pH changes, and non-optimal osmotic conditions. In Escherichia coli, the outer membrane protein OmpA increased biofilm formation on polystyrene, polypropylene, and polyvinyl chloride surfaces while it decreased biofilm formation on glass surfaces. This surface-dependent phenotype was because OmpA inhibits cellulose production by inducing the CpxRA two-component signal transduction pathway, and cellulose inhibits biofilm formation on plastic due to its hydrophilic nature. We discovered, and then engineered, BdcA (formerly YjgI), for biofilm dispersal. We found that in E. coli, BdcA increases motility and extracellular DNA production while it decreases exopolysaccharide production, cell length, and aggregation. We reasoned that the 3, 5-cyclic diguanylic acid (c-di-GMP) levels increase upon deleting bdcA, and showed that BdcA binds c-di-GMP in vitro. In addition, we used protein engineering to evolve BdcA for greater c-di-GMP binding and found that the single amino acid change E50Q causes nearly complete biofilm dispersal. We isolated Proteus mirabilis from the blowfly Lucilia sericata, which swarmed significantly. By motility screening and complementation with putative interkingdom signal molecules that have been shown to attract flies, we found lactic acid, phenol, NaOH, KOH, putrescine, and ammonia restore the swarming motility of seven different swarming deficient mutants. These mutants and putative signal molecules will be further tested for fly attraction and oviposition. Acetylation of lysine residues is conserved in all three kingdoms although its role in bacteria is not clear. We demonstrated that acetylation enables E. coli to withstand environmental stresses. Specifically, the bacteria became more resistant to heat and oxidative stress. Furthermore, we showed that the increase in oxidative stress resistance is due to the induction of catalase gene katG. Hence we demonstrate for the first time a specific physiological role for acetylation in prokaryotes.

Climate change can affect northern aquatic systems causing changes in the composition of resident species through either evolutionary or ecological processes. Rock pools near Churchill, Manitoba, Canada provide an ideal study system for studying the effect of environmental change in a metacommunity context, since salinity of the pools has increased significantly over the past quarter century, and dispersal between habitats is important in this landscape. I used a field experiment to study how zooplankton communities respond to increased salinity with two levels of dispersal limitation and three seasonal levels. I found that experimental zooplankton communities shifted from freshwater to more saline communities after a time lag of three weeks, and that highly connected pools became more similar to saline control communities faster than isolated pools. Moreover, freshwater communities manipulated later in the season changed faster to saline communities. This study highlights the metacommunity concept as a useful tool for studying environmental change. / This thesis has already been submitted to Graduate Program Services in hard copy and approved, however I was advised that I could upload it for electronic distribution as well.

Ecologists studying acid-damaged zooplankton communities have often documented a time lag in recovery following pH increases. While previous work has provided a solid understanding of the local factors that may delay recovery (e.g. competition), less is known about the role of dispersal. The work in this thesis was conducted to test the hypothesis that dispersal limitation contributes to delays in the recovery of acid-damaged zooplankton communities. To assess the role of dispersal during recovery I pursued three objectives: 1) To measure dispersal in the field and determine the relative importance of various dispersal vectors for contributing acid-sensitive colonists to lakes; 2) to determine if spatial structure in recovering zooplankton communities exists across the landscape independent of environmental gradients; and 3) to determine if an interaction between dispersal and local environmental variables could influence recovery. Data collected for Objective 1 demonstrated that overland dispersal rates for acid-sensitive species in Killarney Park were relatively low, but some species were found emerging from the diapausing egg bank or dispersing through streams to recovering lakes. Spatial modeling and variation partitioning analyses for Objective 2 revealed spatial patterns indicative of dispersal limitation in recovering Killarney Park zooplankton communities. Enclosure experiments conducted for Objective 3 suggested that the colonization of the acid-sensitive copepod Epischura lacustris may be influenced by an interaction between dispersal levels and pH, such that higher dispersal levels may be required for establishment in lakes that are early in the process of pH recovery. Enclosure experiments also indicated that community resistance and low dispersal levels might hinder the reestablishment of the acid-sensitive copepod Skistodiaptomus oregonensis. Taken together, my results strongly suggest that dispersal limitation could contribute to delays in zooplankton community recovery. The recovery of acid-sensitive copepod species may be particularly difficult, as their reestablishment in recovering lakes appears to be influenced by Allee effects, community resistance, and an interaction between pH and dispersal levels. While dispersal rates could be artificially increased by human intervention, this would carry the risk of introducing invasive species. As a result, patience and continued monitoring of recovering lakes may be the best management approaches at this time. / Thesis (Ph.D, Biology) -- Queen's University, 2011-12-20 22:49:05.193

Seed dispersal in aquatic habitats is often considered to be a complex multistage process, where initial seed shadows are redistributed by water (hydrochory). The roles of hydrochory in seed dispersal and influencing population genetic structure were examined in Helmholtzia glaberrima using both ecological and genetic techniques. Ecological experiments showed that water can redistribute seeds and seedlings over local scales and that hydrochory can provide the potential for very long distance seed and seedling dispersal. Patterns of seedling genetic structure were affected by micro-drainages that direct water flow within populations and influence water-borne seed dispersal on a local scale. Strong non-equilibrium dynamics and persistent founder effects were responsible for the patterns of genetic structure observed among established populations of H. glaberrima. Classical metapopulation models best described dispersal patterns, while water-borne seed dispersal could potentially explain patterns of genetic differentiation within a stream system, it could not explain the distribution of genetic variation among stream systems. The current study found that although hydrochory influenced seed dispersal and seedling genetic structure within a population, it had little effect on the spatial pattern of genetic variation among established populations of H. glaberrima. Moreover, even though prolonged buoyancy and viability in water provide the potential for long-distance hydrochory, results presented here do not support the hypothesis that flowing water is an effective long distance seed dispersal vector for H. glaberrima. Taken together, these results suggest that the relative importance of gene flow via water-born seed dispersal in H. glaberrima may be low compared with that of some other riparian species.

The entrainment of microbes from agricultural land into overland flow during rainfall events is recognised as an important source of pathogenic microbes to surface water bodies and yet this transport process is poorly understood. In this study, a method has been developed to separate bacteria into the forms in which they have been postulated to exist in overland flow. Then Escherichia coli was used as a model organism to investigate the transported state of bacteria eroded from cowpats and their subsequent transport in overland flow. Simulated rainfall experiments were used to generate runoff direct from cowpats. Concentrations of E. coli in the runoff direct from cowpats were found to be directly proportional to the concentration in the cowpat, regardless of the age of the cowpat. It was also observed that E. coli were predominantly eroded from cowpats as individual cells. The interactions between E. coli and soil particles in overland flow were then examined in a small laboratory scale model system and showed that E. coli attached to large (>45 [mu]m) soil particles were transported significantly less than unattached cells. However, in the runoff from the model system, E. coli were found to be attached mainly to clay particles that were similar in size to the bacterial cells. Furthermore, the transport of E. coli through the model system appeared to follow the transport of a conservative chemical tracer implying that (a) the cells were being transported as a solute with the bulk of the water flow, and (b) that E. coli attached to small clay particles were as mobile in the overland flow as unattached cells. These observations imply that E. coli predominantly interact with small clay particles that are also being carried along in the overland flow. The transport of E. coli at a larger scale was then investigated using 5-metre long, 1-metre wide buffer strips operated under saturation excess conditions. In buffer strips using intact soils and existing pasture cover, E. coli removal was very poor (26 % removal) at the low flow rate of 2 L min⁻� with no removal observed at the higher flow rates of 6 and 20 L min⁻�. E. coli removal rates were increased to 41 % removal at 2 L min⁻� by cultivating the soils, with the removal rate again decreasing with increasing flow rate. E. coli in the overland flow from the buffer strips did not form into large flocs or attach to large soil particles, but were transported in small neutrally buoyant particles that remain entrained in the overland flow. Under saturation excess runoff conditions, E. coli in overland flow were not effectively removed by buffer strips as the small particles are transported either over the soil surface or, through large pores in the soil. This Thesis has shown that E. coli is transported in overland flow in small particle sizes that are difficult to trap or remove from overland flow thereby explaining the high fluxes of faecal bacteria observed in overland flow from agricultural land.

The Moehau Kiwi Sanctuary is one of five sanctuaries established in 2000 and managed by the Department of Conservation. The objective of the sanctuaries is to protect the most endangered kiwi taxa, and increase kiwi survivorship. Operation Nest Egg (ONE) is a programme utilised by the Moehau Kiwi Sanctuary for artificially incubating abandoned Kiwi eggs and captive rearing chicks until they begin to show a gain in weight. ONE chicks were then released back onto Moehau or adjacent protected areas. Kiwi populations are declining on the mainland at an average of about 3% per year in areas where predators of kiwi are not controlled. The main cause for this decline is chick mortality due to predation by stoats (Mustela erminea). During natal dispersal kiwi are known to disperse significant distances of between 5–20 km, and this has influenced the size of management areas needed for the protection of kiwi (10,000 hectares). The type of forest-cover is an important element in determining where management areas are located, as kiwi has preferences for certain forest types over others. This study conducted at Moehau, Coromandel, on the North Island Brown Kiwi advances our knowledge of kiwi by examining differences in rates and distances of dispersal among chicks, sub-adults, non-territorial and territorial adults, as well as between genders. This study investigates kiwi selective use of roost site types, ground-cover types, forest types and physiographical features. Addressed in this study are differences in dispersal, habitat selection and mortality among age-classes and between genders over the months of the year, and across elevations. Comparisons between ONE and wild-reared kiwi dispersal and mortality are included. Data were collected between 2001 and 2008 from observations of kiwi located during daytime hours. The data recorded included the grid reference, elevation, ground-cover type, forest type, physiography, and the type of roost site. The sample size for this study was significantly larger than for any previous studies thus enabling a greater confidence in estimated dispersal rates and dispersal distances, habitat selection and factors relating to mortality. All wild-reared kiwi displayed dispersal and were not philopatric to their natal area. Dispersal distances were found to be further than previously estimated, with the net distance of natal dispersal differing among age-classes, from an average of 834m (SE +/- 131) for kiwi chicks to 7,553m (SE = +/- 1167) for non-territorial adults. Female sub-adult kiwi dispersed further (7,215m) than male sub-adult kiwi (4,226m) (p = 0.04). The time taken to travel one km during natal dispersal ranged from an average of 131days/km (SE = +/- 9) for chicks to 89 days/km (SE = +/- 13) for sub-adults. Habitat selection has been observed in other studies on kiwi but not specifically for Coromandel North Island Brown Kiwi, and selection for ground-cover types by kiwi when roosting on the surface has never been previously studied. Roost site selection of kiwi differed among age-classes (p <0.001), between gender (p <0.001), and across elevations (p <0.001). Female kiwi were found more often in surface roosts (64%) than hole roosts (32%), and male kiwi were found at similar frequencies in holes (46%) and on the surface (47%). Sub-adults used holes to a greater extent as elevation increased, and selected for sub-alpine forest over broadleaf forest (p <0.001). This study is the first to recognise that selection of ground-cover types by kiwi differs among age-classes (p <0.001). Kiwi chicks were more often found on the surface under dead fern fronds and debris (39%) than other ground-cover types. The mortality rate was highest in chicks (33%), with predation responsible for 60% of these deaths; conservation management techniques were responsible for a further 20% of deaths; the remaining 20% of deaths were due to natural or unknown causes. Summer (December-February) was the season in which 81% of kiwi chick deaths occurred. The high proportion of deaths from monitoring techniques and the use of radio-transmitters (22%) indicates improvements need to be made to current management practices. ONE chicks were found to disperse shorter distances and had a greater mortality rate than wild-reared chicks. Therefore, recommendations are made for changes to ONE management practices. Further recommendations are made for the enhancement of kiwi habitat that could reduce kiwi mortality, and for increasing the habitat available to kiwi, thereby potentially increasing population sizes and/or densities.

Northern bobwhite (Colinus virginianus) and swamp rabbits (Sylvilagus aquaticus) are species both strongly influenced by habitat loss and fragmentation in agricultural landscapes. Population declines for the bobwhite and the paucity of information regarding swamp rabbit prevalence add uncertainty to their potential for persistence in Illinois. Research has indicated that these 2 species rarely disperse long distances. In a metapopulation context, such limitations ultimately dictate species' ability to colonize habitat, thereby affecting their persistence. Since gene flow is one of the consequences of dispersal, I employed genetic investigations of the landscape features that affect gene flow, called landscape genetics, to aid the understanding of factors influencing the persistence of the northern bobwhite and swamp rabbit in an agricultural landscape. Tissue samples were collected from hunter harvested bobwhite in central and southern Illinois during 2007-2008. Tissue from trapped swamp rabbits and fecal pellets from swamp rabbit habitat were collected during 2004-2011 in the southernmost counties of Illinois. Microsatellite genetic markers were analyzed for each species. Bayesian clustering methods were used to find interbreeding groups. Levels of gene flow were assessed with F statistics. Correlations between individual genetic distances and landscape features provided an assessment of geographical attributes affecting gene flow. Northern bobwhite expressed less genetic structure among the southern and central counties of Illinois than expected from their sedentary reputation. Genetic differentiation among pre-defined subpopulations was low (FST <0.05) but significant. Genetic clusters were not tightly linked to geography. Individual-based analysis indicated that distance impacted gene flow more than the distribution of suitable habitat or highway barriers. Additionally, the distribution of suitable habitat on the landscape had a negative affect on gene flow indicating bobwhite may disperse through unsuitable habitat more readily than through suitable habitat. These results suggest that greater area of suitable habitat and improvement of existing habitat may be more beneficial to bobwhite than its arrangement or position on the landscape. Significant genetic structure was observed in swamp rabbits in the Cache River watershed of southernmost Illinois. Bayesian clustering indicated 4 distinct genetic groups inhabited the study area. Such structuring suggests swamp rabbits in the northernmost part of their range experience low connectivity among habitat patches and are consequently at risk for extinction in Illinois. Gene flow of swamp rabbits was tied to watercourses indicating their affinity for a water source impacts their dispersal tendencies. Gene flow was negatively impacted by highway barriers, which may interrupt swamp rabbit dispersal due to their avoidance of roads or land cover associated with roads. Alterations to swamp rabbit habitat that leads to loss, increased fragmentation, or increased road density may have severe negative impacts and should be avoided. Habitat improvement focused closer to watercourses may provide a greater benefit for swamp rabbits.

Typescript. Includes vita and abstract. Bibliography: Includes bibliographical references (leaves 147-153). Description: xi, 153 leaves : ill. ; 29 cm.

Accurate sediment flux histories are critical data for deciphering the relative importance of climate and land use factors such as logging and road construction on sediment production and deposition. We use 210Pb activities derived from sediment cores taken on the tidal flats of the South Slough of the Coos Bay estuary to establish temporal variations in sediment accumulation rates. We determined that average deposition varied between 0.4 and 0.81 cm/yr based on two ~80 cm sediment cores. Sedimentation accumulation rates approached 2.1 cm/yr during the 1960s when a rainfall event of extreme intensity coincided with vigorous timber activity. Following this peak, a >40% reduction in peak lumber harvests in the latter part of the 20th century was accompanied by a decrease in sedimentation rates. Mean monthly rainfall during the same time period remained seasonably constant, indicating that land use is likely the key factor governing variations in sediment accumulation.

Master of Science / Department of Entomology / Thomas W. Phillips / The rusty grain beetle, Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae), is a very common worldwide pest of stored grains. The orientation of C. ferrugineus beetles to various semiochemicals was studied in both the laboratory and field. In laboratory experiments glass two-choice pitfall bioassay dishes were used. Mixed-sex populations of beetles responded positively and significantly to cucujolide I and II separately and in combination compared to controls. Bioassays using the two aggregation pheromones of the lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae). Dominicalure 1 and 2 together elicited unexpected significant attractive responses by C. ferrugineus as did assays with the synthetic pheromones from other species. Bioassays showed that C. ferrugineus were not attracted to either corn meal or rolled oats, but they were attracted to commercial grain-based lures and also to ethanol, a natural fermentation product from grains. Several bioassays were conducted to test the attractiveness of naturally produced beetle volatiles to C. ferrugineus, but these showed no orientation to volatiles from either the beetles or their food only. Field tests were conducted in Kansas to test attractiveness of the synthetic pheromones cucujolide I and II in lures together with wheat versus wheat only as a control using Lindgren funnel traps. Field tests in 2014 with cucujolide II pheromone lures showed a significant response by feral C. ferrugineus when tested against wheat. Other field tests to examine dispersal of C. ferrugineus relative to grain storages showed that more C. ferrugineus were caught on the western side of grain bins compared to other cardinal directions at two different locations. Results from field and laboratory studies suggest that semiochemical-based tools can be developed to study dispersal behavior in field populations of C. ferrugineus.