Department of Biology (Fredericton)
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Testing diagnostic bioindicators in prairie streams: are biological traits and delta 15N of aquatic insects able to detect agricultural impacts?
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by Sophie Nicole Cormier, Agricultural activities in the Red River watershed of Manitoba, Canada, can be significant sources of excess nutrients, sediments and pesticides leading to ecological effects in streams and downstream Lake Winnipeg. In such multiple stressor environments, it is difficult to identify, separate and diagnose the cause of environmental impacts from different agricultural activities using traditional methods (e.g., taxa assemblage). However, ecological function indicators (e.g., functional feeding groups) have potential as diagnostic indicators because they lead to the identification of ecological change pathways. This study evaluated the efficacy of two indicators of ecological function: biological traits and nitrogen isotopic signatures (δ15[15 superscript]N) of benthic macroinvertebrate. Indicator sensitivity was evaluated by their association with human activity gradients that define the type and intensity of human activities (i.e., livestock, wastewater lagoon discharge, crop production). Results indicated that biological traits and δ15[15 superscript]N of BMI were effective diagnostic bioindicators for small scale impacts (e.g., riparian condition) and point sources of stressors (e.g., wastewater discharge). However, catchment scale agricultural activities were not associated with the bioindicators likely because of hydrological factors affecting the timing of stressor transportation in these prairie catchments. This study also demonstrated the importance of testing pathways of human impacts based on conceptual models including the type and magnitude of exposure to human activities and natural gradients.
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The aromatic amino acid responsive TyrR transcription factor of Enterobacter cloacae UW5 : its role in regulation of indole-3-acetic acid biosynthesis and the identification of an expanded regulon using RNA-sequencing
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by Thomas J.D. Coulson, The control of transcription is an important process in all living cells. In the bacterial family Enterobacteriaceae, the transcription factor TyrR controls genes for aromatic amino acid uptake and biosynthesis. In this thesis, I explore the control of genes by TyrR in Enterobacter cloacae UW5, a soil bacterium commonly associated with plant roots that confer beneficial effects on its host and is also an inhabitant of human intestinal microflora and an opportunistic pathogen. Chapter 1 provides a general introduction to bacterial activities in the plant rhizosphere and transcriptional regulation, especially by TyrR. In Chapter 2, I investigated the regulation of two divergently transcribed genes, ipdC and akr, by TyrR. The ipdC gene encodes indolepyruvate decarboxylase for the production of the plant growth hormone indole-3-acetic acid, which plays an important role in the plant beneficial behavior of E. cloacae. TyrR is required for activation of ipdC by binding a single DNA element upstream of the promoter. All three aromatic amino acids act as cofactors for TyrR to induce ipdC expression. Expression of akr, encoding a putative aldo-keto reductase, was repressed by TyrR independently of aromatic amino acids and involved TyrR binding an atypical DNA site within the promoter. In Chapter 3, I assembled the E. cloacae UW5 genome sequence, which revealed genes and pathways that contribute to its plant-associated lifestyle and served as a reference for mapping RNA-sequencing data. In Chapter 4, I delineated the TyrR regulon by comparing transcription profiles in wild-type and tyrR mutant strains of E. cloacae generated through RNA-sequencing. Broad changes in gene expression were identified and several new TyrR members confirmed, including dmpM encoding a methyltransferase that is highly upregulated by tyrosine and phenylalanine, and cpxP and cpxR, which encode components of the envelope stress response. Additionally, pathways for aromatic metabolism, anaerobic respiration, and motility were altered in the tyrR mutant. Chapter 5 summarizes this research that suggests that the E. cloacae TyrR regulon has expanded from that of E. coli to include genes for survival in the diverse environments that this bacterium inhabits and illustrates the expansion and plasticity of transcription factor regulons.
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The biogeographic history and contemporary origins of north american arctic marine macroalgae
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by Trevor T. Bringloe, Arctic coastal communities are expected to change in response to warming
climate trends, and yet basic information is lacking in these systems. Marine macroalgae
provide an opportunity to examine historical migration pathways into the Arctic, and
may serve as a model system for future changes. In this thesis, phylogeographic and
population level biogeographic patterns were examined in Arctic marine macroalgae.
Multiple markers were used to examine phylogeographic patterns in 14 trans-Arctic
lineages of red marine macroalgae and determine what role the opening of the Bering
Strait and Pleistocene glaciation had on contemporary biogeographic distributions.
Results confirmed the opening of the Bering Strait resulted in a predominantly Pacificto-
Arctic/Atlantic movement of species, while Pleistocene glaciation did not appear to
play a significant role in promoting trans-Arctic speciation events. The Last Glacial
Maximum, however, is hypothesized to have extirpated marine coastal populations in
the Northwest Atlantic, with subsequent recolonization out of the Northeast Atlantic.
DNA barcode data were used to determine if trans-Atlantic populations of brown and
red macroalgae were consistent with this hypothesis. Contrary to the historical
consensus, isolation times in 60% of the species examined suggested populations were
not recently derived from Europe. Sequence data were also used to assess recolonization
pathways of marine macroalgae into the Arctic following the Last Glacial Maximum. Of
the 100 species with Arctic populations examined (including brown, green, and red
macroalgae), 39 had uncertain origins, 46 had origins in the North Atlantic, five had
origins in the Pacific and the Atlantic, while the remaining 10 had origins in the North
Pacific. Pacific contributions to Arctic recolonization, however, were inferred in 9 of the 12 best sampled species. Surprisingly, 18 genetic groups and some Arctic haplotypes in
28 species were not assignable to Atlantic or Pacific populations. The results from this
thesis indicated that the Pacific Ocean has played a major role in establishing Arctic and
North Atlantic lineages/populations of marine macroalgae. In addition, some marine
populations may have survived glaciation in the Arctic basin, reducing the role of
recolonization pathways out of the Atlantic and/or Pacific.
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The diversity and taxonomy of Ulva species (Ulvales, Chlorophyta) in the Bay of Fundy (New Brunswick, Canada)
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by Kirby Morrill, Species in the green algal genus Ulva have simple morphologies with few diagnostic features for species identification, and characters used for identification are often subject to high intraspecific variability and plasticity in response to environmental conditions. Routine Ulva species identification using morphological characteristics is therefore challenging even for seasoned phycologists. Molecular techniques (namely, DNA barcoding) are useful for species recognition when morphological investigation alone is inadequate, but molecular work must be accompanied by taxonomic study for accurate morphospecies name application. In this thesis I employed molecular techniques along with observations on biogeography, ecology, and morphology in order to assign meaningful morphospecies names to species of Ulva present in the Bay of Fundy (New Brunswick, Canada). Ten unique genetic groups were identified from the Bay of Fundy: eight genetic groups were assigned existing morphospecies names and the remaining two were assigned provisional species names pending publication.
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The ecological role of the common salt marsh snail, Melampus bidentatus in its northern range, Maritime Canada
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by Allen Derek Beck, The gastropod Melampus bidentatus, an abundant macroinvertebrate and omnivore-detritivore in eastern North American salt marshes, may be influential in marsh dynamics near its northern range limit (Northumberland Strait, Maritime Canada). Through sampling and field experiments, I examined details of and tested possible proximal mechanisms for the snail’s unrestricted within-marsh spatial distribution, and effects of its density on Spartina grass and fungal dynamics. Snail survival (using tethering assays) and movement (using mark-recapture trials) indicated that mortality was very low independent of marsh location and movement was random, both consistent with the snail’s distribution throughout a marsh. In manipulations of snail density, live Spartina grass tended to be temporally variable in the snail’s absence, whereas aboveground dead grass biomass and fungal biomass (as quantified via ergosterol content) tended to decrease with higher snail densities by the end of the plant growing season (September). Conversely, at the end of the fungal decomposition season (November), higher fungal abundance on stems tended to be associated with higher snail densities. Despite high natural variation and consequent low statistical power, results suggested that the snail may negatively affect live grass dynamics, contribute to processing of dead grass biomass, consume fungi, and possibly stimulate fungal growth. My study is an important contribution in determining the role M. bidentatus in Maritime Canadian salt marshes.
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The effect of acclimation temperature and triploidy on hypoxia tolerance in brook charr, Salvelinus fontinalis
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by Rebecca Rae Porter, Triploid fish could be beneficial to aquaculture sustainability due to their effective sterility preventing escaped farmed fish from mating with wild fish. However, experience to date has suggested that they are less tolerant of environmental stressors. The goal of this study was therefore to determine whether acclimation to warm temperature improves the performance of both diploid and triploid brook charr (Salvelinus fontinalis) under conditions of high temperature and hypoxia. A preliminary experiment tested fish of both ploidies acclimated to two different temperatures (15 and 18°C) at a range of test temperatures (ambient, 20, 22, 24, 26, 28, 30°C) to determine the oxygen tension (PO2) at loss of equilibrium and time taken to reach loss of equilibrium, during progressive hypoxia. A follow-up experiment involved first acclimating fish to the same two temperatures and then reacclimating the 18°C fish to 15°C before using the same protocol to test hypoxia tolerance at a narrower range of temperatures (ambient, 24, 26, 28, 30°C). Warm acclimation (18°C) improved high temperature and hypoxia tolerance in both ploidies, but this improvement did not last after reacclimation to cooler temperatures. Triploids had slightly lower hypoxia tolerance in both experiments. This study shows that (1) while increasing acclimation temperature improves tolerance of fish regardless of ploidy in high temperature and hypoxic conditions, the effect is not long-lasting, and (2) the difference in tolerance between ploidies may not be great enough for triploids to have a negative impact on the aquaculture industry and instead should be used to minimize negative impacts caused by farmed salmon mating with wild populations of Atlantic salmon. However, further research needs to be done to optimize this approach for use in the aquaculture industry.
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The effect of triploidy on postprandial metabolism and ammonia excretion in brook charr, Salvelinus fontinalis
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by Nicole Jennifer Daigle, Many studies have attempted to find physiological differences between sterile (triploid) and normal (diploid) salmonids with the goal of increasing triploid performance for aquaculture. The objective of this thesis was to study the effects of triploidy on specific dynamic action (SDA) and net total ammonia nitrogen (TAN) excretion by measuring aerobic metabolic rate (MR) and TAN excretion of brook charr, Salvelinus fontinalis, from 48h before to 48h after being fed a single ration (measured as % body mass; BM). A first experiment determined an appropriate ration size (0.4% BM) and validated the tube-feeding procedure. The process of tube-feeding itself only affected the MR factorial scope, which was significantly higher (by 5%) in the sham-fed group. The second experiment compared the same parameters between ploidies and demonstrated that triploids had significantly lower standard metabolic rates and a higher net TAN excretion than diploids when fed 0.4% BM.
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The genetic and evolutionary basis for somatic cell differentiation in the multicellular alga Volvox carteri: investigations into the regulation of regA expression
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by Stephan Konig, The evolution of life is characterized by a series of major transitions in the complexity of
biological systems. One such transition was from unicellular to multicellular organisms
and involved the evolution of sterile somatic cells-a premier example of cooperation.
The goal of this thesis was to investigate the genetic and evolutionary basis for somatic
cell differentiation in Volvox carteri, a simple multicellular green alga composed of ca.
2,000 somatic cells and up to 16 reproductive cells (gonidia). In V carteri, the terminal
differentiation of small somatic cells involves the expression of regA, a gene coding for a
transcription factor thought to repress nuclear genes required for chloroplast biogenesis
and, thus, for cell growth and division. regA induction is likely dependent on cell size,
but the molecular mechanism whereby cell size is translated into regA expression remains
to be elucidated. This study focused on the regulation of regA expression by employing
mechanistic and evolutionary approaches. Using a regA-/gonidialess double mutant strain
characterized in this study, I showed for the first time that in addition to its
developmental expression, regA can be induced by environmental stimuli, and this
induction is also dependent on cell size. These findings provide support for a previously
proposed hypothesis that regA evolved from an ancestral stress-response gene.
Furthermore, in mutants expressing a non-functional RegA protein, the conditions that
trigger regA expression also induce programmed cell death, which points towards a dual
function for regA in cell fitness: to decrease cell reproduction (by repressing cell growth)
and to increase cell survival (by conferring resistance to stress). Genes with antagonistic
pleiotropic effects on fitness have been proposed to stabilize cooperation, and regA is the
first such example in multicellular organisms with unitary development (i.e., developed from a single cell). To identify transcription factors binding to cis-regulatory elements of
regA I have used yeast one-hybrid assays. No potential candidates were identified,
suggesting that cooperative binding of proteins or multi-protein complexes are involved
in the regulation of regA. Overall, this study provides novel insights into our
understanding of somatic cell differentiation, from both a mechanistic and an
evolutionary perspective., Scanned from archival print submission.
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The geography of diet: diversity in diet and foraging behavior in herring gulls (Larus argentatus) across Atlantic Canada
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By Katherine R. Shlepr, Changes in food availability are thought to be the primary driver of Herring Gull (Larus argentatus) species decline, but empirical evidence linking gull diet to population dynamics is lacking. First, I test the ability of new GPS tracking technology to provide representative data on Herring Gull movement, analyzing the effect of tag deployment on adult behavior and reproductive output. I found that effects were short-term. Secondly, I analyze data from GPS tags deployed on Herring Gulls at two colonies in the Bay of Fundy, Canada, and combine results with those from a more established diet methodology, stable isotope analysis. I found that variation in individual foraging strategy is high, but colony-level differences in diet and foraging location do emerge. This study provides the foundation for understanding how differences in individual foraging strategy may lead to variation in individual reproductive success and the ability to adapt to a changing environment.
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The importance of marine-derived nutrients from anadromous fishes to Atlantic rivers
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by Kurt M. Samways, With the dramatic declines in Atlantic anadromous fishes over the past century it is important to identify the relative roles marine-derived nutrients (MDNs) delivered by these fishes play in influencing freshwater food web dynamics. Rivers in New Brunswick and Nova Scotia, Canada containing Atlantic salmon (Salmo salar), alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax), or sea lamprey (Petromyzon marinus) as the primary anadromous species, were chosen to study their effects on i) primary production/productivity; ii) trophic interactions; and iii) resource quality. To understand the linkages between freshwater and marine ecosystems, observational studies, experimental frameworks, and analytical techniques (including stable isotope and fatty acid analysis) were employed.
Biofilm communities followed a predictable response pattern to MDN inputs, regardless of the fishes spawning strategy, timing, or MDN load being delivered. Biofilm community standing crop and gross primary productivity were greater in sites receiving MDN subsidies than reference sites. The 13C and 15N data showed that MDNs were incorporated into all trophic levels (biofilm, invertebrates, and salmon parr) across streams with anadromous fish spawning. Community-wide niche space (i.e. the trophic diversity among food webs) shifted toward the marine-nutrient source, however the total ecological niche space (i.e. magnitude of trophic diversity) did not always increase with MDN inputs. Exposure to MDN resources from spawning Atlantic salmon led to improved nutritional quality for all biota, as indicated by increased lipid stores in all trophic levels and incorporation of fatty acids. The variability in fatty acid profiles was accredited to inherent differences between trophic groups combined with assimilation of marine-derived fatty acids in the MDN treatments. Precipitous declines in fish populations have resulted in a net loss in MDN loading to a point that may no longer sustain elevated levels of productivity needed for sustaining large fish populations.
The current trend of declining anadromous fish populations in Atlantic Canada means fewer nutrient-rich marine subsidies for stimulating trophic production in these river systems. Marine-derived subsidies (nutrients and lipids) benefit multiple trophic levels of freshwater organisms as well as provide a cross-ecosystem spatial subsidy. In order to maintain ecosystem function and productivity, it is critical to include MDNs for effective ecosystem management and river restoration strategies.
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The information insects leave behind: spatial and temporal variation of benthic assemblages using novel non-invasive methods
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by Zoe Gabrielle O’Malley, Rare and elusive benthic macroinvertebrate (BMI) taxa are difficult to detect and sampling methods often require preserving live specimens, a concern for monitoring species-at-risk. Here, we aim to understand spatial and temporal variation in BMI communities within a complex, understudied river-wetland system using exuviae (shed exoskeletons), environmental DNA (eDNA) water samples and bulk-sequenced benthic samples. Samples were collected across wetland, tributary, and mainstem habitats within the lower Saint John River and Grand Lake Meadows, New Brunswick. Using exuviae, we demonstrate that terrestrial factors (e.g. riparian vegetation community) affect emergent dragonfly community composition more than aquatic factors (e.g. water temperature). Further, BMI communities identified via eDNA water samples did not differ from bulk-sequenced benthic communities, except during higher flow conditions in larger systems. Using non-invasive methods to capture biodiversity allowed us to explore ecological linkages, crossing boundaries between life stages and ecotones, to elucidate mechanisms between spatial and temporal drivers of BMI communities in a complex river-wetland system.
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The role of habitat and dispersal in shaping the biodiversity of riverine insect assemblages
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by Colin Curry, Given limited resources, biomonitoring progrrum are touted as a source of biodiversity
information for conservation planning in riverine ecosystes. However, the degree to
which patterns revealed by biomonitoring are reflected in unsampled mesohabitats and
undersampled taxonomic groups has not been fully addressed. Differences in dispersal
capacity among taxonomic groups, in particular, may result in divergent patterns of
biodiversity at landscape and regional scales. I sought to address the suitability of
biological monitoring data in freshwater biodiversity assessment, and to test the
prediction that the degree of spatial structuring in aquatic insect assemblages is inversely
related to their dispersal capacity. My thesis comprises four articles. The first addresses
whether macroinvertebrate biodiversity patterns in riffles, the target mesohabitat of
Canada's national aquatic biomonitoring program, are reflective of those in riverine
wetlands. The second addresses whether biodiversity in a group of insects that is
abundant in biomonitoring samples (Trichoptera) reflects that of an underrepresented
group (Odonata). The third tests the above prediction by comparing the degree of spatial
structuring in the weakly dispersing Trichoptera and the stronger dispersing Odonata. The
final article investigates regional and national aquatic insect biodiversity patterns utilizing
the national biomonitoring dataset, and seeks to evaluate the influence of scale on the
observation of spatial structuring aquatic insect assemblages. Several key findings
emerged from this work: 1) Patterns of invertebrate taxon richness and beta diversity in
riftles poorly reflect those in riverine wetlands. 2) Odonata and Trichoptera biodiversity
were not always congruent, however, differences in abundance among groups may
account for weak correlations. 3) Both Odonata and Trichoptera assemblages
demonstrate relatively weak spatial structuring at a landscape (ie. 5th order catchment)
scale. The weak explanatory ability of spatial variables was also apparent at a regional
scale, as just one of the Water Survey of Canada sub drainages within the Pacific
drainage demonstrated a significant spatial component in aquatic insect assemblage
variation These findings suggest caution in the application of biomonitoring data to
conservation planning. Although landscape and regional scale structuring of aquatic
insect communities may be weak, it does not preclude the existence of smaller scale
spatial structuring driven by local dispersal processes., Electronic Only., Ph.D. University of New Brunswick, Department of Biology, 2014.
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