128 research outputs found
Factors structuring microbial communities on marine foundation species
No full textThe microbiome of marine organisms contributes to host health and ecosystem processes like nutrient cycling. Despite the importance to healthy ecosystems, little is known about the dynamics and drivers of microbiome variation on marine hosts. In this dissertation, I use longitudinal studies and field-based transplant experiments to assess the factors associated with microbiome change on four coastal foundation species. In the intertidal macroalga Fucus distichus, I characterize temporal dynamics and microbiome variation on host individuals. I show seasonal turnover is a highly significant predictor of microbiome change. Local environmental conditions and host developmental stage also explain some microbiome variation. I test microbiome fidelity to geographically and phenotypically differentiated F. distichus by exposing hosts to new abiotic conditions and microbial source pools. No immediate shifts in microbiome composition occur in five-day transplant experiments, suggesting the established microbiome is buffered against short-term environmental change. I test whether host filtering modulates the shell microbiome of the mussel, Mytilus californianus, and find the microbiome is not specific to living mussels. Instead, it is associated with abiotic conditions that vary across geographic locations and elevation in the intertidal zone. In cultivated kelps, I test if outplanting kelp from controlled hatcheries to open ocean sites alters the microbiome and if host and abiotic factors are correlated with microbiome variation at cultivation sites. Host-species specificity was evident throughout the cultivation process and outplanting is followed by high microbiome turnover. Microbiome variation is more strongly correlated to season than abiotic differences between cultivation sites. Altogether, my findings suggest abiotic factors and host identity influence selective microbiome assembly on coastal foundation species. Seasonal microbiome turnover occurs in multiple hosts and coastal habitats, indicating microbes associated with the prevailing conditions may commonly replace existing members of the microbiome over weeks to months. Within host species, local abiotic conditions and host physiological state are correlated to microbiome variation. This research broadens our understanding of the tempo of microbiome turnover and factors predicting microbial community variation in marine foundation species. It provides necessary foundational knowledge for a holistic understanding of host and ecosystem response to changing oceans.Science, Faculty ofBotany, Department ofGraduat
Diversity of intestinal eukaryotes with a focus on Blastocystis, its relationships with gut bacteria and consequences for the host health
No full textThe intestinal tract of mammals is colonized by a diversity of eukaryotes, including metazoan worms, protists and fungi. Although parasitologists historically identified them as parasites causing diseases, more recent studies suggest they can be commensal or beneficial for the host. Indeed, intestinal eukaryotes can protect against immune-mediated disorders in experimental systems by regulating the host immune system and gut bacterial community and are common in healthy populations. In Chapter 1 (Introduction), I conducted a literature review on the genetic diversity of Blastocystis (classified into 25 subtypes), its host specificity, and its interactions with the gut bacterial community and the host immune system. Previous studies confirm that Blastocystis can cause disease or promote health by regulating the immune system and the gut bacterial community. Variation between studies is linked to various factors, including (i) the host specificity of subtypes and the existence of potential pathogenic subtypes, (ii) the host clinical conditions (IBS, IBD, colitis, …), (iii) Blastocystis duration of colonization and abundance and (iv) co-infections with multiple intestinal eukaryotes. In Chapter 2, using an experimental approach, I demonstrated that Blastocystis subtype 3, a common subtype found in mammals, provided faster recovery against colitis in rats. Recovery was associated with the regulation of the immune system and gut bacterial community and was dependent on the duration of colonization. In Chapter 3, I showed that Blastocystis presence and abundance were associated with the signs of a healthy gut, including higher bacterial diversity, lower levels of pathogenic bacteria and lower levels of gut permeability in stunted and non-stunted children from The Central African Republic and Madagascar. In Chapter 4, I described the intestinal eukaryote community in wild western lowland gorillas and found 40 intestinal eukaryotes. Intestinal eukaryotes were more likely to co-occur, suggesting that they could promote each others’ colonization. Variations in abundance, prevalence and duration of colonization between taxa indicate different levels of host-specificity. My results provide crucial information on the diversity and ecology of intestinal eukaryotes and their potential to regulate the host immune system and gut bacterial community.Science, Faculty ofZoology, Department ofGraduat
Identification of core microbiome on macroalgal species, and microbial manipulation in commercial kelp culture
No full textThere is a growing recognition of the important role that host-associated microbes play in the biology and health of seaweeds. The seaweed cultivation industry is rapidly expanding due to its high demand for various applications and as a nutritious food source. As a result, there is a growing interest in exploring the potential for manipulating the microbiome to improve seaweed aquaculture and identify potential probiotic strains more effectively. Recent studies have highlighted an increase in disease and a decline in crop yields in seaweed aquaculture, which can be attributed to intensified and global distribution. However, our current understanding of the influence of microbes on seaweed cultivation remains limited. The distribution of bacteria within the microbiome of seaweeds naturally varies both in space and time. The core microbiome hypothesis suggests that bacteria consistently present in the microbiome of hosts are more likely to play an important functional role. This makes the core bacteria an appealing target for microbial manipulation. In my research, I aim to test the core microbiome hypothesis, which suggests that the ecological distribution of bacteria can serve as a predictive factor for their influence on host biology. In Chapter 2, I developed a better understanding of the distribution of seaweed-associated bacteria and show how different ways of defining the core microbiome result in different suites of bacteria identified as the core, and conclude that sampling across broader spatial and temporal scales result in a more robust set of core bacteria. I found that most of these core bacteria from Fucus distichus were also widespread across seaweed species. In Chapter 3, I identified core bacteria associated with wild sugar kelp (Saccharina latissima) and their distribution on cultivated S. latissima. I then conducted experimental tests investigating the impact of microbial manipulation on S. latissima biology using bacterial isolates in the cultivation of S. latissima. The results revealed that bacteria can indeed alter growth and development of sugar kelp, and found a positive correlation between bacterial taxa found at high frequency on wild S. latissima and their effect on S. latissima development. Chapter 4 tested the prediction that the bacteria most commonly found on wild kelp (the core) would be more successful at colonizing kelp in laboratory cultures. Overall, my findings suggest that selecting probiotic strains from the core candidates could be a valuable strategy, as they are more likely to influence host biology and colonize kelp in a deterministic manner.Science, Faculty ofBotany, Department ofGraduat
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Diversity of Eukaryotes and Their Genomes
No full textMy dissertation addresses two aspects of eukaryotic evolution, 1) the organization of eukaryotic diversity and 2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes.Organismic and Evolutionary BiologyDoctor of Philosophy (Ph.D.
Effects of human activities, environment, and time on eelgrass-associated epifaunal communities
No full textEelgrass (Zostera marina) is a coastal marine angiosperm found in the Northern Hemisphere and forms expansive meadows in sheltered estuaries and bays, providing habitat for a high diversity of organisms, including algae, invertebrates, microbes, fish, birds, and mammals. It also provides invaluable ecosystem services for humans, including coastal storm protection, carbon sequestration, and nutrient cycling. However, eelgrass meadows are threatened worldwide by numerous anthropogenic activities, including shoreline modification, overfishing, land-based nutrient loading, and climate change. In British Columbia, Canada, eelgrass ecosystems are vulnerable to human activities such as habitat destruction, fishing, and pollution, and warming waters, which can cumulatively lead to negative impacts on eelgrass and associated fauna. To understand how environmental variation and BC-specific human activities affect eelgrass ecosystems temporally and spatially, I used a three-year, monthly observational time series of two trophic groups, statistical modeling, and an experiment to study how eelgrass communities and species interactions vary at the micro and macro scales. I show that eelgrass and epiphytic algae biomass change seasonally, and the timing of their peak biomasses varies interannually and is driven by nutrient availability and mesograzer abundances. I also show that human activities have a negative effect on eelgrass biomass, epiphytic algae, and epifaunal invertebrate abundances and species richness. Lastly, I show the first experimental evidence that eelgrass leaves host a core microbiota, eelgrass leaf-associated microbial communities are primarily driven by their surrounding environment, yet there may be host influence because microbial communities are resistant to environmental change within short periods of time. This research provides new insight to how environmental variability and human activities shape eelgrass-associated epifauna communities. This information can be used to predict how eelgrass ecosystems may change over time, which can help inform management decisions for restoration and conservation practices. Implementing more regulations for coastal anthropogenic activities may help ensure that eelgrass, and the organisms and humans that depend on it, will be sustained well into the future.Science, Faculty ofZoology, Department ofGraduat
Rotalid: light micrograph
No full textApresenta imagem de Rotalid. Este exemplar foi isolado em um sedimento de Eel Pond em Woods Hole, MA, USAComponente Curricular::Educação Superior::Ciências Biológicas::Microbiologi
Miliolid: sem
No full textMostra uma imagem microscópica do calcário Miliolid, que foi isolado de sedimentos marinhos de Eel Pond, em Woods Hole, MA, EUAComponente Curricular::Educação Superior::Ciências Biológicas::Microbiologi
Rotalid: light micrograph
No full textApresenta imagem de Rotalid. Este exemplar foi isolado em um sedimento de Eel Pond em Woods Hole, MA, USAComponente Curricular::Educação Superior::Ciências Biológicas::Microbiologi
Rotalid: light micrograph
No full textApresenta imagem de Rotalid. Este exemplar foi isolado em um sedimento de Eel Pond em Woods Hole, MA, USAComponente Curricular::Educação Superior::Ciências Biológicas::Microbiologi
Miliolid: sem
No full textMostra uma imagem microscópica do calcário Miliolid, que foi isolado de sedimentos marinhos de Eel Pond, em Woods Hole, MA, EUAComponente Curricular::Educação Superior::Ciências Biológicas::Microbiologi
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