Browsing by Author "Hunt, Dana E"

This research examines three potential mechanisms by which bacteria can adapt to different temperatures: changes in strain-level population structure, gene regulation and particle colonization. For the first two mechanisms, I utilize bacterial strains from the Vibrionaceae family due to their ease of culturability, ubiquity in coastal environments and status as a model system for marine bacteria. I first examine vibrio seasonal dynamics in temperate, coastal water and compare the thermal performance of strains that occupy different thermal environments. Our results suggest that there are tradeoffs in adaptation to specific temperatures and that thermal specialization can occur at a very fine phylogenetic scale. The observed thermal specialization over relatively short evolutionary time-scales indicates that few genes or cellular processes may limit expansion to a different thermal niche. I then compare the genomic and transcriptional changes associated with thermal adaptation in closely-related vibrio strains under heat and cold stress. The two vibrio strains have very similar genomes and overall exhibit similar transcriptional profiles in response to temperature stress but their temperature preferences are determined by differential transcriptional responses in shared genes as well as temperature-dependent regulation of unique genes. Finally, I investigate the temporal dynamics of particle-attached and free-living bacterial community in coastal seawater and find that microhabitats exert a stronger forcing on microbial communities than environmental variability, suggesting that particle-attachment could buffer the impacts of environmental changes and particle-associated communities likely respond to the presence of distinct eukaryotes rather than commonly-measured environmental parameters. Integrating these results will offer new perspectives on the mechanisms by which bacteria respond to seasonal temperature changes as well as potential adaptations to climate change-driven warming of the surface oceans.

Aquatic ecosystems are highly dynamic environments, suggesting that resident microbial communities to respond and adapt to these environmental changes. However, despite the frequency of disturbances in aquatic ecosystems such as annual cycles in environmental parameters and episodic storm events, few studies have examined the impacts of disturbances on aquatic microbial communities. In this dissertation, I investigate community- and taxon-level responses to natural and anthropogenic disturbances in the coastal ocean and wetland mesocosms using ribosomal RNA gene library sequencing. In my first chapter, I present an overview on disturbances in microbial communities and describe microbial interaction network-based approaches for predicting disturbance effects. In my second chapter, I use three years of weekly coastal ocean samples to identify transitions between distinct summer- and winter-associated taxa that occur across the microbial community over relatively short time intervals. Using the same time series, I find that episodic disturbances involve in rapid turnover of both abundant and conditionally rare taxa depending on environmental conditions and initial community composition. Finally, I investigate the microbial responses to acute and chronic environmental loading of an emerging contaminant in replicated wetland mesocosms. Despite the antimicrobial properties of silver nanoparticles, community changes in both treatments appear to be dominated by indirect effects through aquatic plant die-off, though the timing, duration, and magnitude of responses vary. Together, my dissertation demonstrates that associations between microbial taxa, environmental factors, and other components of the ecosystem all contribute to community response to disturbance. By exploring community responses to disturbance, new insights can be gained into the resistance and resilience of microbial communities in response to environmental drivers of community change.

My thesis addresses the question of how multiple environmental factors affect microorganisms, at the community, population and transcriptomic levels. I first explored how multiple environmental variables are correlated with microbial community patterns across the nearshore to offshore gradient in the coastal ocean. This study revealed clustering by sampling sites with distinct nearshore, continental shelf and offshore microbiomes. To investiage this phenomenon further, I used Bayesian modeling to reveal distinct taxa relationships with water temperature and distance from shore (a proxy for productivity and nutrients, among other environmental factors): some phylotypes are related to temperature, others to distance from shore and some to both factors. I next examined the influence of historical contingencies (prior environmental conditions) on microbial responses to factorial manipulation of pH (-0.3) and temperature (+ 3 oC) of microbes from our nearshore station (more variable environment) and the farthest offshore station (less variable). While at both stations, warming significantly altered microbial community composition, acidification alone had a minor influence. Compared with nearshore microorganisms, offshore communities exhibited larger changes in composition, taxa abundances, respiration rates and metatranscriptomes, suggesting increased sensitivity of microorganisms from the less variable environment to warming. Finally, I examined potential interactions between nanoparticles and nutrients using wetland manipulation experiments. This study showed the effect of nanoparticles on microbes was strongly dependent on interactions with other components of the system. The addition of the floating plant Egeria densa alone was sufficient to alter the microbiome’s response to nanoparticles, highlighting the importance of biological interactions when predicting microbial responses to environmental changes. This work will improve our understanding of short-term responses of microbial communities to multiple co-occurring environmental changes and help inform climate change and ecosystem models.

As climate change continues to alter our global ecosystem, ecological disturbances will increase in both frequency and intensity. These ecological disturbances have been shown to significantly impact microbial communities, often altering composition and/or function. However, while disturbance events are commonly studied in host-associated and engineered systems, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic ocean. Furthermore, the research that has been performed on marine microbiome responses to perturbation has been limited to the a priori identification of disturbances, limiting the scope of current research to events considered disturbances from the researchers’ perspective (e.g. hurricanes, contamination, etc.). In this dissertation, I investigate ecological disturbances using a microbiome-centered approach focusing on the role of perturbation in shaping marine microbial assemblies. In my first chapter, I provide an overview of current and historical theoretical frameworks in disturbance ecology and discuss the potential limitations of these approaches. In my second chapter, I apply a microbiome-centered approach to identify disturbances in the coastal ocean. Using three years of observations from a coastal time series, we identified ten disturbance events based on the largest week-over-week changes in microbiome composition. These microbiome disturbances were not clearly linked to specific environmental changes and did not exhibit common responsive taxa. Further, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally-abundant phytoplankton. Although large storms can have significant impacts on marine microbiomes, we propose that unmeasured disturbances may have large impacts on the microbiome and may only be detected from a microbial perspective. In my third chapter, I investigate a cyclonic, Gulf Stream frontal eddy as a potential spatial disturbance that can trap and transport microbial communities along this current. By parsing our samples based on microbial community composition, we were able to identify an eddy-specific microbiome even in highly dynamic frontal zones. Furthermore, the eddy microbiome was defined by a higher abundance of a specific high-light Prochlorococcus ASV that was also enriched in slope waters, suggesting that the eddy may harbor signatures of the nearshore community entrapped during eddy formation. Although the eddy microbiome is distinct from the Gulf Stream’s, especially in cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus), it is most similar to the Gulf Stream, suggesting eddy microbiome assembly favors environmental filtering over historical contingencies. In my final chapter, I investigate the proximal drivers of hurricane-driven responses in coastal microbiomes using experimental incubations intended to mimic specific hurricane attributes. Coastal microbiomes experienced either a dilution, intended to mimic the initial dilution of the bacterioplankton community from extensive precipitation, or to a daily addition of dissolved organic matter (DOM) intended to mimic a hurricane-induced phytoplankton bloom. The dilution treatment, which represents a more immediate and stochastic effect of hurricane landfall, led to changes in several taxonomic groups, while the DOM treatment, which represents the more latent and deterministic phase of hurricane effects that peaks days to weeks after landfall induced a consistent change among a few taxa. Thus, manipulating specific hurricane-associated drivers can help to differentiate responses to different hurricane components. Together, my dissertation approaches disturbances in time, space and complexity from a microbiome-centered perspective. By broadening our concept of disturbance to include a microbiome-centered perspective, we can better identify how these events shape the microbiome. As global climate change and the associated increase in ecological disturbances i continues to alter our ecosystems, we must understand the full scope of these disturbance responses and the potential ramifications for critical biogeochemical cycles as we strive to predict and mitigate ecosystem changes.

Empirical studies show coupling between phytoplankton and heterotrophic bacterioplankton across marine ecosystems through correlations between bacterial cell abundances and bulk phytoplankton measurements of chlorophyll-a or primary production. However, it is still not known whether associations between heterotrophic and autotrophic microbes are mediated solely through bulk carbon pools or if specific cellular interactions are involved. We examined the coupling of heterotrophic bacteria and specific phytoplankton populations in a dynamic, coastal ecosystem and explored the phylogenetic diversity of heterotrophic bacteria associated with a model phytoplankton taxon. Using flow cytometry to count distinct microbial groups, we found heterotrophic bacteria and phytoplankton abundances exhibit similar seasonal dynamics at the coastal sampling site, indicative of close coupling between these organisms. Heterotrophic bacterial abundances were more tightly correlated with small eukaryotic phytoplankton than either cyanobacteria group, Prochlorococcus or Synechococcus. Given our finding that associations between bacteria and eukaryotic phytoplankton drive ecologically important heterotroph-phytoplankton coupling, we examined the community composition of heterotrophic bacteria in culture with a model diatom, Thalassiosira rotula using 16S rRNA gene sequencing. Results indicate that strains of T. rotula support unique heterotrophic bacterial taxa but that all T. rotula also associate with a common set of bacterial phylotypes, comprised of members of the Alphaproteobacteria. Characterizing the phylogenetic associations between heterotrophic bacteria and phytoplankton is essential for identifying factors shaping phytoplankton-bacteria interactions and their role in organic matter processing, trophic dynamics and biogeochemical cycles in marine ecosystems.