Browsing by Subject "Microbial ecology"

Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ.

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.

The skin is home to trillions of microbes, many of which are recently implicated in immune system regulation and various health conditions (33). The skin is continuously exposed to the outside environment, inviting microbial transfer between human skin and the people, animals, and surfaces with which an individual comes into contact. Thus, the aim of this study is to assess how different environmental exposures influence skin microbe communities, as this can strengthen our understanding of how microbial variation relates to health outcomes. This study investigated the skin microbial communities of humans and domesticated cattle living in rural Madagascar. The V3 region of the 16S rRNA gene was sequenced from samples of zebu (the domesticated cattle of Madagascar), zebu owners, and non-zebu owners. Overall, human armpits were the least diverse sample site, while ankles were the most diverse. The diversity of zebu samples was significantly different from armpits, irrespective of zebu ownership (one-way ANOVA and Tukey’s HSD, p<0.05). However, zebu owner samples (from the armpit, ankle forearm, and hand) were more similar to other zebu owner samples than they were to zebu, yet no more similar to other zebu owner samples than they were to non-zebu owner samples (unweighted UniFrac distances, p<0.05). These data suggest a lack of a microbial signature shared by zebu owners and zebu, though further taxonomic analysis is required to explain the role of additional environmental variables in dictating the microbial communities of various samples sites. Understanding the magnitude and directionality of microbial sharing has implications for a breadth of microbe-related health outcomes, with the potential to explain mosquito host preference and mitigate the threats of vector-borne diseases.

The human gut is home to trillions of microbes that interact intimately with the host and its diet. An important emergent phenotype by these microbes is colonization resistance, the process by which a microbial community resists colonization of an exogenous microbe. This resistance barrier is critical for protecting humans from infectious enteric pathogens. However, it is detrimental to the deliberate engraftment of probiotics which are live microbes beneficial to the host. The mechanisms behind these barriers have been studied extensively, but the microbiome is a network of many biological nodes and ecological edges that can interact with an invader in numerous ways. Therefore, defining the precise mechanisms for resistance of a specific pathogen or probiotic is challenging, due in large to this combinatorial challenge. In the second chapter of this dissertation, I demonstrate a novel approach that can suggest key taxa or host factors associated with clinical outcomes of interest including colonization resistance. In particular, I leveraged a rare prospective cohort study with machine learning methods for identifying gut bacterial signatures associated with susceptibility to cholera. I demonstrated that the human gut microbiota can predict the susceptibility of its host to the diarrheal disease. One of the predictive gut microbes identified by my model, Paracoccus aminovorans, facilitated the growth of Vibrio cholera, the etiologic agent of cholera, in vitro. My model also linked gut microbiota structure, clinical outcomes, and age. This integrative approach suggested that gastrointestinal immaturity of the host and its gut microbiome may be crucial for resisting colonization of enteric pathogens. The predictive model was also over-represented with members of the Bacteroidetes phylum, including several Bacteroides species. These taxa belong to a genus that is dominant in the gut of human on a western diet. Genomic, biochemical, and metabolic studies have vastly studied the traits of these Bacteroides species and how they interact with the host. As obligate anaerobes that are stably colonized in the human gut, the Bacteroides is an ideal model genus for studying ecological mechanisms of colonization resistance. In the third chapter of this dissertation, I developed a high-throughput rapid approach for inferring the relative abundance of several Bacteroides species in a mixed community grown on single carbon substrates. I validated the utility of this method by investigating whether Bacteroides species cooperate or compete when carbon resources are limited. By profiling the growth of mixed cultures on single carbohydrates, I show that Bacteroides exhibit both patterns of resource cooperation and competition. Together, these chapters show that development and application of novel computational and experimental tools can shed light on the intimate interactions between diet, microbiome, and the host in the context of colonization resistance.