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ItemVariation in Coral Microbiome Composition and Transcriptional Activity of Three Corals over Diel Cycles(Georgia Institute of Technology, 2020-05) Caughman, Alicia MarieUnderstanding the dynamics of coral microbiome composition and function is important because microbiomes play important roles in coral health and metabolism. While numerous long-term studies have investigated changes in the microbiome due to various physical or biotic stressors, little is known about the stability of the coral microbiome over diel cycle. For certain parameters (e.g., temperature, pH), the magnitude of diel fluctuation can exceed that observed in mean values over seasons, especially on shallow reefs. Such short-term environmental heterogeneity can affect longer term trends, for example by influencing the extent to which corals acclimate to stress and increase resilience. This study examined diel dynamics of microbiomes in three coral species (Porites lutea, Porites cylindrica, and Pocillopora damicornis) from a shallow, backreef lagoon in Mo’orea (French Polynesia). Porites is relatively resistant to stress, being one of the last coral genera to succumb to bleaching or several diseases, and one of the more abundant genera of corals remaining on degraded reefs. In contrast, Pocillopora is less resistant to many of these stresses and bleaches easily but is one of the genera that commonly recruits and rebounds rapidly after disturbances or strong stresses. We assessed microbiome taxonomic composition and relative transcriptional activity by analyzing 16S rRNA gene and transcript sequences from six time points over 48 hours for each of these coral species. Results showed that composition in P. damicornis varied significantly over the diel period, while composition in both Porites species remained more stable. However, the taxonomic composition of the transcript pool did not vary significantly over time across all corals sampled. This shows that diel stability of these coral microbiomes is dependent on host species, which could contribute to differences in host responses to environmental stressors.
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ItemMicrobiome variation in wild versus captive spotted eagle ryas (Aetobatus narinari)(Georgia Institute of Technology, 2019-07-30) McWhirt, Mary E.The microbial communities (microbiomes) associated with elasmobranchs are currently not well-understood. The spotted eagle ray (Aetobatus narinari) is a slow-maturing ray that is globally distributed in tropical and warm-temperate waters, and is listed as near-threatened by the IUCN Red List. To evaluate how the environment shapes the spotted eagle ray microbiome, we used 16S rRNA Illumina sequencing to compare the microbiomes of the dorsal skin, gill, and cloaca from a ray population sampled in Sarasota Bay, FL to those from a captive population in the Ocean Voyager exhibit at Georgia Aquarium. Cloaca microbiomes of both populations had the lowest alpha diversity and highest beta diversity. The composition of the gill and skin microbiomes differed between captive and wild populations and are similar to, but distinct from, the water column communities while cloaca microbiomes are more divergent from that of the water. This pattern is consistent with that seen in teleost fishes and marine mammals. These results indicate a dual role for body niche and environmental conditions in shaping ray microbiomes and identify key taxa that may be important to the health of the rays.
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ItemMicrobiome community change in the guts of marine fish: feeding and life stage transition as significant organizing factors(Georgia Institute of Technology, 2018-11-08) Parris, Darren J.All animals harbor microbial communities (microbiomes) that play vital roles in host health, development, behavior, and evolution. Determining the processes that regulate microbiome diversity and function is therefore a central question in biology. Numerous investigations have sought to quantify the influence of factors such as diet, host genotype, and environment on gut microbiome assembly, taxonomic composition, and function (Spor et al. 2011, Koenig et al. 2011, Myles et al. 2013). However, these studies have been mostly limited to a handful of model or commercially important host systems. We remain naïve in our understanding of how the importance of different microbiome assembly processes might vary among diverse hosts. This is especially true for the most phylogenetically and ecologically diverse of the vertebrate groups, teleost fishes. In this dissertation, I first describe compositional changes in the gut microbiome associated with the transition from a pelagic larval stage to reef settlement in damselfish (Pomacentridae) and cardinalfish (Apogonidae). Results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families. Next, I use the clownfish Premnas biaculeatus to test how diversity, predicted gene content, and gene transcription of the microbiome vary over a diurnal period following a feeding event. Results confirm feeding as a major restructuring force in intestinal microbiomes over a short timeframe (hours). Finally, I describe ongoing work to characterize the phylogenetic novelty and functional capability of a fish-associated Endozoicomonas bacterium. While this genus has been identified as a symbiont of marine invertebrates, its role in the guts of fish remains unknown. Together, these studies advance our understanding of the diversity and potential function of the fish microbiome, setting the stage for studies to identify the microbiome’s effect on fish health and ecology.
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ItemApplied bioinformatics for exploring diversity patterns in meta-omic data(Georgia Institute of Technology, 2018-04-25) Ranjan, PiyushThis thesis explores the utility of applied bioinformatic approaches to better understand sequence space and phylogenetic diversity in meta-omic clinical and environmental datasets. In three chapters, the thesis describes how applied bioinformatic techniques can be used to 1) identify and quantify sequence variation in the form of insertions and deletions generated as an effect of off-target activity by CRISPR-Cas9 nuclease using high throughput targeted gene amplicon sequencing; 2) identify and quantify the abundance of elements of the bacterial defense systems, CRISPRs, to explore viral-microbe interaction dynamics in natural microbial communities living in marine oxygen minimum zones using high-throughput metagenome sequencing; and 3) investigate phylogenetic variation in an underexplored phylum of bacteria, Atribacteria, that are found as dominant members of microbial communities in methane hydrate-bearing marine sediments again using high-throughput metagenome sequencing.
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ItemUnrecognized diversity of microbes linking methanotrophy to nitrogen loss in marine oxygen minimum zones(Georgia Institute of Technology, 2017-11-13) Padilla, Cory CruzMethane (CH4) is a potent greenhouse gas with 25 times the warming potential of carbon dioxide (CO2) on a per mol basis. Marine oxygen minimum zones (OMZs) are enriched in CH4 compared to oxygenated water columns and are predicted to expand under global warming. OMZs are also key sites for microbially-mediated nitrogen (N) loss, which has been shown in other systems to be linked to CH4 consumption. Diverse groups of microorganisms mediate the global cycling of both CH4 and N. Microbial genes encoding the enzyme used in CH4 oxidation, particulate methane monooxygenase (pmo), have previously been detected in OMZs. However, the genomic diversity and ecological importance of the OMZ CH4-cycling community are unclear, as is the mechanism by which CH4 consumption is carried out by these microbes. This thesis uses a combination of metagenomics, metatranscriptomics, and biogeochemical measurements to explore the activity and diversity of methanotrophic microbes in OMZs. OMZs were found to harbor at least two metabolic strategies for CH4 consumption. First, we found evidence that bacteria belonging to the recently discovered NC10 phylum are present and transcriptionally active at the functionally anoxic core of the OMZ. NC10 bacteria link anaerobic CH4 oxidation to nitrite (NO2-)-driven denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes mediating this unique methanotrophic pathway. Second, metagenomic binning uncovered a separate and distinct methanotrophic strategy that is present and active within and just below the oxycline. In this strategy, gammaproteobacteria, designated phylogenetically as belonging to the OPU3 clade, were found to carry and express genes for methanotrophy and partial denitrification, thereby supporting respiration under low O2 concentrations and allowing for available O2 to be used directly for CH4 oxidation. These findings confirm OMZs as a niche for diverse and previously overlooked forms of denitrification-linked methanotrophy. Further characterization of these niches and the environmental constraints on OMZ CH4 consumption is critical for predicting the effects of OMZ expansion on global C cycling, greenhouse gas consumption, and N loss.
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ItemSignificant changes in microbial community composition in the Gulf of Mexico "Dead Zone" over a diel cycle(Georgia Institute of Technology, 2014-05-02) Cartee, John C.The structure and diversity of microbial communities associated with the oxygen minimum zone located on the Louisiana Shelf in the northern Gulf of Mexico deadzone was studied through amplicon analysis of the 16S rRNA gene. The oxygen minimum zone located on the Louisiana Shelf is a region of reduced oxygen concentrations, containing dynamic and diverse microbial communities that thrive under microaerophilic and anaerobic conditions. The Gulf of Mexico contains one of the largest zones of coastal hypoxia (region of reduced dissolved oxygen concentrations) which is dominated by complex microbial communities that contribute to marine biogeochemical cycling on a global scale. Here we used next-generation sequencing technology to track the microbial community at a single site over a day-night (diel) cycle. Two varying depths were used to collect seawater samples which were used for amplicon sequencing of the 16S rRNA gene (rDNA). By comparing our genetic data to coupled measurements of oxygen and nutrients, we determined how microbial community composition changes in response to day-night gradients and to environmental variation in oxygen and substrate availability.
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ItemThe Effects of Variation in Electron Donor Concentration and Type on Deep-Sea Endosymbiont Community Composition and Gene Expression(Georgia Institute of Technology, 2014-05-02) Shockey, Abigail C.Chemosynthetic symbioses are among the most prevalent microbial symbioses found in marine systems. These associations often dominate reducing environments such as hydrothermal vents, where they play critical roles in biogeochemical cycling. Among the diverse number of organisms that participate in chemosynthetic symbioses is Ifremeria nautilei, a gastropod found surrounding the deep-sea hydrothermal vents of the South Pacific Ocean. Little is known about how chemosynthetic symbiont community composition and gene expression change in response to gradients of electron donors in the vent environment. Understanding these changes offers significant insight into the environmental conditions and physiological mechanisms necessary to sustain the relationship present between host and symbiont. To address this question, individual Ifremeria were collected from the Lau Basin hydrothermal vent system and placed in pressurized, sterile aquaria under the following conditions: i) no electron donor, ii) 100 µM hydrogen sulfide, iii) 300 µM hydrogen sulfide, iv) 300 µM thiosulfate. Stable carbon isotope (13C) incorporation rates were determined for each condition, with 300 µM thiosulfate yielding the highest average rate of carbon incorporation. Amplicon (16S rRNA gene) and metatranscriptomic sequencing were used to compare the phylogenetic diversity and differential gene expression of the symbiotic communities in gill tissue excised from Ifremeriain each treatment. Amplicon analyses revealed two major symbiont lineages within the phylum γ-proteobacteria: putative sulfur-oxidizing symbionts of the Chromatiales and methane-oxidizing symbionts of the Methylococcales. Of these, Chromatiales symbionts dominated, consisting of a single operational taxonomic unit (OTU) representing 81.2-99.6% of the symbiont population. Methylococcales symbionts were represented by two distinct OTUs (0.003-17.5% of sequences) and were present in all host individuals, excluding those exposed to 300uM hydrogen. Preliminary results of the metatranscriptome analysis confirm the expression of genes from both symbiont pools, including genes mediating sulfur oxidation and methane oxidation, despite an assumed lack of methane in the treatments. Genes for sulfur oxidation were ten-fold higher in abundance than those for methane oxidation. These results confirm that Ifremeria engages in a "dual" symbiont strategy using thiotrophic and methanotrophic partners and that this community may be sensitive to changes in electron donor availability, due potentially to symbiont competition within the host, host sanctions of symbiont "cheaters," or direct effects of substrate (sulfide) toxicity.