The colonial, N2 fixing cyanobacterium Trichodesmium is a keystone species in oligotrophic ocean ecosystems. Trichodesmium is responsible for approximately 50% of the total biologically fixed N2 in the ocean, and this “new” nitrogen fuels primary productivity and the amount of carbon sequestered by the ocean. Trichodesmium does not exist in isolation. Colonies occur ubiquitously with an assemblage of epibiotic microorganisms that are distinct from planktonic microbes and modulated across environments, yet the implications of this relationship have not been explored. In this thesis, the ecology, physiology, and potential geochemical impact of interactions within the Trichodesmium host-microbiome system were examined across three different oligotrophic ocean environments. First, to establish the metabolic diversity contributed by the microbiome to Trichodesmium consortia, a whole community metagenomic sequencing approach was used across a transect the western North Atlantic. This study demonstrated that the microbiome contributes a large amount of unique functional potential and is modulated across a geochemical gradient. In the following study, metatranscriptomics was used to show that such metabolic potential in Trichodesmium and the microbiome was expressed and modulated across the environment. Colonies were sampled in the western tropical South Pacific and gene expression dynamics indicated co-limitation by iron and phosphorus, and revealed a mechanism for phosphate reduction by Trichodesmium and subsequent utilization by the microbiome. These activities were verified with phosphate reduction rate measurements and indicated cryptic phosphorus cycling within colonies. Next, the suite of potential physiological interactions between host and microbiome was assessed with metatranscriptome sequencing on high frequency samples of Trichodesmium colonies from the North Pacific subtropical gyre. Synchronized day-night gene expression periodicity between consortia members indicated tightly linked metabolisms. The functional annotations of these synchronous genes indicated intra-consortia cycling of nitrogen, phosphorus and iron, as well as a microbiome dependence on Trichodesmium-derived cobalamin—interactions that could alter the transfer of these resources to the surrounding water column. In the final study, the effect of the microbiome on Trichodesmium N2 fixation was assessed. Using colonies obtained from the North Atlantic, activity in the microbiome was selectively modified using quorum sensing acyl homoserine lactone cell-cell signaling, a mechanism that Trichodesmium itself does not possess. These experiments indicated that the microbiome has the potential to increase or decrease Trichodesmium N2 fixation to a degree that rivals the effects of alterations in nutrient concentration, but at a more rapid rate. In all, the research presented in this thesis demonstrates the integral importance of the microbiome to Trichodesmium physiology and ecology, highlighting the importance of an unexplored facet of marine microbial systems that likely influences the biogeochemistry of the planet.

The discovery of deep-sea hydrothermal vents in 1977 revealed an ecosystem supported by chemosynthesis with a rich diversity of invertebrates, Archaea and Bacteria. While the invertebrate vent communities are largely composed of endemic species and exist in different biogeographical provinces, the possible factors influencing the distribution patterns of free-living Archaea and Bacteria are still being explored. In particular, how differences in the geologic setting of vent fields influence microbial communities and populations associated with active vent deposits remains largely unknown. The overall goal of the studies presented in this dissertation was to examine the links between the geologic setting of hydrothermal vent fields and microorganisms associated with actively venting mineral deposits at two levels of biological organization. At the community level, bar-coded pyrosequencing of a segment of the archaeal and bacterial 16S rRNA gene was employed to characterize and compare the microbial communities associated with numerous deposits from several geochemically different vent fields. Results from these studies suggest that factors influencing end-member fluid chemistry, such as host-rock composition and degassing of magmatic volatiles, help to structure the microbial communities at the vent field scale. At the population level, targeted cultivation-dependent and -independent studies were conducted in order to expand our understanding of thermoacidophily in diverse hydrothermal environments. Results of these studies expanded the phylogenetic and physiological diversity of thermoacidophiles in deep-sea vent environments and provided clues to factors that are influencing the biogeography of an important thermoacidophilic archaeal lineage. Overall, these studies have increased our understanding of the interplay between geologic processes and microorganisms in deep-sea hydrothermal environments.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 155-181). / This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R² of 1.0), with a dynamic range from 10²-10⁶ cells/ml. Genotypes with >/=~80% average nucleotide identity to those targeted crosshybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R²=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions. / by Virginia Rich. / Ph.D.

In aquatic environments the availability of nitrogen (N) generally limits primary production. N2-fixing prokaryotes (diazotrophs) can convert N2 gas into ammonium and provide significant input of N into the oceans. Cyanobacteria are thought to be the main N2-fixers but diazotrophs also include a wide range of heterotrophic bacteria. However, their activity and regulation in the water column is largely unknown. In this thesis the distribution, diversity, abundance, and activity of marine and estuarine heterotrophic diazotrophs was investigated. With molecular methods targeting the nifH gene, encoding the nitrogenase enzyme for N2 fixation, it was shown that diverse nifH genes affiliating with heterotrophic bacteria were ubiquitous in surface waters from ten marine locations world-wide and the estuarine Baltic Sea. Through enrichment cultures of Baltic Sea surface water in anaerobic N-free medium, heterotrophic N2 fixation was induced showing that there was a functional N2-fixing community present and isolates of heterotrophic diazotrophs were obtained. In Sargasso Sea surface waters, transcripts of nifH related to heterotrophic bacteria were detected indicating heterotrophic N2-fixing activity. Nitrogenase expression is thought to be highly regulated by the availability of inorganic N and the presence of oxygen. Low oxygen zones within the water column can be found in association with plankton. The presence of diazotrophs as symbionts of heterotrophic dinoflagellates was investigated and nifH genes related to heterotrophic diazotrophs rather than the cyanobacterial symbionts were found, suggesting that a symbiotic co-existence prevailed. Oxic-anoxic interfaces could also be potential sites for heterotrophic N2 fixation. The Baltic Sea contains large areas of anoxic bottom water. At the chemocline and in anoxic deep water heterotrophic diazotrophs were diverse, abundant and active. These findings extend the currently known regime of N2 fixation to also include ammonium-rich anaerobic waters. The results of this thesis suggest that heterotrophic diazotrophs are diverse and widely distributed in marine and estuarine waters and that they can also be active. However, limits in the knowledge on their physiology and factors which regulate their N2 fixation activity currently prevent an evaluation of their importance in the global marine N budget.

In aquatic environments the availability of nitrogen (N) generally limits primary production. N2-fixing prokaryotes (diazotrophs) can convert N2 gas into ammonium and provide significant input of N into the oceans. Cyanobacteria are thought to be the main N2-fixers but diazotrophs also include a wide range of heterotrophic bacteria. However, their activity and regulation in the water column is largely unknown. In this thesis the distribution, diversity, abundance, and activity of marine and estuarine heterotrophic diazotrophs was investigated. With molecular methods targeting the nifH gene, encoding the nitrogenase enzyme for N2 fixation, it was shown that diverse nifH genes affiliating with heterotrophic bacteria were ubiquitous in surface waters from ten marine locations world-wide and the estuarine Baltic Sea. Through enrichment cultures of Baltic Sea surface water in anaerobic N-free medium, heterotrophic N2 fixation was induced showing that there was a functional N2-fixing community present and isolates of heterotrophic diazotrophs were obtained. In Sargasso Sea surface waters, transcripts of nifH related to heterotrophic bacteria were detected indicating heterotrophic N2-fixing activity. Nitrogenase expression is thought to be highly regulated by the availability of inorganic N and the presence of oxygen. Low oxygen zones within the water column can be found in association with plankton. The presence of diazotrophs as symbionts of heterotrophic dinoflagellates was investigated and nifH genes related to heterotrophic diazotrophs rather than the cyanobacterial symbionts were found, suggesting that a symbiotic co-existence prevailed. Oxic-anoxic interfaces could also be potential sites for heterotrophic N2 fixation. The Baltic Sea contains large areas of anoxic bottom water. At the chemocline and in anoxic deep water heterotrophic diazotrophs were diverse, abundant and active. These findings extend the currently known regime of N2 fixation to also include ammonium-rich anaerobic waters. The results of this thesis suggest that heterotrophic diazotrophs are diverse and widely distributed in marine and estuarine waters and that they can also be active. However, limits in the knowledge on their physiology and factors which regulate their N2 fixation activity currently prevent an evaluation of their importance in the global marine N budget.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), February 2013. / "February 2013." Cataloged from PDF version of thesis. / Includes bibliographical references. / Intact polar diacylglycerolipids (IP-DAGs) were used to study microbial dynamics in the surface ocean. IP-DAGs from surface ocean seawater were quantified using high performance liquid chromatography-mass spectrometry (HPLC-MS), after first developing a sensitive, high throughput molecular ion independent triple quadrupole MS method for quantification. Using this analytical technique I examined the distribution of the nine most abundant classes of IPDAGs across the Mediterranean, and found that phospholipids as a percent of total IP-DAGs correlated with phosphate concentration. Furthermore, phospholipids were a higher percent of total particulate phosphorus where phosphate was higher, ranging from 1-14%. Thus IP-DAGs can play not only a significant but also a dynamic role in defining planktonic nutrient needs and cellular C:N:P ratios in the environment. Additionally, microcosm incubations were amended with phosphate and ammonium, and in the course of several days this elicited a shift in the ratios of IP-DAGs. This study was the first to demonstrate the dynamic response of membrane lipid composition to changes in nutrients in a natural, mixed planktonic community, and indicated that the change in IP-DAG ratios in response to changing nutrients may be a useful indicator of microbial nutrient stress. In the surface waters of the western North Atlantic I used three experimental approaches to identify the microbial sources of the nine most abundant classes of IP-DAGs. Phytoplankton are the primary source of one class of sulfolipid, sulfoquinovosyldiacylglycerol, and one class of betaine lipid, diacylglyceryl-trimethyl-homoserine, while heterotrophic bacteria are the dominant source of the phospholipids phosphatidylglycerol and phosphatidylethanolamine. In regrowth experiments in the Sargasso Sea and the North Pacific I demonstrated that phospholipid specific production rate is representative of heterotrophic bacterial cell specific growth rate. I measured phospholipid specific production rate and bacterial production rate using uptake of 3H-leucine (³H-Leu) and 3H-thymidine (³H-TdR) across the North Atlantic, across the Mediterranean, and in the North Pacific subtropical gyre. I found that phospholipid specific production rates estimate heterotrophic bacterial cell specific growth rates that are on the order of 1 per day, an order of magnitude faster than cell specific growth rates suggested by uptake of ³H-Leu and ³H-TdR. / by Kimberly J. Popendorf. / Ph.D.

Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of hypoxia and anoxia, events that are detrimental to larger macro-faunal species. Microbial communities, however, are metabolically diverse, capable of utilizing alternative electron donors and acceptors, and can withstand transient periods of low dissolved oxygen. Understanding the phylogenetic and metabolic diversity of microorganisms in these environments is important for assessing the impact hypoxic events have on local and global biogeochemistry. Several molecular ecology tools were used to answer questions about the distribution patterns and activities of microorganisms residing along the coast of Oregon in this dissertation. Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. However, substantial depth dependent changes were observed, with samples collected in the bottom boundary layer (BBL) displaying significant differences from those collected in the surface layer. Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. Thaumarchaea displayed significant depth dependent increases during the summer, and were detected at maximal frequencies during periods of hypoxia, suggesting that nitrification maybe influenced by local changes in dissolved oxygen. Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. Samples collected during the spring, prior to upwelling clustered independently of those collected during the summer, during a period of upwelling, and did not display any clear stratification. Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. Overall, these observations suggest that depth impacts microbial community diversity, metabolic potential, and transcriptional activity in shallow areas of the Northeast Pacific Ocean. The increase in lithotrophic genes and transcripts in the BBL suggests that this microbial community includes many organisms that are able to use inorganic electron donors for respiration. We speculate that the dissolved organic material in the BBL is semi-labile and not available for immediate oxidation, favoring the growth for microorganisms that are able to use alternative electron donors. / Graduation date: 2012

Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. Where terrestrial ecology draws from landscape theory and practice to address issues of scale, the pelagic seascape concept is still in its infancy. We have applied the patch mosaic paradigm of landscape ecology to the study of the seasonal and interannual variability of the North Pacific to facilitate comparative analysis between pelagic ecosystems and provide spatiotemporal context for eulerian time-series studies. Using multivariate, 13-year climatologies of sea surface temperature, photosynthetically active radiation, and chlorophyll a derived from remote sensing observations, we classified hierarchical seascapes at monthly and interannual scales. These dynamic, objectively-determined seascapes offer improved hydrographic coherence relative to oceanic regions with subjectively defined and static boundaries (Chapter 2) and represent unique biogeochemical functioning (Chapter 2) and microbial communities (Chapter3). Furthermore they provide consilience between satellite studies and in situ observations (Chapter 4) and allow for objective comparison of ecosystem forcing (Chapters, 4 and 5). In Chapter 2, we rigorously tested the assumption that satellite-derived seascapes describe regions of biogeochemical coherence. The seasonal cycle of the North Pacific was characterized at three levels of spatiotemporal hierarchy and broader relevance of monthly ���resolved seascapes was assessed through analysis of variance (ANOVA) and multiple linear regression (MLR) analyses of nutrient, primary productivity, and pCO��� data. Distinct nutrient and primary productivity regimes were well-characterized in the coarsest two levels of hierarchy (ANOVA, R�� = 0.5-0.7). Finer scale partitioning was more relevant for pCO���. MLR analyses revealed differential forcing on pCO��� across seascapes and hierarchical levels and a 33 % reduction in mean model error with increased partitioning (from 18.5 ��atm to 12.0 ��atm pCO���). In Chapter 3 we verified the seascapes with in situ collections of microbial abundance and structure. Flow cytometry data was collected from two long term time series and several cruises spanning thousand kilometers of the NE Pacific; these data allowed us to quantify spatiotemporal patterns. In addition, multiple response permutation analysis revealed differences in community structure across discrete seascapes, in terms of both absolute and relative abundances. Principal component analysis of the assemblage supported seascape divisions and revealed structure along environmental gradients with strong associations with chlorophyll a and sea surface temperature and, to a lesser extent, with mixed layer depth and mean photosynthetically active radiation in the mixed layer. Differences of assemblage structure between seascapes and strength of environmental forcing were strong in the subarctic and transition zones, but less pronounced in the subtropics, suggesting satellite-detected changes in bulk properties that may be associated with local physiology or interannual shifts in seascape boundaries. Based on the work presented in Chapter 4, we discovered that interannual shifts in the boundaries of a transition seascape and two distinct oligotrophic subtropical seascapes affect the variability observed at benchmark time series Station ALOHA; the latter two seascapes oscillate in their contributions to the expansion of the entire subtropics. On interannual scales, in situ phytoplankton abundance (as measured by chl-a), net primary productivity (NPP), and the relative abundance of eukaryotic phytoplankton and Synechococcus sp. increased during periods of encroachment by the transition seascape. Conversely, the relative abundance of Prochlorococcus increased and chl ���a and NPP decreased when the highly oligotrophic seascape encroached on Station ALOHA. The dynamic range (~6 million km��) of subtropical expansion is born almost entirely by the transition zone - resulting in a transfer of ~1.2 Pg of total primary C production between a system primed for export production and one dominated by the microbial loop. In Chapter 5, we investigated multiple factors that contribute to the effectiveness of the biological pump in the transition seascape. Near-continuous measurements of net primary production (NPP), net community production (NCP) and several ecophysiological variables were collected in across subarctic, transition, and subtropical seascapes of the Northeast Pacific during August and September of 2008. Mesoscale processes and shifts in community structure contributed to high export efficiency in the subtropical seascape; the convergence of assemblage structure, high biomass, moderate NPP: NCP and high NCP contributed to biologically mediated air-sea exchange in the transition seascape. Furthermore, NPP and NCP were strongly spatially coupled in both the transition (r[subscript 1, 39]=0.70; p<0.0001) and subtropical seascapes (r[subscript 1, 45]= 0.68, p<0.0001), suggesting the possibility for empirical modeling efforts. This dissertation provides a first step to characterize the seascape variability in the NE Pacific and to understand the modulation of primary and export production in a critical transition region. The multivariate seascape approach described here provides spatiotemporal context for in situ studies and allows objective comparisons of systems' responses to climatic forcing. An integrated ocean observing system will require insight from in situ observations and experiments, ecosystem models, and satellite remote sensing. The results highlighted in this dissertation suggest that the pelagic seascape framework, through its capacity to scale both context and mechanism, may serve as an important and unifying component of such an observing system. / Graduation date: 2013