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• 21. [Article] The Interplay Between Landscape Structure and Biotic Interactions

  Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of ...

  Citation × Citation Citation Abstract Copy Title: The Interplay Between Landscape Structure and Biotic Interactions Author: Zarnetske, Phoebe, Baiser, Benjamin, Strecker, Angela L., Record, Sydne, Belmaker, Jonathan, Tuanmu, Mao-Ning Year: 2017 Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of biotic interactions: patch size and habitat amount, isolation of patches, barriers to dispersal and movement, persistence of landscape structure, and landscape complexity. In addition, these aspects of landscape structure influence the strength and outcome of biotic interactions. Whereas most research focuses on the effects of the abiotic environment on species and their biotic interactions, research on foundation species and ecosystem engineers demonstrates the important influence of biotic interactions on landscape structure itself, including effects on landscape complexity, extent of habitat, and the structure of landscape features. In this review, we describe ecological theories that lay the foundation for interplay between landscape structure and biotic interactions, and summarize these connections across an array of interacting species in freshwater, marine, and terrestrial systems. We end with suggestions for integrating the fields of landscape ecology and community ecology to better understand the connections between landscape structure and biotic interactions and better predict their dynamics in light of global change. Title: The Interplay Between Landscape Structure and Biotic Interactions Author: Zarnetske, Phoebe, Baiser, Benjamin, Strecker, Angela L., Record, Sydne, Belmaker, Jonathan, Tuanmu, Mao-Ning Year: 2017 Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of biotic interactions: patch size and habitat amount, isolation of patches, barriers to dispersal and movement, persistence of landscape structure, and landscape complexity. In addition, these aspects of landscape structure influence the strength and outcome of biotic interactions. Whereas most research focuses on the effects of the abiotic environment on species and their biotic interactions, research on foundation species and ecosystem engineers demonstrates the important influence of biotic interactions on landscape structure itself, including effects on landscape complexity, extent of habitat, and the structure of landscape features. In this review, we describe ecological theories that lay the foundation for interplay between landscape structure and biotic interactions, and summarize these connections across an array of interacting species in freshwater, marine, and terrestrial systems. We end with suggestions for integrating the fields of landscape ecology and community ecology to better understand the connections between landscape structure and biotic interactions and better predict their dynamics in light of global change. Close

• 22. [Article] Microbial Ecology of Active Marine Hydrothermal Vent Deposits: The Influence of Geologic Setting on Microbial Communities

  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 ...

  Citation × Citation Citation Abstract Copy Title: Microbial Ecology of Active Marine Hydrothermal Vent Deposits: The Influence of Geologic Setting on Microbial Communities Author: Flores, Gilberto Eugene Year: 2011 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. Title: Microbial Ecology of Active Marine Hydrothermal Vent Deposits: The Influence of Geologic Setting on Microbial Communities Author: Flores, Gilberto Eugene Year: 2011 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. Close

• 23. [Article] Oregon's Fish and Wildlife in a Changing Climate

  Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and ...

  Citation × Citation Citation Abstract Copy Title: Oregon's Fish and Wildlife in a Changing Climate Author: Hixon, Mark A., Gregory, Stanley V., Robinson, W. Douglas, Baker, C. Scott, Batchelder, Harold P., Epps, Clinton, Garcia, Tiffany S., Haig, Susan M., Letelier, Ricardo M., Lytle, David A., Menge, Bruce A., Miller, Jeffery C., Noakes, David L.G., Peterson, William T., Rice, James M., Rumrill, Steven S., Schreck, Carl B., Suryan, Robert M., Sytsma, Mark D., White, Angelicque E. Year: 2010 Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and coastal ocean. Oregon is one of the most ecologically diverse states in the country. The state’s robust biodiversity, some of which is already threatened or endangered -- inhabits complex and dynamic ecosystems that we have only begun to understand, let alone examine in terms of climate change.It is clear that the abundance and distribution of species are shifting already and will shift more rapidly as habitats on land, in freshwater, and in the sea are altered due to increasing temperatures and related environmental changes. It remains to be seen if past changes are all tied to global climate change or if they are a result of some other variability, but they represent a proxy for how species may shift in a warmer climate. Among the observed species changes: Insects are moving in from the south of Oregon, frogs are reproducing earlier in the year and land birds are shifting their distributions northward and migrating earlier. Freshwater fish are losing their cool-water habitats. In the marine environment, algal blooms have increased (figure 11) and the highly predatory Humboldt squid have shifted their distribution from subtropical and tropical regions, making an appearance off the coast of Oregon in the last few years. In a warmer climate, plant and animal species may have to shift upward or northward on land or deeper at sea for survival. Rare or endangered species may become less abundant or extinct; insect pests, invasive species and harmful algal blooms may become more abundant. Declines in the abundance of species may be caused directly by physiological stress related to changes in temperature, water availability, and other environmental shifts, and/or indirectly by habitat degradation and negative interactions with species that are benefited by climate change (diseases, parasites, predators, and competitors). Understanding the responses of Oregon’s fish and wildlife to climate change will require a better understanding of smaller organisms and insects and ocean species. Knowledge of ecological interactions will be crucial for understanding the related effects of climate change (increased predation or competition, for example). Management and natural resource polices that protect intact ecosystems are a tool for adaptation; native species can live and migrate to these safe refugia. Title: Oregon's Fish and Wildlife in a Changing Climate Author: Hixon, Mark A., Gregory, Stanley V., Robinson, W. Douglas, Baker, C. Scott, Batchelder, Harold P., Epps, Clinton, Garcia, Tiffany S., Haig, Susan M., Letelier, Ricardo M., Lytle, David A., Menge, Bruce A., Miller, Jeffery C., Noakes, David L.G., Peterson, William T., Rice, James M., Rumrill, Steven S., Schreck, Carl B., Suryan, Robert M., Sytsma, Mark D., White, Angelicque E. Year: 2010 Chapter 7 in: The Oregon Climate Change Assessment Report Oregon's fish and wildlife include animals on land, fish and other species in rivers and lakes, and various kinds of sea life in estuaries and coastal ocean. Oregon is one of the most ecologically diverse states in the country. The state’s robust biodiversity, some of which is already threatened or endangered -- inhabits complex and dynamic ecosystems that we have only begun to understand, let alone examine in terms of climate change.It is clear that the abundance and distribution of species are shifting already and will shift more rapidly as habitats on land, in freshwater, and in the sea are altered due to increasing temperatures and related environmental changes. It remains to be seen if past changes are all tied to global climate change or if they are a result of some other variability, but they represent a proxy for how species may shift in a warmer climate. Among the observed species changes: Insects are moving in from the south of Oregon, frogs are reproducing earlier in the year and land birds are shifting their distributions northward and migrating earlier. Freshwater fish are losing their cool-water habitats. In the marine environment, algal blooms have increased (figure 11) and the highly predatory Humboldt squid have shifted their distribution from subtropical and tropical regions, making an appearance off the coast of Oregon in the last few years. In a warmer climate, plant and animal species may have to shift upward or northward on land or deeper at sea for survival. Rare or endangered species may become less abundant or extinct; insect pests, invasive species and harmful algal blooms may become more abundant. Declines in the abundance of species may be caused directly by physiological stress related to changes in temperature, water availability, and other environmental shifts, and/or indirectly by habitat degradation and negative interactions with species that are benefited by climate change (diseases, parasites, predators, and competitors). Understanding the responses of Oregon’s fish and wildlife to climate change will require a better understanding of smaller organisms and insects and ocean species. Knowledge of ecological interactions will be crucial for understanding the related effects of climate change (increased predation or competition, for example). Management and natural resource polices that protect intact ecosystems are a tool for adaptation; native species can live and migrate to these safe refugia. Close

• 24. [Article] Microbial Biogeochemistry of Boiling Springs Lake: a Physically Dynamic, Oligotrophic, Low-p H Geothermal Ecosystem

  Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. ...

  Citation × Citation Citation Abstract Copy Title: Microbial Biogeochemistry of Boiling Springs Lake: a Physically Dynamic, Oligotrophic, Low-p H Geothermal Ecosystem Author: Siering, Patricia Lynne, Wolfe, Gordon V., Wilson, Mark S., Yip, A. N., Carey, Cynthia M., Wardman, Colin D., Shapiro, Russell Scott, Stedman, Kenneth M., Kyle, Jennifer E., Yuan, Tong, Van Nostrand, Joy D., He, Zhili, Zhou, Jizhong Year: 2013 Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 [degrees]C, but temperatures reach 93 [degrees]C locally. We extracted DNA from water and sediments collected from warm (52 [degrees]C) and hot (73-83 [degrees]C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle. Title: Microbial Biogeochemistry of Boiling Springs Lake: a Physically Dynamic, Oligotrophic, Low-p H Geothermal Ecosystem Author: Siering, Patricia Lynne, Wolfe, Gordon V., Wilson, Mark S., Yip, A. N., Carey, Cynthia M., Wardman, Colin D., Shapiro, Russell Scott, Stedman, Kenneth M., Kyle, Jennifer E., Yuan, Tong, Van Nostrand, Joy D., He, Zhili, Zhou, Jizhong Year: 2013 Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 [degrees]C, but temperatures reach 93 [degrees]C locally. We extracted DNA from water and sediments collected from warm (52 [degrees]C) and hot (73-83 [degrees]C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle. Close

• 25. [Article] New Insights into the Controls and Mechanisms of Plankton Productivity Along the US West Coast

  During the lifetime of the National Science Foundation's Coastal Ocean Processes program, four experiments were conducted on the US West Coast in the northern California Current System. Although each project ...

  Citation × Citation Citation Abstract Copy Title: New Insights into the Controls and Mechanisms of Plankton Productivity Along the US West Coast Author: Kudela, Raphael M., Banas, Neil S., Barth, John A., Frame, Elizabeth R., Jay, David A., Largier, John L., Lessard, Evelyn J., Peterson, Tawnya D., Vander Woude, Andrea J. Year: 2008 During the lifetime of the National Science Foundation's Coastal Ocean Processes program, four experiments were conducted on the US West Coast in the northern California Current System. Although each project had a unique scientific focus, all four addressed the mechanisms causing eastern boundary current systems in general, and the California Current System in particular, to be biologically rich, from phytoplankton to apex predators. Taken together, findings from these projects provide new insights into the canonical view that upwelling systems are simple wind-driven "conveyor belts," bringing cold, nutrient-rich waters to the well-lit surface ocean where biological organisms flourish. We highlight new insights and advances gained from these programs, including recognition that (a) elements other than nitrogen, particularly iron, may limit the base of the food chain, and (b) the source of these nutrients is not solely a result of wind-driven Ekman transport. The importance of retentive features has clearly emerged, whether these are associated with topography, bathymetry, or more transient features such as river plumes. These new insights into the drivers and fate of this high biological productivity should greatly improve current and future generations of ecosystem models and provide a better understanding of the unique physical-biological coupling that makes the California Current System so rich. Title: New Insights into the Controls and Mechanisms of Plankton Productivity Along the US West Coast Author: Kudela, Raphael M., Banas, Neil S., Barth, John A., Frame, Elizabeth R., Jay, David A., Largier, John L., Lessard, Evelyn J., Peterson, Tawnya D., Vander Woude, Andrea J. Year: 2008 During the lifetime of the National Science Foundation's Coastal Ocean Processes program, four experiments were conducted on the US West Coast in the northern California Current System. Although each project had a unique scientific focus, all four addressed the mechanisms causing eastern boundary current systems in general, and the California Current System in particular, to be biologically rich, from phytoplankton to apex predators. Taken together, findings from these projects provide new insights into the canonical view that upwelling systems are simple wind-driven "conveyor belts," bringing cold, nutrient-rich waters to the well-lit surface ocean where biological organisms flourish. We highlight new insights and advances gained from these programs, including recognition that (a) elements other than nitrogen, particularly iron, may limit the base of the food chain, and (b) the source of these nutrients is not solely a result of wind-driven Ekman transport. The importance of retentive features has clearly emerged, whether these are associated with topography, bathymetry, or more transient features such as river plumes. These new insights into the drivers and fate of this high biological productivity should greatly improve current and future generations of ecosystem models and provide a better understanding of the unique physical-biological coupling that makes the California Current System so rich. Close

• 26. [Article] Direct and Indirect Effects of an Invasive Planktonic Predator on Pelagic Food Webs

  The relative importance of top-down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded ...

  Citation × Citation Citation Abstract Copy Title: Direct and Indirect Effects of an Invasive Planktonic Predator on Pelagic Food Webs Author: Strecker, Angela L., Beisner, Beatrix E., Arnott, Shelley E., Paterson, Andrew M., Winter, Jennifer G., Johannsson, Ora E., Yan, Norman D. Year: 2011 The relative importance of top-down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded reference lakes. The non-native invertebrate predator Bythotrephes had significant effects on zooplankton community size structure, rotifers, and phytoplankton taxonomic composition, but no significant effects on crustacean zooplankton taxonomic and functional group composition. Part of the variation in phytoplankton communities was explained by the presence of the invader. Because Bythotrephes is generally known to be a carnivore and to not consume phytoplankton, this effect is likely mediated by the zooplankton community’s response to environmental gradients. Although Bythotrephes appears to indirectly alter phytoplankton composition in invaded lakes, there was no evidence of a trophic cascade, and edible phytoplankton biovolume did not increase in invaded lakes. These complex direct and indirect interactions suggest that effects of invaders may be highly context-dependent, and therefore pose a significant challenge for predicting wider community and ecosystem responses. Title: Direct and Indirect Effects of an Invasive Planktonic Predator on Pelagic Food Webs Author: Strecker, Angela L., Beisner, Beatrix E., Arnott, Shelley E., Paterson, Andrew M., Winter, Jennifer G., Johannsson, Ora E., Yan, Norman D. Year: 2011 The relative importance of top-down invader effects relative to environmental drivers was determined by sampling crustacean zooplankton, rotifer, and phytoplankton communities in a set of invaded and noninvaded reference lakes. The non-native invertebrate predator Bythotrephes had significant effects on zooplankton community size structure, rotifers, and phytoplankton taxonomic composition, but no significant effects on crustacean zooplankton taxonomic and functional group composition. Part of the variation in phytoplankton communities was explained by the presence of the invader. Because Bythotrephes is generally known to be a carnivore and to not consume phytoplankton, this effect is likely mediated by the zooplankton community’s response to environmental gradients. Although Bythotrephes appears to indirectly alter phytoplankton composition in invaded lakes, there was no evidence of a trophic cascade, and edible phytoplankton biovolume did not increase in invaded lakes. These complex direct and indirect interactions suggest that effects of invaders may be highly context-dependent, and therefore pose a significant challenge for predicting wider community and ecosystem responses. Close

• 27. [Article] The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats

  Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation ...

  Citation × Citation Citation Abstract Copy Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Close

• 28. [Article] Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents

  Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal ...

  Citation × Citation Citation Abstract Copy Title: Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents Author: Rutherford, Alexander Fenner Year: 2014 Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood. The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota. Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields. There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source. Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale. Title: Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents Author: Rutherford, Alexander Fenner Year: 2014 Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood. The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota. Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields. There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source. Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale. Close