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Author: Alexander Theodore Neu Publisher: ISBN: Category : Languages : en Pages : 186
Book Description
Ecological communities have been shown to vary in some predictable ways through space, time, and along environmental gradients, suggesting there may be underlying "rules" in ecology which govern these patterns and processes. However, nearly all our knowledge of these trends comes from studies of large eukaryotes such as plants and animals, and we know very little about how these eukaryotic patterns compare to those of bacteria and archaea, the most dominant life forms on the planet. The goal of this dissertation is to determine whether ecological patterns that are evident in plants and animals are also applicable to host-associated microbes. First, I investigated whether these microbes exhibit large-scale spatial trends in diversity and community composition that are concordant with those of their eukaryotic hosts. Specifically, I investigated changes in community composition across a marine biogeographic boundary and changes in diversity along a latitudinal transect. Results showed that microbiome compositions varied significantly between geographic sites, but that the identity of the host species played a greater role than geography in determining community composition. Further, microbes associated with the California mussel, Mytilus californianus, did not show a traditional latitudinal diversity gradient, and latitudinal diversity patterns varied based on microbial group and host body site. Next, I investigated whether host-associated microbial communities vary over time and in response to environmental change in similar ways to their eukaryotic hosts. I found that over an 11-year period, and in response to environmental change, microbial communities of the bean clam, Donax gouldii, significantly differed in composition, but not in richness. Further, I found that microbes did not regularly diverge in concordance with their intertidal gastropod hosts in the ~3.5 million years since the closure of the Isthmus of Panama, though this was dependent on the host taxa and the body site from which the microbes were collected. Finally, I investigated whether current methodologies for determining the core microbiome are guided by ecological and evolutionary principles and identify critical areas for future research. Overall, this dissertation shows that large-scale patterns in host-associated microbial taxa are often context-dependent and distinct from those of their hosts.
Author: Alexander Theodore Neu Publisher: ISBN: Category : Languages : en Pages : 186
Book Description
Ecological communities have been shown to vary in some predictable ways through space, time, and along environmental gradients, suggesting there may be underlying "rules" in ecology which govern these patterns and processes. However, nearly all our knowledge of these trends comes from studies of large eukaryotes such as plants and animals, and we know very little about how these eukaryotic patterns compare to those of bacteria and archaea, the most dominant life forms on the planet. The goal of this dissertation is to determine whether ecological patterns that are evident in plants and animals are also applicable to host-associated microbes. First, I investigated whether these microbes exhibit large-scale spatial trends in diversity and community composition that are concordant with those of their eukaryotic hosts. Specifically, I investigated changes in community composition across a marine biogeographic boundary and changes in diversity along a latitudinal transect. Results showed that microbiome compositions varied significantly between geographic sites, but that the identity of the host species played a greater role than geography in determining community composition. Further, microbes associated with the California mussel, Mytilus californianus, did not show a traditional latitudinal diversity gradient, and latitudinal diversity patterns varied based on microbial group and host body site. Next, I investigated whether host-associated microbial communities vary over time and in response to environmental change in similar ways to their eukaryotic hosts. I found that over an 11-year period, and in response to environmental change, microbial communities of the bean clam, Donax gouldii, significantly differed in composition, but not in richness. Further, I found that microbes did not regularly diverge in concordance with their intertidal gastropod hosts in the ~3.5 million years since the closure of the Isthmus of Panama, though this was dependent on the host taxa and the body site from which the microbes were collected. Finally, I investigated whether current methodologies for determining the core microbiome are guided by ecological and evolutionary principles and identify critical areas for future research. Overall, this dissertation shows that large-scale patterns in host-associated microbial taxa are often context-dependent and distinct from those of their hosts.
Author: China Hanson Publisher: ISBN: 9781267819116 Category : Languages : en Pages : 173
Book Description
Biogeography, the study of species distributions over space and time, provides valuable information on the factors controlling biodiversity. Microorganisms are now widely recognized as exhibiting biogeographic patterns similar to larger organisms. However, the biogeography of viruses has been slower to develop despite their important role in ecosystems. After first proposing a theoretical framework with which to study microbial biogeographic patterns, the goal of this dissertation was to demonstrate whether an ecologically important subset of viruses - cyanophages, or viruses that infect the marine cyanobacterium, Synechococcus - also exhibit such patterns. I isolated cyanophages every month for three years in Southern California, and at one point in time at two additional locations in the coastal U.S.I then taxonomically characterized nearly 4,000 isolates by amplifying and sequencing a cyanophage-specific marker gene in each isolate. To more accurately detect possible spatial patterns, I also characterized a subset of isolates for their host range phenotypes, which provided additional biological variability than could be assessed by the marker gene alone. I found that coastal marine cyanophage communities are both temporally dynamic as well as spatially structured. Within the regional scale of Southern California, these communities were strikingly seasonal - that is, their composition changed in tune with the seasons in an annually recurring manner. I found that this seasonal pattern over three years was primarily related to forecasted UV irradiance, with UV explaining nearly 33% of the temporal variation in cyanophage composition. Moreover, I found that at larger spatial scales, cyanophage community composition was also highly structured in space, both taxonomically and phenotypically. These results provide strong evidence that phages exhibit spatial and temporal biogeographic patterns. Because phages are susceptible to degradation by light, the results further suggest that their distributional patterns may be partially driven by selective environmental factors, namely UV radiation, acting directly on phages; rather than solely being influenced by the presence of susceptible hosts. The library of isolates collected here offers a unique opportunity to test this hypothesis. Overall, this work adds to the growing evidence that all microbes, including phages, exhibit biogeographic patterns that are in large part driven by environmental selection.
Author: Publisher: ISBN: 9780438629073 Category : Languages : en Pages : 171
Book Description
Kelp forest ecosystems are distributed on the rocky reefs of coastal regions worldwide. Kelps (order Laminariales) are a diverse group of brown macroalgae containing numerous species including giant kelp, Macrocystis pyrifera. The giant kelp dominates the kelp forests of southern California, engineering complex three-dimensional habitat which provides foundational shelter, nursery, and nutrients to marine organisms including invertebrates, fish, and marine mammals. While the kelp forests of southern California are well-regarded for their ecological and economic importance, traditional ecological surveys have ignored the most abundant fraction within the ecosystem - microbes. Microbes, including bacteria, archaea, and micro-eukaryotes, are present on all submerged surfaces in marine ecosystems, including microbiomes on macroorganisms. Microbes serve key ecological roles, including cycling of nutrients such as carbon and nitrogen to higher trophic levels within the ecosystem. Host-associated microbes have a symbiotic relationship with the host, providing environmentally-limited nutrients and protection from pathogen invasion in exchange for settlement substrate and host-derived metabolic exudates. Despite the known importance of microbes in marine ecosystems, microbes are absent from classic ecological models describing the top-down and bottom-up regulating forces structuring kelp populations. Thus, for my dissertation I aimed to address the lack of knowledge on the microbial ecology of southern California kelp forests, including the interactions between the predominant macroalgae and the associated microbiomes. In Chapter 1, I established a baseline description of the taxonomic structure and functional potential of microbial communities residing within the Macrocystis pyrifera-dominated kelp forest of Point Loma, CA, and identified sources of variation in microbiome profiles. The Point Loma kelp forest is subject to fluctuations in environmental conditions resulting from seasonality and stratification, which has an influence on kelp forest productivity. However, the potential direct and indirect effects of altered kelp forest environmental conditions on the microbial community structure and function has yet to be described, and as such I aimed to address this for Chapter 1. I sampled microbiomes from both the M. pyrifera biofilm and the adjacent water column seasonally over a three year investigation (2013-2016). I described the microbiomes in great depth using culture-independent whole genome shotgun metagenomics, and assessed the spatial and temporal variability in microbiome composition, function, and diversity. The microbiomes of the kelp and water were distinct in both taxonomic composition and functional potential. Kelp microbiomes remained stable across vertical depth, did not change significantly across season, and were not influenced by biophysical measurements of the surrounding environmental conditions. In contrast, the water-associated microbiomes varied significantly across depth with distinct community profiles above and below the thermocline stratification, showed significant changes across season, and seasonal changes within microbiome structure were strongly correlated with biophysical measurements of kelp forest productivity. Overall, my results showed that while free-living microbiomes were structured by the surrounding environmental conditions, host factors outweighed environmental factors in structuring hostassociated microbiomes. In Chapter 2, I examined the potential shifts in the baseline kelp forest microbiomes resulting from disturbance caused by the spread of an invasive alga, and the potential microbial influence in the alga's invasion strategy. This investigation took place at Santa Catalina Island within the Channel Islands 40 km offshore southern California, throughout the progression of the species invasion (2014-2018). Catalina Island has historically boasted dense populations of the native alga Macrocystis pyrifera, but has undergone disturbance due to the invasion and spread of invasive alga, Sargassum horneri. Invasive species cause significant alterations to ecosystems with both physical and chemical influences which deter and inhibit recovery of native species; however, whether there is a microbial influence in the invasion strategy of alga S. horneri is unknown. First, I described the microbiome of the invasive S. horneri and compared it to the native M. pyrifera, and found the microbiomes of the two macroalgal species to be distinct; specifically, the S. horneri microbiome was enriched in potentially pathogenic Vibrios. Next, I identified the potential for S. horneri presence to induce changes in the surrounding microbiomes. In 2018 as the native alga M. pyrifera was attempting to recover from disturbance, M. pyrifera and S. horneri existed in an interface at some sites. Where the two were in direct contact, I observed evidence of tissue bleaching and deterioration of the native alga, and investigated whether this detriment was a direct result of microbial pathogens. I did not find evidence of S. horneri microbiome inoculation onto the adjacent M. pyrifera; rather, the bleached M. pyrifera showed dysbiosis where the microbiome was lost completely compared to healthy M. pyrifera individuals nearby. However, I did find evidence of S. horneri microbiome inoculation onto the benthic substrate directly below the invasive alga, which resulted in an enrichment of Vibrios compared to the microbiome from benthic substrate beneath native M. pyrifera, and the enrichment of Vibrios on the benthic substrate occurred concurrently with a lack of native algal recovery at those locations. My findings suggest that the invasive species S. horneri has altered the baseline microbiome structure in the kelp forest, and the induced microbial changes may have an ongoing influence on the native species as they attempt to recover from disturbance. In Chapter 3, I investigated the microbial influence on a key stage of recruitment of the giant kelp, Macrocystis pyrifera. Macroalgae, including kelps, rely on recruitment processes to maintain adult populations and recover from disturbances. During kelp recruitment processes, microscopic propagules are released into the kelp forest water column where they are suspended until settlement onto the benthic substrate. Microscopic propagules are highly susceptible to abiotic conditions including UV irradiation, temperature, and nutrients, and biotic conditions including grazing. However, the influence of microbes on kelp propagule success has not been widely studied. Given that microbes are abundant in marine ecosystems (106 cells per ml of seawater) and are present on every submerged surface, microbes are likely to interact with kelp propagules during recruitment processes. For this investigation I reared M. pyrifera microscopic propagules in laboratory microcosms and exposed them to environmentally-sourced microbial communities within treatments. First, I investigated whether the presence of microbes influenced M. pyrifera propagules, and found that removing microbes in seawater increased propagule recruitment success. I then assessed the propagule success when exposed to a nearshore (Point Loma, CA) microbial community compared to an offshore (Santa Catalina Island, CA) microbial community, at multiple levels of microbial abundance. At the time the experiment was conducted, Catalina Island fostered a pristine kelp forest with lower anthropogenic influence compared to the nearshore Point Loma kelp forest. The nearshore (Point Loma) microbial community treatments yielded similar results to the first experiment, where removing microbes resulted in higher kelp propagule success. In contrast, kelp propagules exposed to offshore (Catalina) microbes had the greatest success when microbes were present at intermediate abundances, rather than removed completely. In both treatments, a microbialization of the seawater resulted in observed morphological detriment to kelp propagules. This study suggests that kelp forest microbes have an influence on a key stage of kelp recruitment, and the composition of the microbial community is important in recruitment success. Collectively, my dissertation shows that microbes influence kelp forest ecosystem dynamics and must be incorporated into future population and community models for a more holistic description of the ecosystem.
Author: Jackie Zorz Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Bacteria are important members of every marine ecosystem and the composition of their communities has implications for global biogeochemical cycling. The Northwest Atlantic Ocean is an ecologically and economically significant region that exhibits wide ranges in physiochemical parameters that vary seasonally. In this thesis the bacterial community structure of two areas within the Northwest Atlantic Ocean, the Scotian Shelf and the Bedford Basin, were analyzed using 16S rRNA gene sequencing. The Scotian Shelf was analyzed spatially over two time points. Environmental parameters of the region, seasonality, and depth were found to heavily influence community structure. In the Bedford Basin, a weekly bacterial time series was established and the first year of data from the deepest samples were analyzed. The deep basin exhibited seasonal patterns with respect to community similarity, diversity, and composition. Overall, these datasets provide novel information regarding community composition and drivers of community shifts in this region.
Author: Jessica A. Bryant Publisher: ISBN: Category : Languages : en Pages : 233
Book Description
Microorganisms support all life in the oceans and are fundamental to maintaining a habitable biosphere on Earth. However an understanding of their taxonomic and functional distributions across space and time are just beginning to emerge and numerous niches within the marine environment are still awaiting exploration. The motivation for this thesis is to improve our understanding of distributions of microbes and their metabolic potential at Station ALOHA, a long-term study site representative of the North Pacific Subtropical Gyre (NPSG). We observed changes in diversity and community composition at Station ALOHA across time, ocean depth and on plastic debris, a new anthropogenically derived niche in the NPSG. Despite surface waters only experiencing mild seasonal variation in the abiotic environment, using near monthly picoplankton samples collected across a 2-year period at 25m depth, we observed that microbial community composition correlated with solar irradiance, thereby demonstrating seasonal trends. Ocean surface microbes are known to differ fundamentally from those found in the ocean's interior, yet the nature of the transitions from shallow to deep surface water communities is not well understood. Using a high resolution depth series across twelve time points, we observed that microbial communities partitioned into four groups that consisted of all samples above the deep chlorophyll maximum (DCM), 125m samples below the DCM, all 200 m samples and all 500, 770 and 1000m samples. Our data also revealed a sharp discontinuity in genomic traits including GC%, genome size and proteome elemental composition spanning the DCM, suggesting that nitrogen limitation was key to shaping this sharp genomic transition zone across disparate clades. In contrast, we observed that plastic debris in the NPSG forms a habitat for complex microbial assemblages that have organisms, lifestyles and metabolic pathways that are distinct and potentially less nutrient limited than picoplankton in the surrounding water column. Taken together this work helps expand our understanding of spatial and temporal distributions of microorganisms at Station ALOHA and can help direct future microbial oceanography surveys, highlighting new directions for future research.
Author: Liat Shenhav Publisher: ISBN: Category : Languages : en Pages : 102
Book Description
Microbial communities can undergo rapid changes, that can both cause and indicate host disease, rendering longitudinal microbiome studies key for understanding microbiome-associated disorders. However, most standard statistical methods, based on random samples, are not applicable for addressing the methodological and statistical challenges associated with repeated, structured observations of a complex ecosystem. Therefore, to elucidate how and why our microbiome varies in time, and whether these trajectories are consistent across humans, we developed new methods for modeling the temporal and spatial dynamics of microbial communities. We developed a method to identify 'time-dependent' microbes (Shenhav et al., PLoS Computational Biology 2019) and showed that their temporal patterns differentiate between the developing microbial communities of infants and those of adults. We also developed models to deconvolute the dynamics of microbial community formation. Using these methods, we found significant differences between vaginally- and cesarean-delivered infants in terms of initial colonization and succession of their gut microbial community (Shenhav et al., Nature Methods 2019) as well as the trajectories of these communities in the first years of life (Martino*, Shenhav* et al., Nature Biotechnology). These models, designed to identify and predict time-dependent patterns, will help researchers better understand the temporal nature of the human microbiome from the time of its formation at birth and throughout life.
Author: Claudia Maturana Martínez Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Southern high latitudes marine ecosystems (HLME) are highly sensitive to climate change, impacting physical, chemical, and biological processes, however, their prominent role in climate modulation and water masses circulation, contrast with the relatively low number of studies on their functioning. Relatively few studies on bacterioplankton community structure have been reported for southern Chilean Patagonia and for the Southern Ocean (SO) on a large scale, and none have targeted the active fraction of the bacterioplankton community. We used 16S rRNA sequencing to analyze and describe the community structure of the active bacterioplankton communities in southern HLME. The main objective of this thesis was to characterize de diversity and abundance of bacterioplankton communities along environmental and geographical gradients in southern HLME. First, we investigated whether nearby fjords of the southern Chilean Patagonia, with similar climate and location but different freshwater inflows, had different communities. Second, we investigated interannual changes experienced by the bacterioplankton community of the Yendegaia fjord. Third, we examined the large-scale spatial structure of the bacterioplankton community along a transect across the Pacific sector of the SO. Ours results show that southern polar bacterioplanktonic communities are structured according to physical, chemical, and biological parameters characteristic of the area. In addition, we also demonstrated that changes in environmental, spatial, and temporal parameters affect the structure of bacterioplanktonic communities. Thus, highlighting the importance of microbial ecology studies in areas sensitive to global climate change such as southern HLME.
Author: Erin Coleen Herder Publisher: ISBN: Category : Languages : en Pages :
Book Description
Benthic fauna are a crucial part of the marine ecosystem providing many ecosystem services. Unfortunately, Arctic coastal marine environments are under tremendous pressure from changing climate conditions and it is becoming increasingly important to understand community changes occurring in these environments. Long-term ecological studies in the Canadian Arctic are rare, however, Frobisher Bay provides a unique opportunity to study long-term change in the marine benthos because historical benthic community datasets exist for this region. We focused on the molluscs as indicators of long-term change by comparing community temporal and spatial changes between 1967-1976 and 2016. Significant changes in community composition were observed between these two time periods and shifts in functional trait characteristics were also observed. These changes coincided with long-term environmental change in the region. Our results highlight the need for long-term systematic sampling which is fundamental to our understanding of Arctic marine ecosystems and for identifying long-term ecosystem change.
Author: Alexander Theodore Neu
Author: Alexander Theodore Neu
Author: China Hanson
Author: Mireia Mestre Martín
Author: 
Author: Jackie Zorz
Author: Jessica A. Bryant
Author: Liat Shenhav
Author: Claudia Maturana Martínez
Author: Zachary Adam Kerrigan
Author: Erin Coleen Herder