Download or read book Spatiotemporal Variability of Bacterial Communities in Marine and Freshwater Ecosystems of California written by Melissa Lynne Partyka and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Microorganisms are fundamental members of aquatic and marine ecosystems capable of affecting the macroecology of these systems by serving as the foundation of complex food chains, biogeochemical processes, and disease dynamics. Though recognized as foundational, scientists continue to struggle to apply basic ecological concepts of like community, spatiotemporal variability, gradients, and disturbance regimes to microorganisms in meaningful ways due to the vast differences in scale between macrobial sampling designs and microbial existence. However, until new ecological concepts have been generated for understanding microbial populations, we must continue to sample varied habitats at multiple spatial and temporal scales with the hope of capturing both unique and common characteristics of these communities that will allow us to predict their responses to a changing environment. The ability to predict microbial behavior has particular importance for human health; for that reason, this research focused on bacterial members of the greater microbial community that have been associated with illness and disease in humans utilizing both culture and molecular techniques followed by multiple-regression analyses. In Chapter 1, the intention was to examine bacterial populations at broad spatial and temporal scales within 6 freshwater reservoirs in the foothills of the Sierra Nevada Mountains. We sought to understand whether microbial water quality within reservoirs was driven by upstream conditions and subsequently predictive of downstream outcomes. Specifically, this research sought to understand the variability of fecal indicator bacteria (Escherichia coli and fecal coliforms) and pathogens (E. coli O157:H7, Non-O157 shiga toxin-producing E. coli and Salmonella) along both horizontal and vertical profiles within California reservoirs as it related to upstream river sources and downstream irrigation water supplies. Continued monitoring and modeling of both bacterial indicators and enteric pathogens are critical to our ability to estimate the risk of surface irrigation water supplies and make appropriate management decisions. In this study, the extreme variability in microbial populations across both space and time made successful predictions largely impossible and underlined the extreme importance of sampling these dynamic communities at scales where their behavior can be observed, particularly where human health may be impacted. I sought to further refine the scale of examination in Chapter 2 which moved from the freshwater of the Sierras to the marine habits of coastal California. In these systems the bacterial genus Vibrio is both endemic and occasionally pathogenic. Thus, we strove for greater understanding of how four members of Vibrio, V. alginolyticus, V. parahaemolyticus, V. cholerae, and V. vulnificus, referred to as “the big four” of global human illness, interact with their environment and respond to changing conditions. We examined finer-scale spatial and temporal variability of the “big four” in one bay of Northern California, Tomales Bay, highly popular with tourists and known as a premier region for shellfish production. As with Chapter 1, bacterial populations were highly dynamic in both space and time. However, these data were more easily modeled by capturing weekly, daily, and occasionally hourly changes to the environment during seasonal storms and sub-meter differences in sediment characteristics during acute tidal cycles. As with the previous chapter, pathogen prevalence or concentration in water, sediment, or shellfish did not correlate (p>0.1) with concentrations of fecal indicator bacteria, suggesting the need for revisions to the current regulatory monitoring efforts. For the third and final chapter I chose to manipulate the environment experienced by microorganisms in a manner that is common to intertidal sand and mudflats along most coastlines, recreational clamming activity. The impact of physical disturbance by clamming activity on microbial communities of intertidal sand flats has received relatively little attention, though the state of California estimates that 20-40K clams are taken from California bays annually, suggesting many people are performing the behavior and a large volume of sediment is being moved. I examined these impacts through a replicated cross-factorial longitudinal experiment on two emergent islands at the mouth of Tomales Bay. By following these exact sites through time we were able to reveal a wealth diversity within a single species of Vibrio, V. alginolyticus, and examine how that diversity changed through recurring tidal cycles. Further, while it was apparent that our targeted species were not significantly (p>0.05) impacted by our experimental disturbances, there were clear differences in the responses of indicator bacteria (fecal coliforms and enterococci) and vibrios by location and across time. These data illustrate that a great deal remains to be discovered about human influence over microbial communities in coastal systems, opening the door for further refinement in study designs. Taken as a whole, this series of studies has helped to further highlight the need of studies that examine microbial populations not only at scales that are relevant to the organism under investigation, but to the humans that may encounter them and fall ill. I sought to provide suggestion to aid the regulatory community in modifying current guidelines in the interest of public health and to encourage the ecological community to continue to evaluate the impact of scale on our ability to make inferences and gain understanding of these unseen and complex microbial communities.

Download or read book Mechanisms Shaping Spatial and Temporal Variations in Marine Microbial Niches written by Alaina Noel Smith and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine microbial communities are crucial to ecosystem function and productivity, but their spatial and temporal distributions are highly variable. Microbes exhibit unique environmental preferences, called niches, that drive observable distribution patterns across space and time. However, it's not well understood how much and at what scales external biotic and abiotic influences, such as competition and dispersal affect microbial distributions. It's expected that microbial distributions are going to change as a result of anthropogenic climate changes, such as increase sea surface temperatures and increased water column stratification. However, current predictive models rely on some assumptions about niches, such as niche stability over time, that have not been broadly tested or observed. This thesis aims to elucidate the mechanisms that shape spatial and temporal variability in marine microbial niches across three distinct chapters. The first chapter asks how the laboratory expectations and observations of niches in the field compare for a globally important genus of cyanobacteria Prochlorococcus. The second chapter asks how temporal variability and dispersal shape microbial realized niches across a latitudinal gradient by utilizing a simplified metacommunity model. The final chapter asks if and how microbial niches have adapted to spatial and temporal environmental change in the California Current Ecosystem. Understanding the mechanisms behind microbial distributions can influence our mitigation and management of broader ecosystem changes such as food web dynamics and carbon export.

Download or read book Ecosystems of California written by Harold Mooney and published by Univ of California Press. This book was released on 2016-01-19 with total page 1008 pages. Available in PDF, EPUB and Kindle. Book excerpt: This long-anticipated reference and sourcebook for CaliforniaÕs remarkable ecological abundance provides an integrated assessment of each major ecosystem typeÑits distribution, structure, function, and management. A comprehensive synthesis of our knowledge about this biologically diverse state, Ecosystems of California covers the state from oceans to mountaintops using multiple lenses: past and present, flora and fauna, aquatic and terrestrial, natural and managed. Each chapter evaluates natural processes for a specific ecosystem, describes drivers of change, and discusses how that ecosystem may be altered in the future. This book also explores the drivers of CaliforniaÕs ecological patterns and the history of the stateÕs various ecosystems, outlining how the challenges of climate change and invasive species and opportunities for regulation and stewardship could potentially affect the stateÕs ecosystems. The text explicitly incorporates both human impacts and conservation and restoration efforts and shows how ecosystems support human well-being. Edited by two esteemed ecosystem ecologists and with overviews by leading experts on each ecosystem, this definitive work will be indispensable for natural resource management and conservation professionals as well as for undergraduate or graduate students of CaliforniaÕs environment and curious naturalists.

Download or read book Microbial Ecology of the Oceans written by Josep M. Gasol and published by John Wiley & Sons. This book was released on 2018-01-31 with total page 663 pages. Available in PDF, EPUB and Kindle. Book excerpt: The newly revised and updated third edition of the bestselling book on microbial ecology in the oceans The third edition of Microbial Ecology of the Oceans features new topics, as well as different approaches to subjects dealt with in previous editions. The book starts out with a general introduction to the changes in the field, as well as looking at the prospects for the coming years. Chapters cover ecology, diversity, and function of microbes, and of microbial genes in the ocean. The biology and ecology of some model organisms, and how we can model the whole of the marine microbes, are dealt with, and some of the trophic roles that have changed in the last years are discussed. Finally, the role of microbes in the oceanic P cycle are presented. Microbial Ecology of the Oceans, Third Edition offers chapters on The Evolution of Microbial Ecology of the Ocean; Marine Microbial Diversity as Seen by High Throughput Sequencing; Ecological Significance of Microbial Trophic Mixing in the Oligotrophic Ocean; Metatranscritomics and Metaproteomics; Advances in Microbial Ecology from Model Marine Bacteria; Marine Microbes and Nonliving Organic Matter; Microbial Ecology and Biogeochemistry of Oxygen-Deficient Water Columns; The Ocean’s Microscale; Ecological Genomics of Marine Viruses; Microbial Physiological Ecology of The Marine Phosphorus Cycle; Phytoplankton Functional Types; and more. A new and updated edition of a key book in aquatic microbial ecology Includes widely used methodological approaches Fully describes the structure of the microbial ecosystem, discussing in particular the sources of carbon for microbial growth Offers theoretical interpretations of subtropical plankton biogeography Microbial Ecology of the Oceans is an ideal text for advanced undergraduates, beginning graduate students, and colleagues from other fields wishing to learn about microbes and the processes they mediate in marine systems.

Download or read book The Ocean and Cryosphere in a Changing Climate written by Intergovernmental Panel on Climate Change (IPCC) and published by Cambridge University Press. This book was released on 2022-04-30 with total page 755 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Intergovernmental Panel on Climate Change (IPCC) is the leading international body for assessing the science related to climate change. It provides policymakers with regular assessments of the scientific basis of human-induced climate change, its impacts and future risks, and options for adaptation and mitigation. This IPCC Special Report on the Ocean and Cryosphere in a Changing Climate is the most comprehensive and up-to-date assessment of the observed and projected changes to the ocean and cryosphere and their associated impacts and risks, with a focus on resilience, risk management response options, and adaptation measures, considering both their potential and limitations. It brings together knowledge on physical and biogeochemical changes, the interplay with ecosystem changes, and the implications for human communities. It serves policymakers, decision makers, stakeholders, and all interested parties with unbiased, up-to-date, policy-relevant information. This title is also available as Open Access on Cambridge Core.

Download or read book Microbial Ecology of the California Current Ecosystem written by Sara Renee Rivera and published by . This book was released on 2020 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: The southern CCS (sCCS), part of the California Current Ecosystem (CCE), is home to the California Cooperative Oceanic Fisheries Investigation (CalCOFI) survey program and the California Current Ecosystem Long Term Ecological Research (CCE-LTER) program. CalCOFI, begun in 1949, was designed as a survey program, sampling the same stations each quarter; whereas, the CCE-LTER program was designed to study interactions between various physical perturbations and ecosystem processes using Lagrangian cycles. The goal of this thesis was to examine microbial dynamics within these two programs and present a model for carbon fluxes into and out of the bacterial compartment. Chapter 1 'binned' findings from CCE-LTER cruises into the relevant CalCOFI climatology and hydrography allowing the mechanistic studies into microbial dynamics enabled by the CCE-LTER program to be interpreted in the context of long-term observations. For example, the underlying mechanism of the enhanced microbial loop hypothesis, originally based on CalCOFI data, was supported using bacterial production data from CCE-LTER cycles in 2017. Additionally, the picoplankton community responded to broad climate variability with increased abundances and shifts in spatial distribution following a switch to the positive phase of the Pacific Decadal Oscillation at the end of 2013. Using the binned oceanic regions designated in Chapter 1, Chapter 2 showed that including the bacterial component in the food web strengthened previous conclusions that the nearshore is net autotrophic, providing excess carbon available to be laterally exported to the offshore. Examination of the westward propagating 2017 Morro Bay filament supported the hypothesis that lateral transport of organic material could support offshore, net heterotrophic communities. Bacterial production was strongly correlated to organic carbon pools, as observed in Chapter 3. Bottom-up control of bacterial production across the CCE was comparable to global trends, but did not scale with net primary production, perhaps due to enhanced grazing nearshore. Furthermore, the observed temperature control of bacterial production was a proxy for the role of upwelling and substrate production, not metabolic rate. Strong bottom-up controls and weak temperature controls observed during the 2014 warm anomaly suggest future warming and stratification within the sCCS could be rapidly experienced by the bacterial community.

Download or read book Applied Environmental Genomics written by Oliver F... Berry and published by CSIRO PUBLISHING. This book was released on 2023-12 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA is the essence of life and the original ‘big data’. New technologies are allowing scientists to access and make sense of this information like never before, and they are using it to solve the world’s greatest environmental challenges. Applied Environmental Genomics synthesises the latest and most exciting uses of genomic technologies for environmental science and management. With an emphasis on diversity of applications and real-world demonstrations, leading researchers have contributed detailed chapters on innovative approaches to obtaining critical management-relevant information about the natural world. These chapters are complemented by perspective sections written by environmental managers who describe their experiences using genomics to support evidence-based decisions. Ideal for students, researchers and professionals working in natural resource management and policy, Applied Environmental Genomics is a comprehensive introduction to a fast-moving field that is transforming the practice of environmental management, with profound relevance to industry, government and the public.

Download or read book The Prokaryotes written by Edward F. DeLong and published by Springer. This book was released on 2014-10-13 with total page 567 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Prokaryotes is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters. Different from other resources, this new Springer product includes not only taxonomy, but also prokaryotic biology and technology of taxa in a broad context. Technological aspects highlight the usefulness of prokaryotes in processes and products, including biocontrol agents and as genetics tools. The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology; Part 2 describes the known properties of specific taxonomic groups. Two completely new sections have been added to Part 1: bacterial communities and human bacteriology. The bacterial communities section reflects the growing realization that studies on pure cultures of bacteria have led to an incomplete picture of the microbial world for two fundamental reasons: the vast majority of bacteria in soil, water and associated with biological tissues are currently not culturable, and that an understanding of microbial ecology requires knowledge on how different bacterial species interact with each other in their natural environment. The new section on human microbiology deals with bacteria associated with healthy humans and bacterial pathogenesis. Each of the major human diseases caused by bacteria is reviewed, from identifying the pathogens by classical clinical and non-culturing techniques to the biochemical mechanisms of the disease process. The 4th edition of The Prokaryotes is the most complete resource on the biology of prokaryotes. The following volumes are published consecutively within the 4th Edition: Prokaryotic Biology and Symbiotic Associations Prokaryotic Communities and Ecophysiology Prokaryotic Physiology and Biochemistry Applied Bacteriology and Biotechnology Human Microbiology Actinobacteria Firmicutes Alphaproteobacteria and Betaproteobacteria Gammaproteobacteria Deltaproteobacteria and Epsilonproteobacteria Other Major Lineages of Bacteria and the Archaea

Download or read book Freshwater Microbiology written by Suhaib A. Bandh and published by Academic Press. This book was released on 2019-08-01 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: Freshwater Microbiology: Perspectives of Bacterial Dynamics in Lake Ecosystems provides a comprehensive and systematic analysis of microbial ecology in lakes. It offers basic information on how well the bacterial community composition varies along the spatio-temporal and trophic gradients along with the evaluation of the bioindicator species of bacteria so as to act as a key to predict the trophic status of lake ecosystems. The book helps to identify the factors of potential importance in structuring the bacterial communities in lakes as it delves into the dynamics and diversity of bacterial community composition in relation to various water quality parameters. It helps to identify the possibility of bioremediation plans and devising future policy decisions, with better conservation and management practices. - Provides a comprehensive and systematic analysis of microbial ecology - Helps to identify the factors of potential importance in structuring the bacterial community composition - Gives insight into the bacterial diversity of freshwater lake ecosystems along with their industrial potential - Caters to the needs and aspirations of students and professional researchers

Download or read book Multivariate Analysis of Ecological Data using CANOCO 5 written by Petr Šmilauer and published by Cambridge University Press. This book was released on 2014-04-17 with total page 375 pages. Available in PDF, EPUB and Kindle. Book excerpt: An accessible introduction to the theory and practice of multivariate analysis for graduates, researchers and professionals dealing with ecological problems.

Download or read book Aeolian Dust and Dust Deposits written by Kenneth Pye and published by Elsevier. This book was released on 2015-07-14 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Aeolian Dust and Dust Deposits explores the entrainment, dispersion, and deposition of aeolian dust and dust deposits, with emphasis on transport and deposition of dust derived by deflation of surface sediments and soils. Topics covered range from the mechanisms of fine-particle formation to dust sources, sinks, and rates of deposition. Dust-transporting wind systems are also discussed, along with the grain size, mineralogy, and chemical composition of aeolian dust. Comprised of nine chapters, this book begins with an overview of the general nature and significance of windborne dust as well as the importance of aeolian dust and loess. The next chapter deals with the mechanisms underlying the formation of fine particles, including glacial grinding, frost and salt weathering, and fluvial comminution. The reader is then introduced to dust entrainment, transport, and deposition, together with dust sources, sinks, and rates of deposition. Subsequent chapters focus on the implications of dust deflation, transport, and deposition; dust deposition in the oceans; and loess distribution and the thickness and morphology of loess deposits. This monograph is written primarily for research workers and advanced students in sedimentology, geomorphology, and Quaternary studies, but is also likely to be of value to soil scientists, meteorologists, planetary geologists, engineers, and others concerned with environmental management.

Download or read book Microbes Among Marine Giants written by and published by . This book was released on 2018 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Encyclopedia of Metagenomics written by Karen E. Nelson and published by Springer. This book was released on 2015-02-18 with total page 1528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Download or read book Microbiology of the Rapidly Changing Polar Environments written by Julie Dinasquet and published by Frontiers Media SA. This book was released on 2018-07-05 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine and freshwater polar environments are characterized by intense physical forces and strong seasonal variations. The persistent cold and sometimes inhospitable conditions create unique ecosystems and habitats for microbial life. Polar microbial communities are diverse productive assemblages, which drive biogeochemical cycles and support higher food-webs across the Arctic and over much of the Antarctic. Recent studies on the biogeography of microbial species have revealed phylogenetically diverse polar ecotypes, suggesting adaptation to seasonal darkness, sea-ice coverage and high summer irradiance. Because of the diversity of habitats related to atmospheric and oceanic circulation, and the formation and melting of ice, high latitude oceans and lakes are ideal environments to investigate composition and functionality of microbial communities. In addition, polar regions are responding more dramatically to climate change compared to temperate environments and there is an urgent need to identify sensitive indicators of ecosystem history, that may be sentinels for change or adaptation. For instance, Antarctic lakes provide useful model systems to study microbial evolution and climate history. Hence, it becomes essential and timely to better understand factors controlling the microbes, and how, in turn, they may affect the functioning of these fragile ecosystems. Polar microbiology is an expanding field of research with exciting possibilities to provide new insights into microbial ecology and evolution. With this Research Topic we seek to bring together polar microbiologists studying different aquatic systems and components of the microbial food web, to stimulate discussion and reflect on these sensitive environments in a changing world perspective.

Download or read book A Comparative Study of the Bacterial Communities in California Vernal Pools written by Dana Lynn Carper and published by . This book was released on 2013 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbes usually provide important functions as the basal trophic level of ecosystems. Their high reproduction and dispersal capabilities can result in their ubiquity. The "everything is everywhere" hypothesis of bacterial biogeography has been challenged recently by an indication that abiotic factors determine bacterial communities. Vernal pools are insulated environments, which can function similar to islands in regard to the movement of organisms. An alternative hypothesis is that vernal pools in close proximity will have increased movement of organisms from one to the other, while pools that are further away would have less flow of organisms resulting in closer pools supporting similar bacterial communities. California vernal pool communities (primarily plants) have been researched at the local and landscape level but little to no characterization of the microbial community has been done. For this environment it is hypothesized that there will be a difference in the bacterial communities in different California vernal pool ecosystems (CVPE) and that the difference will be driven by location or abiotic factors. Six vernal pools from three different sites were used to evaluate whether location or abiotic factors drive bacterial community structure. Two vernal pools were sampled from each of these three locations; Mather Field Air Force Base, Travis Air Force Base and Beale Air Force Base. Turbidity, pH, phosphates and conductivity were used as abiotic factors. All of the bacterial analysis was carried out using community analysis techniques including; community level physiological profiles, terminal restriction fragment length polymorphism and next generation sequencing. Bacterial cells in each sample were enumerated using fluorescent staining and flow cytometry. Biolog EcoPlate(TM) were used to assess differences in metabolism for the communities. Terminal restriction fragment length polymorphism (t-RFLP) and next generation sequencing (NGS) were used to evaluate bacterial community diversity. Water samples contained between 4x107 and 6x107 cells per ml of water. Clustering analysis using the Biolog EcoPlate(TM) data showed two distinct groups: one contained Travis2, and both Beale pools and the other containing Travis1 and both Mather pools. Principal component analysis (PCA) was conducted showing the same grouping. Axis 1 showed a moderate negative correlation with phosphates (r = -0.473, r2 = 0.223, tau = -0.200) and axis two showed strong negative correlations with phosphates (r= -0.760, r2 = 0.577, tau= -0.333) and pH (r = -0795, r2= 0.632, tau= -0.733). t-RFLP showed differences dependent on the enzyme used, with all enzymes showing low values of the Bray-Curtis index of similarity. The highest value produced was from using the restriction enzyme RsaI between Travis1 and Travis2 (0.37). NGS showed six main classes of bacteria found in each pool, although relative abundance of each differed between pools: Spartobacteria, Verrucomicrobiae, Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Sphingobacteria. All are common freshwater bacteria, which generally function in degradation of organic matter. The Bray-Curtis Index of similarity was higher using NGS data, with the highest value being 0.89 between Travis1 and Beale2. A PCA was conducted using NGS data also showing correlations with pH, phosphates and turbidity. UniFrac Unweighted Pair Group Method with Arithmetic Mean (UPGMA), resulted in two strongly supported groups one containing the Travis pools and the other containing the Beale and Mather pools. This indicates that an evolutionary significant branch was found in the Travis pools, which was not located in the rest of the pools. All of this data together supports the idea that there are differences in the bacterial communities in CVPE and that the data supports that abiotic factors are driving those differences. Further research will be needed to understand any biogeographical patterns, since only a few pool exhibited biogeographical influences.

Download or read book Selected Water Resources Abstracts written by and published by . This book was released on 1990 with total page 972 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Biodiversity Conservation and Ecological Function Restoration in Freshwater Ecosystems written by Min Zhang and published by Frontiers Media SA. This book was released on 2023-03-13 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: