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Author: Patricia Quynh-Giao Tran
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Microbial communities are made up of microscopic organisms: viruses, bacteria, archaea, eukaryotes, and fungi. Their ability to exist under various and sometimes extreme conditions allows them to thrive in all corners of the environment. Aquatic environments cover 70% of the earth's surface and much of it is undergoing drastic human-impacted change. Rises in atmospheric temperature are leading to an increase in surface water temperatures, which leads to a cascade of ecological impacts, including oxygen depletion through physical and biological means. In this dissertation, I demonstrate how microbial communities, particularly bacteria, archaea, and phages (viruses that can impact prokaryotes) impact biogeochemical cycling in anoxic lakes. Using holistic approaches that cover both cultivation-dependent and independent methods, I aim to expand the way we approach studying microbial communities by leveraging interdisciplinary strengths to demonstrate that microbes and phages are interacting members that are highly dynamic in time and space. In Chapter 1 (Introduction), I summarize the role of freshwater lakes in biogeochemical cycling by focusing on the transformations that occur in the water column. For context, I compare and contrast some of the physical features of Lake Tanganyika and Lake Mendota, the two study sites in this work. I then give a broad summary of what is known about microbial and viral function in anoxic lakes. Together, these form the rationale for the next chapters. In Chapter 2, I used physiological and genomic evidence to characterize bacteria that were able to produce hydrogen sulfide under oxic conditions, a process typically associated with dissimilatory sulfate reduction which occurs under anoxic conditions. This work demonstrates and expands the spatiotemporal scope of hydrogen sulfide sources and sinks in the environment. In Chapter 3, I used genome-resolved metagenomics to characterize the potential contribution of bacteria and archaea in Lake Tanganyika, a permanently anoxic lake that happens to be one of the world's deepest and oldest lakes. This revealed that the anoxic hypolimnion of Lake Tanganyika had an extremely high proportion of Archaea, and endemic microorganisms, compared to other freshwater lakes worldwide, giving insight into the interplay between long-term anoxia and evolution. In Chapter 4, I provide a commentary that argues for a holistic way to study biogeochemical cycling: from an organismal and methodological perspective. In Chapter 5, I apply this holistic framework to assess the impact and interactions between phage and prokaryotes on biogeochemical cycling in a seasonally anoxic freshwater lake. We found that the bacterial community was sensitive to deoxygenation but the viral community was not. A broad range of bacterial taxa were infected by phages, but phages were highly specific. Phage-impacted bacteria were active in methane, sulfur, and nitrogen metabolism. Finally, time-series phage activity data showed the dynamic impact of phage-host interactions for nutrient cycling. Overall, the knowledge and framework generated in these studies improves our understanding of complex multi-kingdom species interactions and their associations with microbiology, ecology, and biogeochemistry in anoxic environments.
Author: Patricia Quynh-Giao Tran
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Microbial communities are made up of microscopic organisms: viruses, bacteria, archaea, eukaryotes, and fungi. Their ability to exist under various and sometimes extreme conditions allows them to thrive in all corners of the environment. Aquatic environments cover 70% of the earth's surface and much of it is undergoing drastic human-impacted change. Rises in atmospheric temperature are leading to an increase in surface water temperatures, which leads to a cascade of ecological impacts, including oxygen depletion through physical and biological means. In this dissertation, I demonstrate how microbial communities, particularly bacteria, archaea, and phages (viruses that can impact prokaryotes) impact biogeochemical cycling in anoxic lakes. Using holistic approaches that cover both cultivation-dependent and independent methods, I aim to expand the way we approach studying microbial communities by leveraging interdisciplinary strengths to demonstrate that microbes and phages are interacting members that are highly dynamic in time and space. In Chapter 1 (Introduction), I summarize the role of freshwater lakes in biogeochemical cycling by focusing on the transformations that occur in the water column. For context, I compare and contrast some of the physical features of Lake Tanganyika and Lake Mendota, the two study sites in this work. I then give a broad summary of what is known about microbial and viral function in anoxic lakes. Together, these form the rationale for the next chapters. In Chapter 2, I used physiological and genomic evidence to characterize bacteria that were able to produce hydrogen sulfide under oxic conditions, a process typically associated with dissimilatory sulfate reduction which occurs under anoxic conditions. This work demonstrates and expands the spatiotemporal scope of hydrogen sulfide sources and sinks in the environment. In Chapter 3, I used genome-resolved metagenomics to characterize the potential contribution of bacteria and archaea in Lake Tanganyika, a permanently anoxic lake that happens to be one of the world's deepest and oldest lakes. This revealed that the anoxic hypolimnion of Lake Tanganyika had an extremely high proportion of Archaea, and endemic microorganisms, compared to other freshwater lakes worldwide, giving insight into the interplay between long-term anoxia and evolution. In Chapter 4, I provide a commentary that argues for a holistic way to study biogeochemical cycling: from an organismal and methodological perspective. In Chapter 5, I apply this holistic framework to assess the impact and interactions between phage and prokaryotes on biogeochemical cycling in a seasonally anoxic freshwater lake. We found that the bacterial community was sensitive to deoxygenation but the viral community was not. A broad range of bacterial taxa were infected by phages, but phages were highly specific. Phage-impacted bacteria were active in methane, sulfur, and nitrogen metabolism. Finally, time-series phage activity data showed the dynamic impact of phage-host interactions for nutrient cycling. Overall, the knowledge and framework generated in these studies improves our understanding of complex multi-kingdom species interactions and their associations with microbiology, ecology, and biogeochemistry in anoxic environments.
Author: United States. Environmental Protection Agency. Office of Water Program Operations
Publisher:
ISBN:
Category : Biochemical cycles
Languages : en
Pages : 264
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Author: H.W. PAERL
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: David L. Kirchman
Publisher: OUP Oxford
ISBN: 0191624225
Category : Science
Languages : en
Pages : 597
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Book Description
Microbial ecology is the study of interactions among microbes in natural environments and their roles in biogeochemical cycles, food web dynamics, and the evolution of life. Microbes are the most numerous organisms in the biosphere and mediate many critical reactions in elemental cycles and biogeochemical reactions. Because microbes are essential players in the carbon cycle and related processes, microbial ecology is a vital science for understanding the role of the biosphere in global warming and the response of natural ecosystems to climate change. This novel textbook discusses the major processes carried out by viruses, bacteria, fungi, protozoa and other protists - the microbes - in freshwater, marine, and terrestrial ecosystems. It focuses on biogeochemical processes, starting with primary production and the initial fixation of carbon into cellular biomass, before exploring how that carbon is degraded in both oxygen-rich (oxic) and oxygen-deficient (anoxic) environments. These biogeochemical processes are affected by ecological interactions, including competition for limiting nutrients, viral lysis, and predation by various protists in soils and aquatic habitats. The book neatly connects processes occurring at the micron scale to events happening at the global scale, including the carbon cycle and its connection to climate change issues. A final chapter is devoted to symbiosis and other relationships between microbes and larger organisms. Microbes have huge impacts not only on biogeochemical cycles, but also on the ecology and evolution of more complex forms of life, including Homo sapiens..
Author: Igor Markelov
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Lakes are ecologically, economically, and culturally significant resources that are, at the same time, very fragile and sensitive to human disturbances. During the last decades, intensified urbanization and discharge of nutrients lead to the increase of lake eutrophication in many regions of the world. Moreover, biogeochemical cycles within the lakes are changing due to climate warming, which increases water temperature and affects physical and hydrological lake regimes. In this thesis, I investigate a vast scope of the natural and anthropogenic processes affecting the biogeochemical cycles in lakes at different scales. In particular, I examine the cascading effect of the climate, regional weather, human interventions, and microbial control on phosphorus dynamics in lakes. In Chapter 2, I demonstrate that on the lake scale, phosphorus cycle is driven by internal loading and iron recycling, while it is vulnerable to the reduction of ice cover. To achieve that, I expand the existing MyLake model by incorporating a sediment diagenesis module. Moreover, I develop the continuous reaction network that couples biogeochemical reactions taking place both in water column and sediment. In the modeling scenarios, I assess the importance of the sediment processes and the effects of the climatic and anthro- pogenic drivers on water quality in Lake Vansjø, Norway. I also highlight the importance of phosphorus accumulation within the lake that controls timing and magnitude of bio- geochemical lake responses to external forcing. This includes projected changes in the air temperature, absence of ice cover, and potential management practices. In Chapter 3, I contribute to the long-standing understanding that on the scales of microbial systems, the respiration reactions exert substantial control on biogeochemi- cal cycles by regulating the availability of the electron donors and acceptors, secondary minerals, adsorption sites, and alkalinity. Moreover, I develop a new conceptual model to simulate the preferential catabolic reaction pathways based on power produced in reactions. In contrast to common kinetic rate expressions, I demonstrate that new ther- modynamically based formulations can be applied to describe the microbial respiration of arbitrary large reaction networks. New approach substantially improves the robustness, transferability, and allows the generalization of the model-derived parameters. In Chapter 4, I show that on the regional scale, weather defines hydrodynamic flush rates and water circulation patterns, which, in turn, control the phosphorus transport in Lake Erie, Canada. Specifically, precipitation controls the release of phosphorus from the watershed in the spring, while wind governs the water circulation and transport of the phosphorus released from sediment in the central basin during summer. I also illustrate that climate and weather in the upper Laurentian Great Lakes regulate changes in the water level of Lake Erie. Overall, this thesis improves the fundamental understanding of the phosphorus cycle in lakes, which is being controlled by numerous biogeochemical and physical processes at various scales. In particular, I show that the climate has a cascading effect on the phosphorus cycle in lakes. First, climate controls regional precipitation, wind, and air temperature, which in turn control phosphorus supply from the watershed and basin- wide phosphorus transport. Second, being vulnerable to climate warming, the duration of ice cover impacts the phosphorus cycle through changes in light attenuation, water temperature, mixing regimes, and water column ventilation. Lastly, local environmental perturbations (e.g., pH, temperature, or redox state) define thermodynamic properties of the sediment, which control microbial metabolism and, therefore, the internal phosphorus loading. Finally, this thesis provides new open-source tools for reactive transport simula- tions in lakes as well as in saturated media. In addition to the coupled lake-sediment model developed in Chapter 3, I develop a computer program PorousMediaLab, which performs biogeochemical simulations in water-saturated media and described In Chapter 5. PorousMediaLab is the core component of the numerical investigations presented in the thesis. For example, PorousMediaLab is applied in Chapter 2 to design and test the initial reaction network, calculate fluxes at the sediment-water interface, and estimate re- action timescales. In Chapter 3, PorousMediaLab is used to simulate the reaction rates of batch and one-dimensional sediment column using a novel approach based on the thermo- dynamic switch function. In Chapter 4, PorousMediaLab is used to build a mass balance model and to improve the current understanding of the inter-basin exchange. Both tools are open-source, and they are available online.
Author: Trevor C. Charles
Publisher: Springer
ISBN: 3319615106
Category : Science
Languages : en
Pages : 256
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Book Description
In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.
Author: David C. Sigee
Publisher: John Wiley & Sons
ISBN: 0470026472
Category : Science
Languages : en
Pages : 516
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Book Description
This unique textbook takes a broad look at the rapidly expanding field of freshwater microbiology. Concentrating on the interactions between viruses, bacteria, algae, fungi and micro-invertebrates, the book gives a wide biological appeal. Alongside conventional aspects such as phytoplankton characterisation, seasonal changes and nutrient cycles, the title focuses on the dynamic and applied aspects that are not covered within the current textbooks in the field. Complete coverage of all fresh water biota from viruses to invertebrates Unique focus on microbial interactions including coverage of biofilms, important communities on all exposed rivers and lakes. New information on molecular and microscopical techniques including a study of gene exchange between bacteria in the freshwater environment. Unique emphasis on the applied aspects of freshwater microbiology with particular emphasis on biodegradation and the causes and remediation of eutrophication and algal blooms.
Author: K. Ramesh Reddy
Publisher: CRC Press
ISBN: 0429531931
Category : Science
Languages : en
Pages : 926
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Book Description
The globally important nature of wetland ecosystems has led to their increased protection and restoration as well as their use in engineered systems. Underpinning the beneficial functions of wetlands are a unique suite of physical, chemical, and biological processes that regulate elemental cycling in soils and the water column. This book provides an in-depth coverage of these wetland biogeochemical processes related to the cycling of macroelements including carbon, nitrogen, phosphorus, and sulfur, secondary and trace elements, and toxic organic compounds. In this synthesis, the authors combine more than 100 years of experience studying wetlands and biogeochemistry to look inside the black box of elemental transformations in wetland ecosystems. This new edition is updated throughout to include more topics and provide an integrated view of the coupled nature of biogeochemical cycles in wetland systems. The influence of the elemental cycles is discussed at a range of scales in the context of environmental change including climate, sea level rise, and water quality. Frequent examples of key methods and major case studies are also included to help the reader extend the basic theories for application in their own system. Some of the major topics discussed are: Flooded soil and sediment characteristics Aerobic-anaerobic interfaces Redox chemistry in flooded soil and sediment systems Anaerobic microbial metabolism Plant adaptations to reducing conditions Regulators of organic matter decomposition and accretion Major nutrient sources and sinks Greenhouse gas production and emission Elemental flux processes Remediation of contaminated soils and sediments Coupled C-N-P-S processes Consequences of environmental change in wetlands# The book provides the foundation for a basic understanding of key biogeochemical processes and its applications to solve real world problems. It is detailed, but also assists the reader with box inserts, artfully designed diagrams, and summary tables all supported by numerous current references. This book is an excellent resource for senior undergraduates and graduate students studying ecosystem biogeochemistry with a focus in wetlands and aquatic systems.
Author: Ramesh D. Gulati
Publisher: Springer
ISBN: 3319491431
Category : Science
Languages : en
Pages : 405
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Book Description
This volume presents recent advances in the research on meromictic lakes and a state-of-the art overview of this area. After an introduction to the terminology and geographic distribution of meromictic lakes, three concise chapters describe their physical, chemical and biological features. The following eight chapters present case studies of more than a dozen meromictic lakes, showing the variety of physical and biochemical processes that promote meromixis. The result is a broad picture of the ecology and biochemistry of meromictic lakes in tropical and cold regions, in man-made pit lakes and euxinic marine lakes, and in freshwater as well as hypersaline lakes. In the final chapter the editors provide a synthesis of the topic and conclude that the study of meromictic lakes also offers new insights into the limnology of inland lakes. The book appeals to researchers in the fields of ecology, limnology, environmental physics and biophysics.
Author: Geoffrey Michael Gadd
Publisher: Cambridge University Press
ISBN: 1107320747
Category : Science
Languages : en
Pages : 504
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Book Description
Fungi play important roles in the cycling of elements in the biosphere but are frequently neglected within microbiological and geochemical research spheres. Symbiotic mycorrhizal fungi are responsible for major transformations and redistribution of inorganic nutrients, while free-living fungi have major roles in the decomposition of organic materials, including xenobiotics. Fungi are also major biodeterioration agents of stone, wood, plaster, cement and other building materials, and are important components of rock-inhabiting microbial communities. The aim of this book is to promote further understanding of the key roles that free-living and symbiotic fungi (in mycorrhizas and lichens) play in the biogeochemical cycling of elements, the chemical and biological mechanisms that are involved, and their environmental and biotechnological significance. Where appropriate, relationships with bacteria are also discussed to highlight the dynamic interactions that can exist between these major microbial groups and their integrated function in several kinds of habitat.
