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Intra- and inter-species interactions in microbial communities

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194490 Year: Pages: 149 DOI: 10.3389/978-2-88919-449-0 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Microbiology --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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Recent developments in various “OMICs” fields have revolutionized our understanding of the vast diversity and ubiquity of microbes in the biosphere. However, most of the current paradigms of microbial cell biology, and our view of how microbes live and what they are capable of, are derived from in vitro experiments on isolated strains. Even the co-culturing of mixed species to interrogate community behavior is relatively new. But the majority of microorganisms lives in complex communities in natural environments, under varying conditions, and often cannot be cultivated. Unless we obtain a detailed understanding of the near-native 3D ultrastructure of individual community members, the 3D spatial community organization, their metabolic interdependences, coordinated gene expression and the spatial organization of their macromolecular machines inventories as well as their communication strategies, we won’t be able to truly understand microbial community life. How spatial and also temporal organization in cell–cell interactions are achieved remains largely elusive. For example, a key question in microbial ecology is what mechanisms microbes employ to respond when faced with prey, competitors or predators, and changes in external factors. Specifically, to what degree do bacterial cells in biofilms act individually or with coordinated responses? What are the spatial extent and coherence of coordinated responses? In addition, networks linking organisms across a dynamic range of physical constraints and connections should provide the basis for linked evolutionary changes under pressure from a changing environment. Therefore, we need to investigate microbial responses to altered or adverse environmental conditions (including phages, predators, and competitors) and their macromolecular, metabolic responses according to their spatial organization. We envision a diverse set of tools, including optical, spectroscopical, chemical and ultrastructural imaging techniques that will be utilized to address questions regarding e.g. intra- and inter-organism interactions linked to ultrastructure, and correlated adaptive responses in gene expression, physiological and metabolic states as a consequence of the alterations of their environment. Clearly strategies for co-evolution and in general the display of adaptive strategies of a microbial network as a response to the altered environment are of high interest. While a special focus will be placed on terrestrial sole-species or mixed biofilms, we are also interested in aquatic systems, biofilms in general and microbes living in symbiosis. In this Research Topic, we wish to summarize and review results investigating interactions and possibly networks between microbes of the same or different species, their co-occurrence, as well as spatiotemporal patterns of distribution. Our goal is to include a broad spectrum of experimental and theoretical contributions, from research and review articles to hypothesis and theory, aiming at understanding microbial interactions at a systems level.

The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193462 Year: Pages: 195 DOI: 10.3389/978-2-88919-346-2 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Oceanography --- Science (General)
Added to DOAB on : 2016-03-10 08:14:32
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Biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment. The aim of this Research Topic is to highlight recent advances in our knowledge of the pathways and controls of microbially-catalyzed hydrocarbon degradation in marine ecosystems, with emphasis on the response of microbial communities to the Deepwater Horizon oil spill in the Gulf of Mexico. In this Research Topic, we encouraged original research and reviews on the ecology of hydrocarbon-degrading bacteria, the rates and mechanisms of biodegradation, and the bioremediation of discharged oil under situ as well as near in situ conditions.

Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450954 Year: Pages: 154 DOI: 10.3389/978-2-88945-095-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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Filamentous phage (genus Inovirus) infect almost invariably Gram-negative bacteria. They are distinguished from all other bacteriophage not only by morphology, but also by the mode of their assembly, a secretion-like process that does not kill the host. “Classic” Escherichia coli filamentous phage Ff (f1, fd and M13) are used in display technology and bio/nano/technology, whereas filamentous phage in general have been put to use by their bacterial hosts for adaptation to environment, pathogenesis, biofilm formation, horizontal gene transfer and modulating genome stability. Many filamentous phage have a “symbiotic” life style that is often manifested by inability to form plaques, preventing their identification by standard phage-hunting techniques; while the absence or very low sequence conservation between phage infecting different species often complicates their identification through bioinformatics. Nevertheless, the number of discovered filamentous phage is increasing rapidly, along with realization of their significance. “Temperate” filamentous phage whose genomes are integrated into the bacterial chromosome of pathogenic bacteria often modulate virulence of the host. The Vibrio cholerae phage CTXf genome encodes cholera toxin, whereas many filamentous prophage influence virulence without encoding virulence factors. The nature of their effect on the bacterial pathogenicity and overall physiology is the next frontier in understanding intricate relationship between the filamentous phage and their hosts. Phage display has been widely used as a combinatorial technology of choice for discovery of therapeutic antibodies and peptide leads that have been applied in the vaccine design, diagnostics and drug development or targeting over the past thirty years. Virion proteins of filamentous phage are integral membrane proteins prior to assembly; hence they are ideal for display of bacterial surface and secreted proteins. The use of this technology at the scale of microbial community has potential to identify host-interacting proteins of uncultivable or low-represented community members. Recent applications of Ff filamentous phage extend into protein evolution, synthetic biology and nanotechnology. In many applications, phage serves as a monodisperse long-aspect nano-scaffold of well-defined shape. Chemical or chenetic modifications of this scaffold are used to introduce the necessary functionalities, such as fluorescent labels, ligands that target specific proteins, or peptides that promote formation of inorganic or organic nanostructures. We anticipate that the future holds development of new strategies for particle assembly, site-specific multi-functional modifications and improvement of existing modification strategies. These improvements will render the production of filamentous-phage-templated materials safe and affordable, allowing their applications outside of the laboratory.

Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics

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ISBN: 9783038429753 9783038429760 Year: Pages: VIII, 286 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Chemical Engineering
Added to DOAB on : 2018-07-04 13:24:50
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Investigating the microbiome is on the frontier of science. It has the potential to resolve many issues in the realms of energy, food, human health, the environment, and biotechnology. Scientists are trying to understand, in a fundamental way, how microbes influence each other and how they organize into interaction networks. These are the keys to predicting and engineering community function and properties of the microbiome. In this regard, mathematical modeling and computational analysis play an increasing role. This book is a collection of contributions from lead scientists in the field. It provides innovative approaches and fresh perspectives for modeling environmental communities and engineered microbial consortia. Reading this book will give researchers a solid look at cutting-edge science in microbial community modeling, and at the remaining challenges such modeling poses.

Carbon, Nitrogen and Phosphorus Cycling in Forest Soils

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ISBN: 9783038976820 / 9783038976837 Year: Pages: 238 DOI: 10.3390/books978-3-03897-683-7 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Forestry
Added to DOAB on : 2019-06-26 08:44:06
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The majority of carbon stored in the soils of the world is stored in forests. The refractory nature of some portions of forest soil organic matter also provides the slow, gradual release of organic nitrogen and phosphorus to sustain long term forest productivity. Contemporary and future disturbances, such as climatic warming, deforestation, short rotation sylviculture, the invasion of exotic species, and fire, all place strains on the integrity of this homeostatic system of C, N, and P cycling. On the other hand, the CO2 fertilization effect may partially offset losses of soil organic matter, but many have questioned the ability of N and P stocks to sustain the CO2 fertilization effect.

Keywords

carbon distribution index --- moisture gradient --- soil organic matter fraction --- soil degradation --- soil available nitrogen --- soil available phosphorus --- temperature --- stand density --- charcoal --- forest soil --- carbon mineralization --- microbial activity --- nitrification --- polyphenols --- temperature --- soil microbial communities --- PLFA --- seasons --- nitrogen dynamics --- gross nitrogen transformations --- Daxing’an Mountains --- climatic factors --- soil nutrients --- forest types --- principal component analyses --- soil structure --- soil pH --- Oxisol --- variable-charge soils --- aluminum accumulator --- seasonal trends --- beech forests --- soil enzymes --- organic matter --- multilevel models --- near natural forest management --- Pinus massoniana plantation --- Cunninghamia lanceolata plantation --- soil greenhouse gas flux --- biolability --- tree-DOM --- dissolved organic matter (DOM) --- carbon --- dissolved organic carbon (DOC) --- stemflow --- throughfall --- alpine forest --- ammonia-oxidizing bacteria --- ammonia-oxidizing archaea --- ammonium --- nitrate --- revegetation --- microbial biomass --- chloroform fumigation extraction --- enzyme activities --- stoichiometric homeostasis --- the Three Gorges Reservoir --- Eucalyptus sp. --- wood volume --- second production cycle --- annual increment average --- soil fertility --- nutrient cycling --- Chamaecyparis forest --- humic substances --- 31P nuclear magnetic resonance spectroscopy (31P NMR) --- P species --- topography --- net primary productivity --- climate zone --- climate --- soil N --- litter N --- climate change --- manuring --- manure pelleting --- northern temperate --- pyrolysis --- information review --- leaf N:P ratio --- P resorption efficiency --- soil P fractions --- P stock --- stand age

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