Search results: Found 6

Listing 1 - 6 of 6
Sort by
Intra- and inter-species interactions in microbial communities

Authors: --- ---
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
License:

Loading...
Export citation

Choose an application

Abstract

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.

Archaeal Cell Envelope and Surface Structures

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197736 Year: Pages: 178 DOI: 10.3389/978-2-88919-773-6 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
License:

Loading...
Export citation

Choose an application

Abstract

Prokaryotes have a complex cell envelope which has several important functions, including providing a barrier that protects the cytoplasm from the environment. Along with its associated proteinaceous structures, it also ensures cell stability, facilitates motility, mediates adherence to biotic and abiotic surfaces, and facilitates communication with the extracellular environment. Viruses have evolved to take advantage of cell envelope constituents to gain access to the cellular interior as well as for egress from the cell. While many aspects of the biosynthesis and structure of the cell envelope are similar across domains, archaeal cell envelopes have several unique characteristics including, among others, an isoprenoid lipid bilayer, a non-murein-based cell wall, and a unique motility structure, (important features that give archaeal cell envelopes characteristics that are significantly different from those of bacterial cell envelopes – possibly out). Recent analyses have revealed that the cell envelopes of distantly related archaea also display an immense diversity of characteristics. For instance, while many archaea have an S-layer, the subunits of S-layers of various archaeal species, as well as their posttranslational modifications, vary significantly. Moreover, like gram-negative bacteria, recent studies have shown that some archaeal species also have an outer membrane. In this collection of articles, we include contributions that focus on research that has expanded our understanding of the mechanisms underlying the biogenesis and functions of archaeal cell envelopes and their constituent surface structures.

Keywords

pili --- Flagella --- archaella --- Archaea --- S-layer --- Cytochromes --- membrane --- hami --- Biofilms --- Surface structures

Microbiology of the Rapidly Changing Polar Environments

Authors: --- --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455133 Year: Pages: 315 DOI: 10.3389/978-2-88945-513-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Oceanography --- Microbiology
Added to DOAB on : 2019-01-23 14:53:42
License:

Loading...
Export citation

Choose an application

Abstract

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.

DNA Replication Origins in Microbial Genomes

Author:
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197798 Year: Pages: 115 DOI: 10.3389/978-2-88919-779-8 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
License:

Loading...
Export citation

Choose an application

Abstract

DNA replication, a central event for cell proliferation, is the basis of biological inheritance. Complete and accurate DNA replication is integral to the maintenance of the genetic integrity of organisms. In all three domains of life, DNA replication begins at replication origins. In bacteria, replication typically initiates from a single replication origin (oriC), which contains several DnaA boxes and the AT-rich DNA unwinding element (DUE). In eukaryotic genomes, replication initiates from significantly more replication origins, activated simultaneously at a specific time. For eukaryotic organisms, replication origins are best characterized in the unicellular eukaryote budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. The budding yeast origins contain an essential sequence element called the ARS (autonomously replicating sequence), while the fission yeast origins consist of AT-rich sequences. Within the archaeal domain, the multiple replication origins have been identified by a predict-and-verify approach in the hyperthermophilic archaeon Sulfolobus. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several short repetitive DNA sequences, known as origin recognition boxes (ORBs). It appears that archaea have a simplified version of the eukaryotic replication apparatus, which has led to considerable interest in the archaeal machinery as a model of that in eukaryotes. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. Therefore, intensive studies have been carried out in the last two decades. The pioneer work to identify bacterial oriCs in silico is the GC-skew analysis. Later, a method of cumulative GC skew without sliding windows was proposed to give better resolution. Meanwhile, an oligomer-skew method was also proposed to predict oriC regions in bacterial genomes. As a unique representation of a DNA sequence, the Z-curve method has been proved to be an accurate and effective approach to predict bacterial and archaeal replication origins. Budding yeast origins have been predicted by Oriscan using similarity to the characterized ones, while the fission yeast origins have been identified initially from AT content calculation. In comparison with the in silico analysis, the experimental methods are time-consuming and labor-intensive, but convincing and reliable. To identify microbial replication origins in vivo or in vitro, a number of experimental methods have been used including construction of replicative oriC plasmids, microarray-based or high-throughput sequencing-based marker frequency analysis, two-dimensional gel electrophoresis analysis and replication initiation point mapping (RIP mapping). The recent genome-wide approaches to identify and characterize replication origin locations have boosted the number of mapped yeast replication origins. In addition, the availability of increasing complete microbial genomes and emerging approaches has created challenges and opportunities for identification of their replication origins in silico, as well as in vivo and in vitro. The Frontiers in Microbiology Research Topic on DNA replication origins in microbial genomes is devoted to address the issues mentioned above, and aims to provide a comprehensive overview of current research in this field.

Thermophiles and Thermozymes

Author:
ISBN: 9783038978169 9783038978176 Year: Pages: 198 DOI: 10.3390/books978-3-03897-817-6 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General)
Added to DOAB on : 2019-04-25 16:37:17
License:

Loading...
Export citation

Choose an application

Abstract

Interest in the study of life in hot environments, both with respect to the inhabiting microorganisms and the enzymes they produce, is currently very high. The biological mechanisms responsible for the resistance to high temperatures are not yet fully understood, whereas thermostability is a highly required feature for industrial applications. In this e-book, the invited authors provide diverse evidence contributing to the understanding of such mechanisms and the unlocking of the biotechnological potential of thermophiles and thermozymes.

Carbon, Nitrogen and Phosphorus Cycling in Forest Soils

Author:
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
License:

Loading...
Export citation

Choose an application

Abstract

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

Listing 1 - 6 of 6
Sort by
Narrow your search