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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.

Microbial responses to environmental changes

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197231 Year: Pages: 261 DOI: 10.3389/978-2-88919-723-1 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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Advances in next generation sequencing technologies, omics, and bioinformatics are revealing a tremendous and unsuspected diversity of microbes, both at a compositional and functional level. Moreover, the expansion of ecological concepts into microbial ecology has greatly advanced our comprehension of the role microbes play in the functioning of ecosystems across a wide range of biomes. Super-imposed on this new information about microbes, their functions and how they are organized, environmental gradients are changing rapidly, largely driven by direct and indirect human activities. In the context of global change, understanding the mechanisms that shape microbial communities is pivotal to predict microbial responses to novel selective forces and their implications at the local as well as global scale. One of the main features of microbial communities is their ability to react to changes in the environment. Thus, many studies have reported changes in the performance and composition of communities along environmental gradients. However, the mechanisms underlying these responses remain unclear. It is assumed that the response of microbes to changes in the environment is mediated by a complex combination of shifts in the physiological properties, single-cell activities, or composition of communities: it may occur by means of physiological adjustments of the taxa present in a community or selecting towards more tolerant/better adapted phylotypes. Knowing whether certain factors trigger one, many, or all mechanisms would greatly increase confidence in predictions of future microbial composition and processes. This Research Topic brings together studies that applied the latest molecular techniques for studying microbial composition and functioning and integrated ecological, biogeochemical and/or modeling approaches to provide a comprehensive and mechanistic perspective of the responses of micro-organisms to environmental changes. This Research Topic presents new findings on environmental parameters influencing microbial communities, the type and magnitude of response and differences in the response among microbial groups, and which collectively deepen our current understanding and knowledge of the underlying mechanisms of microbial structural and functional responses to environmental changes and gradients in both aquatic and terrestrial ecosystems. The body of work has, furthermore, identified many challenges and questions that yet remain to be addressed and new perspectives to follow up on.

Molecular Ecology and Genetic Diversity of the Roseobacter Clade

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455386 Year: Pages: 138 DOI: 10.3389/978-2-88945-538-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2019-01-23 14:53:42
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Marine bacteria and archaea are key players in the biogeochemical cycling of nitrogen, carbon, and other elements. One important lineage of marine bacteria is the Roseobacter group. Members of this clade are the most abundant bacteria in marine ecosystems constituting up to 25% of the marine bacterioplankton. They have been detected in various marine habitats from coastal regions to deep-sea sediments and from polar regions to tropical latitudes. These bacteria are physiologically and genetically very versatile. Utilization of several organic and inorganic compounds, sulfur oxidation, aerobic anoxygenic photosynthesis, carbon monoxide oxidation, DMSP demethylation, and production of secondary metabolites are some of the important functional traits found in this clade. Moreover, several isolates are available allowing in-depth analysis of physiological and genetic characteristics. Although the Roseobacter group has been intensively studied in recent years, our understanding of its ecological contributions and the evolutionary processes shaping the genomes of this clade is still rather limited.

Current Challenges and Future Perspectives on Emerging Bioelectrochemical Technologies

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199044 Year: Pages: 121 DOI: 10.3389/978-2-88919-904-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2016-01-19 14:05:46
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The increasing demand for energy worldwide, currently evaluated at 13 terawatts per year, has triggered a surge in research on alternative energy sources more sustainable and environmentally friendly. Bio-catalyzed electrochemical systems (BESs) are a rapidly growing biotechnology for sustainable production of bioenergy and/or value-added bioproducts using microorganisms as catalysts for bioelectrochemical reactions at the electrode surface. In the last decades, this biotechnology has been intensively studied and developed as a flexible and practical platform for multiple applications such as electricity production, wastewater treatment, pollutants remediation, desalination and production of biogas, biofuels, or other commodities. BESs could have a critical impact on societies in many spheres of activity and become one of the solutions to reform our petroleum-based economy. However, BESs research has so far been limited to lab scale with the notable exceptions of pilot scale microbial fuel cells for brewery and winery wastewater treatment coupled with electricity generation. In general, more knowledge has to be acquired to overcome the issues that are stymieing BESs development and commercialization. For example, it is critical to understand better microbial physiology including the mechanisms responsible for the transfer of electrons between the microbes and the electrodes to start optimizing the systems in a more rational manner. There are many BES processes and for each one of them there is a multitude of biological and electrochemical specifications to investigate and adjust such as the nature of the microbial platform, electrode materials, the reactor design, the substrate, the medium composition, and the operating conditions. The ultimate goal is to develop highly energy efficient BESs with a positive footprint on the environment while maintaining low cost and generating opportunities to create value. BESs are complex systems developed with elements found in multiple fields of science such as microbiology, molecular biology, bioinformatics, biochemistry, electrochemistry, material science and environmental engineering. Given the high volume of research activities going on in the field of BESs today, this e-book explores the current challenges, the more recent progresses, and the future perspectives of BESs technologies. The BESs discussed here include microbial fuel cells, microbial electrolysis cells, microbial electrosynthesis cells, microbial electroremediation cells, etc.

Conflict and Cooperation in Microbial Societies

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451432 Year: Pages: 119 DOI: 10.3389/978-2-88945-143-2 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The most evident aspect of biodiversity is the variety of complex forms and behaviors among organisms, both living and extinct. Comparative molecular and physiological studies show that the evolution of complex phenotypic traits involves multiple levels of biological organization (i.e. genes, chromosomes, organelles, cells, individual organisms, species, etc.). Regardless of the specific molecular mechanisms and details, the evolution of different complex biological organizations share a commonality: cooperation and conflict among the parts of the biological unit under study. The potential for conflict among parts is abundant. How then do complex systems persist, given the necessity of cooperative behavior for their maintenance, when the potential for conflict occurs across all levels of biological organization? In this Research Topic and eBook we present ideas and work on the question, how coexistence of biological components at different levels of organization persists in the face of antagonistic, conflicting or even exploitative behavior of the parts? The goal of this topic is in presenting examples of cooperation and conflict at different levels of biological organization to discuss the consequences that this “tension” have had in the diversification and emergence of novel phenotypic traits. Exemplary cases are studies investigating: the evolution of genomes, formation of colonial aggregates of cells, biofilms, the origin and maintenance of multicellular organisms, and the stable coexistence of multispecies consortia producing a cooperative product. Altogether, we hope that the contributions to this Research Topic build towards mechanistic knowledge of the biological phenomenon of coexistence in the face of conflict. We believe that knowledge on the mechanisms of the origin and evolutionary maintenance of cooperation has implications beyond evolutionary biology such as novel approaches in controlling microbial infections in medicine and the modes by studies in synthetic biology are conducted when designing economically important microbial consortia.The most evident aspect of biodiversity is the variety of complex forms and behaviors among organisms, both living and extinct. Comparative molecular and physiological studies show that the evolution of complex phenotypic traits involves multiple levels of biological organization (i.e. genes, chromosomes, organelles, cells, individual organisms, species, etc.). Regardless of the specific molecular mechanisms and details, the evolution of different complex biological organizations share a commonality: cooperation and conflict among the parts of the biological unit under study. The potential for conflict among parts is abundant. How then do complex systems persist, given the necessity of cooperative behavior for their maintenance, when the potential for conflict occurs across all levels of biological organization? In this Research Topic and eBook we present ideas and work on the question, how coexistence of biological components at different levels of organization persists in the face of antagonistic, conflicting or even exploitative behavior of the parts? The goal of this topic is in presenting examples of cooperation and conflict at different levels of biological organization to discuss the consequences that this “tension” have had in the diversification and emergence of novel phenotypic traits. Exemplary cases are studies investigating: the evolution of genomes, formation of colonial aggregates of cells, biofilms, the origin and maintenance of multicellular organisms, and the stable coexistence of multispecies consortia producing a cooperative product. Altogether, we hope that the contributions to this Research Topic build towards mechanistic knowledge of the biological phenomenon of coexistence in the face of conflict. We believe that knowledge on the mechanisms of the origin and evolutionary maintenance of cooperation has implications beyond evolutionary biology such as novel approaches in controlling microbial infections in medicine and the modes by studies in synthetic biology are conducted when designing economically important microbial consortia.

Microbial symbiosis of marine sessile hosts - Diversity and function

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196814 Year: Pages: 108 DOI: 10.3389/978-2-88919-681-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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Modern molecular -omics tools (metagenomics, metaproteomics etc.) have greatly contributed to the rapid advancement of our understanding of microbial diversity and function in the world’s oceans. These tools are now increasingly applied to host-associated environments to describe the symbiotic microbiome and obtain a holistic view of marine host-microbial interactions. Whilst all eukaryotic hosts are likely to benefit from their microbial associates, marine sessile eukaryotes, including macroalgae, seagrasses and various invertebrates (sponges, acidians, corals, hydroids etc), rely in particular on the function of their microbiome. For example, marine sessile eukaryotes are under constant grazing, colonization and fouling pressure from the millions of micro- and macroorganisms in the surrounding seawater. Host-associated microorganisms have been shown to produce secondary metabolites as defense molecules against unwanted colonization or pathogens, thus having an important function in host health and survival. Similarly microbial symbionts of sessile eukaryotes are often essential players in local nutrient cycling thus benefiting both the host and the surrounding ecosystem. Various research fields have contributed to generating knowledge of host-associated systems, including microbiology, biotechnology, molecular biology, ecology, evolution and biotechnology. Through a focus on model marine sessile host systems we believe that new insight into the interactions between host and microbial symbionts will be obtained and important areas of future research will be identified. This research topic includes original research, review and opinion articles that bring together the knowledge from different aspects of biology and highlight advances in our understanding of the diversity and function of the microbiomes on marine sessile hosts.

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.

The microbial nitrogen cycle

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194124 Year: Pages: 174 DOI: 10.3389/978-2-88919-412-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2015-12-10 11:59:06
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Nitrogen is an essential element in biological systems, and one that often limits production in both aquatic and terrestrial systems. Due to its requirement in biological macromolecules, its acquisition and cycling have the potential to structure microbial communities, as well as to control productivity on the ecosystem scale. In addition, its versatile redox chemistry is the basis of complex biogeochemical transformations that control the inventory of fixed nitrogen, both in local environments and over geological time. Although many of the pathways in the microbial nitrogen cycle were described more than a century ago, additional fundamental pathways have been discovered only recently. These findings imply that we still have much to learn about the microbial nitrogen cycle, the organisms responsible for it, and their interactions in natural and human environments. Progress in nitrogen cycle research has been facilitated by recent rapid technological advances, especially in genomics and isotopic approaches. In this Research Topic, we reviewed the leading edge of nitrogen cycle research based on these approaches, as well as by exploring microbial processes in modern ecosystems.

Synthetic biology applications in industrial microbiology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193424 Year: Pages: 129 DOI: 10.3389/978-2-88919-342-4 Language: English
Publisher: Frontiers Media SA
Subject: Environmental Sciences --- Biotechnology --- General and Civil Engineering --- Microbiology --- Science (General)
Added to DOAB on : 2016-03-10 08:14:32
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Exponentially increasing information on biological organisms coupled with increasing computational power in the past decade have broadened the perspective of fundamental biological research, bringing about considerable promise and unprecedented potential for practical applications in biotechnology. As one emergent discipline, synthetic biology aims to design and engineer novel biologically-based parts, devices, and systems, in addition to redesigning existing, natural biological systems. Although previously relegated to demonstration studies, more recent research in synthetic biology has focused on the rational engineering of industrial microorganisms with the potential to address many of society’s critical challenges. Within the realm of industrial microbiology, progress in the field of synthetic biology has enabled the development of, for example, new biosynthetic pathways for the production of renewable fuels and chemicals, programmable logic controls to regulate and optimize cell function, and robust microbes for the destruction of harmful environmental contaminants. Some of the exciting examples included producing anti-malarial drug, anti- cancer taxol precursor and various biofuel molecules in E. coli and yeast. In addition, these researches have also greatly enhanced our understanding of the cellular machinery and its regulation in some of the industry important microbes, laying an important foundation for further design and engineering of biological function for even greater application. For these reasons, we present here a collection of articles from the leading edge of the field of synthetic biology, with a specific focus on the development in industrial microorganisms. It is the intent of this collection to reach a wide audience whose interests and expertise spans from development of novel synthetic biology methodologies and theories (both experimental and computational) to practical applications seeking to address issues facing the world today.

Hydrothermal microbial ecosystems

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196821 Year: Pages: 284 DOI: 10.3389/978-2-88919-682-1 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2016-04-07 11:22:02
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