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Omics for environmental engineering and microbiology systems
\"Bioremediation using microbes is a sustainable technology for biodegradation of target compounds and OMICS approach gives more clarity on these microbial communities. This book provides insights into the complex behavior of microbial communities and identifies enzymes/metabolites and their degradation pathways. It describes the application of microbes and their derivatives for bioremediation of potentially toxic and novel compounds. It highlights existing technologies along with industrial practices and real-life case studies. Features: Includes recent research and development in the areas of OMICS and microbial bioremediation. Covers the broad environmental pollution control approach such as metagenomics, metabolomics, fluxomics, bioremediation, and biodegradation of industrial wastes. Reviews metagenomics and waste management, and recycling for environmental cleanup. Describes the metagenomic methodologies and best practices, from sample collection to data analysis for taxonomies. Explores various microbial degradation pathways and detoxification mechanisms for organic and inorganic contaminants of wastewater with their gene expression. This book aims at Graduate students and researchers in environmental engineering, soil remediation, hazardous waste management, environmental modeling, and wastewater treatment\"-- Provided by publisher.
Book
The assembly of microbial communities on red sandstone surfaces was shaped by dispersal limitation and heterogeneous selection
Minimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.
Journal Article
The Andromeda evolution
\"In 1967, an extraterrestrial microbe came crashing down to Earth and nearly ended the human race. Accidental exposure to the particle--designated The Andromeda Strain--killed every resident of the town of Piedmont, Arizona, save for an elderly man and an infant boy. Over the next five days, a team of top scientists assigned to Project Wildfire worked valiantly to save the world from an epidemic of unimaginable proportions. In the moments before a catastrophic nuclear detonation, they succeeded. In the ensuing decades, research on the microparticle continued. And the world thought it was safe ... Deep inside Fairchild Air Force Base, Project Eternal Vigilance has continued to watch and wait for the Andromeda Strain to reappear. On the verge of being shut down, the project has registered no activity--until now. A Brazilian terrain-mapping drone has detected a bizarre anomaly of otherworldly matter in the middle of the jungle, and, worse yet, the tell-tale chemical signature of the deadly microparticle. With this shocking discovery, the next-generation Project Wildfire is activated, and a diverse team of experts hailing from all over the world is dispatched to investigate the potentially apocalyptic threat. But the microbe is growing--evolving. And if the Wildfire team can't reach the quarantine zone, enter the anomaly, and figure out how to stop it, this new Andromeda Evolution will annihilate all life as we know it\"-- Provided by publisher.
Book
Microplastics provide new microbial niches in aquatic environments
Microplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase.Key Points• Bacteria are mainly studied in community analyses: fungi are neglected.• Microbial colonization of microplastics depends on substrate, location and time.• Community ecology is a promising approach to investigate microbial colonization.• Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.
Journal Article
A multidimensional perspective on microbial interactions
Beyond being simply positive or negative, beneficial or inhibitory, microbial interactions can involve a diverse set of mechanisms, dependencies and dynamical properties. These more nuanced features have been described in great detail for some specific types of interactions, (e.g. pairwise metabolic cross-feeding, quorum sensing or antibiotic killing), often with the use of quantitative measurements and insight derived from modeling. With a growing understanding of the composition and dynamics of complex microbial communities for human health and other applications, we face the challenge of integrating information about these different interactions into comprehensive quantitative frameworks. Here, we review the literature on a wide set of microbial interactions, and explore the potential value of a formal categorization based on multidimensional vectors of attributes. We propose that such an encoding can facilitate systematic, direct comparisons of interaction mechanisms and dependencies, and we discuss the relevance of an atlas of interactions for future modeling and rational design efforts.
Journal Article
Microbiology of green fuels
\"A key priority in today's society is the implementation of a sustainable bio-based economy. For such a goal, the production of renewable bioproducts such as biofuels to replace fossil-derived compounds is crucial. In this context, the utilization of microorganisms for the production of biofuels from renewable resources is advantageous in terms of environmental sustainability and it is expected to play an important role in bioeconomy in the near future. In this sense, green fuel synthesis from agro-industrial organic wastes by microorganisms will boost circular economy. The success of the biotechnological biofuel production process requires, however, conversion microorganism capable of both efficiently assimilating the major derived carbon sources and diverting their metabolites towards the specific fuel. This book aims to show recent advances in the production of green fuels by means of microorganisms. Promising processes and microorganisms involved in the biofuel production will be provided and discussed to give and in-depth overview of the state of the art with broad spectrum of microorganisms and biofuels. For the sustainability of green fuel technologies, the book will also address biosafety of different production technologies and, social and political interest in promoting green fuels. These facts make this book very valuable for biofuels companies and scientific community\"-- Provided by publisher.
Book
Integrated network analysis reveals the importance of microbial interactions for maize growth
milk*Microbes play a critical role in soil global biogeochemical circulation and microbe–microbe interactions have also evoked enormous interests in recent years. Utilization of green manures can stimulate microbial activity and affect microbial composition and diversity. However, few studies focus on the microbial interactions or detect the key functional members in communities. With the advances of metagenomic technologies, network analysis has been used as a powerful tool to detect robust interactions between microbial members. Here, random matrix theory-based network analysis was used to investigate the microbial networks in response to four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) over two growth cycles from October 2012 to September 2014. The results showed that the topological properties of microbial networks were dramatically altered by green manure fertilization. Microbial network under milk vetch amendment showed substantially more intense complexity and interactions than other fertilization systems, indicating that milk vetch provided a favorable condition for microbial interactions and niche sharing. The shift of microbial interactions could be attributed to the changes in some major soil traits and the interactions might be correlated to plant growth and production. With the stimuli of green manures, positive interactions predominated the network eventually and the network complexity was in consistency with maize productivity, which suggested that the complex soil microbial networks might benefit to plants rather than simple ones, because complex networks would hold strong the ability to cope with environment changes or suppress soil-borne pathogen infection on plants. In addition, network analyses discerned some putative keystone taxa and seven of them had directly positive interactions with maize yield, which suggested their important roles in maintaining environmental functions and in improving plant growth.
Journal Article
Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities
Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (
rrn
) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level
rrn
copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on
rrn
copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the
rrn
copy number, ecological interaction, and nutrient availability.
Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.
Journal Article