Download or read book Marine Microbial Metabolomics written by Angela Kelsey Boysen and published by . This book was released on 2020 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microorganisms control the flux of energy, stored as organic matter, into the ocean through the cumulative effects of individual metabolisms and community interactions. Metabolites are the currency of microbial metabolism, are carefully regulated to meet the metabolic demands of organisms living in dynamic environments, and reflect cellular status and metabolic strategies for nutrient acquisition, energy storage, redox maintenance, and more. This dissertation focuses on developing metabolomics techniques for the marine environment and using them to study microbial dynamics over time and space to identify compounds that are key microbial currencies. In order to study natural populations of marine microbes, I developed a method for targeted and untargeted metabolomics data acquisition and analysis with the unique challenges of marine samples in mind (Chapter 2). I use this method to study the influence of the diel cycle on the marine microbial community at Station ALOHA in the North Pacific Subtropical Gyre, ultimately showing synchrony of daytime anabolism and nighttime catabolism as seen through diel oscillations of ubiquitous metabolites including cofactors and vitamins. Through pairing metabolite and gene expression data, I demonstrate the strategies that specific photoautotrophs use to manage the daily fluctuations in solar energy (Chapter 3). To examine how microorganisms respond to other environmental forcings, I investigate the metabolism of microbial communities across the North Pacific Transition Zone and identify metabolic currencies used by those communities to adapt to varying nutrient supply (Chapter 4). Nutrient amendment experiments show the dominance of nitrogen limitation throughout this region and the potential for iron-nitrogen co-limitation near the subtropical chlorophyll front. Finally, in order to explore the potential for metabolites to be nutrient sources to the microbial community, I investigate the ability of natural microbial communities to use the abundant osmolyte glycine betaine. I determine the kinetics of uptake and identify the metabolic uses of glycine betaine in two different natural microbial communities and show that its use as a nutrient differs depending on DIN availability (Chapter 5). In full, this dissertation provides some of the first metabolomics measurements in the natural marine environment and identifies and explores the roles of key organic molecules in shaping the microbial community structure and function.
Download or read book Marine Microbial Diversity as a Source of Bioactive Natural Products written by Didier Stien and published by MDPI. This book was released on 2020-06-17 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: A trillion different microbial species have been evolving for some 3.5 billion years, producing ever more complex active secondary metabolites. The sea is a cauldron of a great diversity of useful and valuable compounds. This Special Issue focused on studies of marine microbe natural products for discovering compounds useful to humankind. Papers were collected that provide up-to-date information regarding the characterization of marine microbes’ metabolic diversity and the evaluation of the therapeutic potential of marine microbes’ metabolites. Most of the articles in this book deal with marine fungi, biological and chemical diversity, and their active metabolites. This may be a sign that marine fungi have been under studied to date and are perceived by many researchers as an important source of discovery in this field. A best practices guide for the isolation of marine fungi from different matrixes and their conservation is also presented. The comparison of the phylogenetic and metabolomic profiles of microalgae from different lineages provides novel insights into the potential of chemotaxonomy in marine phytoplankton, showing a good overlap of phylogenetic and chemotaxonomic signals.
Download or read book The Marine Microbiome written by Lucas J. Stal and published by Springer. This book was released on 2016-06-03 with total page 501 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the state-of-the-art concerning the ‘marine microbiome’ and its uses in biotechnology. The first part discusses the diversity and ecology of marine microorganisms and viruses, including all three domains of life: Bacteria, Archaea, and Eukarya. It discusses whether marine microorganisms exist and, if so, why they might be unique. The second part presents selected marine habitats, their inhabitants and how they influence biogeochemical cycles, while the third discusses the utilization of marine microbial resources, including legal aspects, dissemination, and public awareness. The marine microbiome is the total of microorganisms and viruses in the ocean and seas and in any connected environment, including the seafloor and marine animals and plants. The diversity of microbial life remains unquantified and largely unknown, and could represent a hidden treasure for human society. Accordingly, this book is also intended to connect academics and industry, providing essential information for microbiologists from both fields.
Download or read book Natural Product Genomics and Metabolomics of Marine Bacteria written by and published by . This book was released on 2022-02-24 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Marine Microbial Diversity as a Source of Bioactive Natural Products written by Didier Stien and published by . This book was released on 2020 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: A trillion different microbial species have been evolving for some 3.5 billion years, producing ever more complex active secondary metabolites. The sea is a cauldron of a great diversity of useful and valuable compounds. This Special Issue focused on studies of marine microbe natural products for discovering compounds useful to humankind. Papers were collected that provide up-to-date information regarding the characterization of marine microbes' metabolic diversity and the evaluation of the therapeutic potential of marine microbes' metabolites. Most of the articles in this book deal with marine fungi, biological and chemical diversity, and their active metabolites. This may be a sign that marine fungi have been under studied to date and are perceived by many researchers as an important source of discovery in this field. A best practices guide for the isolation of marine fungi from different matrixes and their conservation is also presented. The comparison of the phylogenetic and metabolomic profiles of microalgae from different lineages provides novel insights into the potential of chemotaxonomy in marine phytoplankton, showing a good overlap of phylogenetic and chemotaxonomic signals.
Download or read book Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts written by Lynsey MacIntyre and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Metabolomics written by and published by BoD – Books on Demand. This book was released on 2020-07-01 with total page 114 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is mainly for researchers interested in the new developments and applications of metabolomics. It is also important for physicians using metabolomic approaches in the diagnosis of diseases or treatment, and for postgraduate students starting their research projects on metabolomics. The book is divided into two sections as indicated from its title, namely: new insights into biology and new insights into medicine. It gives examples of the different applications of metabolomics from the production of biosurfactants by marine microorganisms to the applications of data from fecal metabolomics, serum metabolomics, and metabolomics of microbiota, as well as the use of Chinese medicines for cancer treatment. Overall, this is a well-written book, containing some very interesting research avenues and cutting-edge approaches. Finally, the editing of this book was of special interest to me and I hope that readers will also find it stimulating.
Download or read book The Power and Promise of Direct Measurements of Metabolites in Marine Systems written by Katherine Rose Heal and published by . This book was released on 2018 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Organic molecules play a myriad of roles in the surface ocean. They are the building blocks of proteins, the alphabet of genetic information, and the language in which microorganisms communicate. The small biomolecules that are the readout of cellular activity, or metabolites, or are of particular interest. Some metabolites like compatible solutes fuel the microbial loop, while others like vitamins act as micronutrients to algae. In this dissertation, I aim to use liquid-chromatography mass-spectrometry (LC-MS) to observe pools of metabolites to answer long-standing questions in microbial ecology and organic matter cycling in the surface ocean, specifically tackling gaps in our knowledge regarding cobalamin (vitamin B12) and microbial metabolomics. In Chapters 2 and 3, I develop and utilize LC-MS techniques to directly measure cobalamin in dissolved and particulate organic matter. These chapters reveal an underappreciated chemical diversity of cobalamin and cobalamin-like compounds in marine systems, revealing that cyanobacteria produce a cobalamin-like compound, pseudocobalamin. I tie this chemical diversity to the biochemistry, ecology, and evolution of marine cobalamin producers in Chapter 3. In Chapters 4 and 5, I use an analytical technique to perform targeted and untargeted metabolomics. These techniques aim to identify and quantify the entire metabolome of an organism (as in Chapter 4) or community (as in Chapter 5). In a controlled laboratory setting, I harness metabolomics to understand how two species of diatoms experience cobalamin limitation; this work is presented in Chapter 4. In Chapter 5, I explore the whole community metabolome across a natural oceanographic gradient in temperature, salinity, and nutrients in the North Pacific Ocean. Here I offer some of the first observations of several metabolites in natural marine systems and hypothesize on their roles in microbial processing of organic matter.
Download or read book Marine OMICS written by Se-Kwon Kim and published by CRC Press. This book was released on 2016-11-18 with total page 922 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides comprehensive coverage on current trends in marine omics of various relevant topics such as genomics, lipidomics, proteomics, foodomics, transcriptomics, metabolomics, nutrigenomics, pharmacogenomics and toxicogenomics as related to and applied to marine biotechnology, molecular biology, marine biology, marine microbiology, environmental biotechnology, environmental science, aquaculture, pharmaceutical science and bioprocess engineering.
Download or read book Microbial Metabolomics written by David J. Beale and published by Springer. This book was released on 2016-12-05 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book brings together contributions from global experts who have helped to facilitate the exciting and rapid advances that are taking place in microbial metabolomics. The main application of this field is in clinical and veterinary microbiology, but there is a great potential to apply metabolomics to help to better understand complex biological systems that are dominated by multiple-species microbial populations exposed to changing growth and nutritional conditions. In particular, environmental (e.g., water, soil), food (e.g., microbial spoilage, food pathogens), and agricultural and industrial applications are seen as developing areas for microbial metabolomics. As such, the book includes contributions with clinical, environmental, and industrial perspectives.
Download or read book Diversity Antimicrobial Activity and Metabolomics Study of Marine Microbes from Puerto Rico and Hawaii written by Ruhnaz Kashfi and published by . This book was released on 2018 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: The need for novel antibacterial compounds has stimulated the exploration of marine environment for bioactive secondary metabolites. However, marine bacterial screening often rediscoveres known species, leading to an inefficient discovery process that is laborious and time consuming. The approach used in this investigation involves genus and possibly species level identification of a large number of samples from diverse locations, mass spectrometry-based finger printing/metabolomic analysis, study of the volatile metabolites and creation and expansion of database containing new actinobacterial species. In this study, replicate samples from 19 geographical locations of Puerto Rico and seven collection sites from Hawaii were analyzed to investigate the diversity of marine actinobacteria regarding antimicrobial properties and growth requirements for bacteria from similar tropical conditions. 16S rRNA sequencing on extracted, PCR amplified DNA samples helped identification at least to the genus level. Chemical fingerprinting, based on chemical analysis of secondary metabolites excreted during cultivation, is one possible discovery tool to explore the chemical picture of the produced set of metabolites without the individual isolation or any prior knowledge about the produced matabolites. Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was found to be an excellent tool for natural product analysis in this study. UPLC-MS analyzed ethyl acetate (EA) extracts of the bacterial samples with data being analyzed using Progenesis QI and Metaboanalyst software. Volatile metabolites from these bacterial strains were analyzed using GC-MS and ChromaTOF software. We used a nonderivatization approach, which allows faster analysis and successful observation of different classes of volatile organic compounds present in these samples. We tested antibacterial activity for each actinobacterial culture using both cell free supernatants and crude extracts against five different antibiotic resistant pathogens. Among 80 initial samples, nine showed antimicrobial activity against Acinetobacter baumannii (AB), Methicillin resistant Staphylococcus aureus (MRSA), and Enterococcus faecalis (EPH) . One strain from Hawaii exhibited broad spectrum activity. Actinobacterial library creation was accomplished using Bruker Biotyper software from samples analyzed in a Bruker UltrafleXtreme, a state of the art MALDI-TOF/TOF system. Extension of the database using samples from different geographical locations, combined with antimicrobial activity testing results will make future identification of new, novel actinobacterial species routine.
Download or read book Marine Microorganisms written by Leo M.L. Nollet and published by CRC Press. This book was released on 2016-09-19 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: The marine environment covers 70% of the earth’s surface and accounts for 98% of the potentially habitable space. The bioactives from marine microorganisms include antibiotic compounds, polysaccharides, inhibitors, enzymes, peptides, and pigments. These are used in various fields of biology that range from nutraceuticals to cosmeceuticals. Recent scientific investigations have revealed that marine microbial compounds exhibit various beneficial biological effects, such as anti-inflammatory, anti-cancer, anti-HIV, anti-hypertensive, and anti-diabetic. Marine Microorganisms: Extraction and Analysis of Bioactive Compounds sheds light on the extraction, clean-up, and detection methods of major compounds from marine organisms. The book includes information on the different classes of marine microorganisms and the different bioactives that can be extracted from bacteria, fungi and microalgae. Divided into 7 chapters, the book covers bioactive marine natural products, such as marine microbes, seaweeds, and marine sponges as potential sources of drug discovery, and focuses on analysis methods of the biocomponents from marine microorganisms. A useful reference tool for researchers and students, this book provides current knowledge about isolation and analysis methods of the bioactives and provides insight into the various bioactives of marine microbes toward nutraceutical and pharmaceutical development.
Download or read book Reproducible and Automated Analysis of Metabolomics Data to Assess the Biosynthetic Capacities of Organisms in Microbial Communities written by Mahnoor Zulfiqar and published by . This book was released on 2024* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The thesis entitled "Reproducible and automated analysis of metabolomics data to assess the biosynthetic capacities of organisms in microbial communities", investigates the role of marine microbial communities in maintaining ecological balance through the exchange of metabolites. High-throughput omics techniques have transformed microbial research, where metabolomics is crucial to elucidate and analyzes these metabolites that are involved in the metabolic exchange and hence, affect our ecosystem. We developed Metabolome Annotation Workflow (MAW), a workflow for untargeted tandem mass spectrometry data. The workflow takes the tandem mass spectrometry data as input and annotates chemical structures to the metabolites detected in the input spectra. FAIR (Findable, Accessible, Interoperable, Reusable) principles have been implemented to the workflow to enable reproducibility and portability of the workflow across different workflow platforms and operating systems. This workflow was then applied to a marine microalgae, the diatom Skeletonema marinoi to expand the chemical space produced by this diatom. Furthermore, we developed another module of MAW, that detected statistically significant metabolites among co-culture condition of two microorgansism (S. marinoi and a marine haptophyte Prymnesium parvum), to explores chemical interactions between the two organisms to uncover insights into microbial communication.
Download or read book YOUMARES 9 the Oceans Our Research Our Future written by Simon Jungblut and published by Springer Nature. This book was released on 2020-01-01 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book summarizes peer-reviewed articles and the abstracts of oral and poster presentations given during the YOUMARES 9 conference which took place in Oldenburg, Germany, in September 2018. The aims of this book are to summarize state-of-the-art knowledge in marine sciences and to inspire scientists of all career stages in the development of further research. These conferences are organized by and for young marine researchers. Qualified early-career researchers, who moderated topical sessions during the conference, contributed literature reviews on specific topics within their research field. .
Download or read book Linking Microbial Metabolism and Organic Matter Cycling Through Metabolite Distributions in the Ocean written by Winifred M. Johnson (Ph. D.) and published by . This book was released on 2017 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Key players in the marine carbon cycle are the ocean-dwelling microbes that fix, remineralize, and transform organic matter. Many of the small organic molecules in the marine carbon pool have not been well characterized and their roles in microbial physiology, ecological interactions, and carbon cycling remain largely unknown. In this dissertation metabolomics techniques were developed and used to profile and quantify a suite of metabolites in the field and in laboratory experiments. Experiments were run to study the way a specific metabolite can influence microbial metabolite output and potentially processing of organic matter. Specifically, the metabolic response of the heterotrophic marine bacterium, Ruegeria pomeroyi, to the algal metabolite dimethylsulfoniopropionate (DMSP) was analyzed using targeted and untargeted metabolomics. The manner in which DMSP causes R. pomeroyi to modify its biochemical pathways suggests anticipation by R. pomeroyi of phytoplankton-derived nutrients and higher microbial density. Targeted metabolomics was used to characterize the latitudinal and vertical distributions of particulate and dissolved metabolites in samples gathered along a transect in the Western Atlantic Ocean. The assembled dataset indicates that, while many metabolite distributions co-vary with biomass abundance, other metabolites show distributions that suggest abiotic, species specific, or metabolic controls on their variability. On sinking particles in the South Atlantic portion of the transect, metabolites possibly derived from degradation of organic matter increase and phytoplankton-derived metabolites decrease. This work highlights the role DMSP plays in the metabolic response of a bacterium to the environment and reveals unexpected ways metabolite abundances vary between ocean regions and are transformed on sinking particles. Further metabolomics studies of the global distributions and interactions of marine biomolecules promise to provide new insights into microbial processes and metabolite cycling.
Download or read book Grand Challenges in Marine Biotechnology written by Pabulo H. Rampelotto and published by Springer. This book was released on 2018-05-15 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves as essential reading for research scientists and biotechnologists from both academia and industry working in marine biotechnology and related disciplines. The book discusses recent advances and challenges in terms of science, technology, innovation, and policy for the development of the field; and how marine biotechnology may provide new solutions to some of the grand challenges faced by our society. Written in an accessible language, the book is also recommended as a reference text for decision-makers in government and non-governmental organizations in their efforts to foster the development of a global blue economy. With less than 5 % of the vast and rich marine environment explored, our seas and oceans represent a virtually unexplored resource for the discovery of novel product, processes, and development of bio-inspired synthetic drugs with biotechnological potential. As such, the marine environment has been considered Earth's last frontier of exploration. Recent advances in molecular techniques are providing the necessary tools to access on a larger scale the still-untapped ocean resources and, consequently, unveil the promise of the blue biotechnology. Governments are recognizing the potential of marine biotechnology to provide solutions to some of the Grand Challenges of the 21st Century such as sustainable energy and food sources, identification of novel drugs for improved health treatments, and providing new industrial materials and processes. For this reason, advances in marine biotechnology may foster the much-needed source of innovation and economic growth in many countries, and pave the way towards the development of a global blue economy, i.e. a new economic model based on the sustainable exploration of our ocean ecosystems.
Download or read book Chemical Ecology of Marine Microbial Communities written by Alyssa Marie Demko and published by . This book was released on 2021 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine sediments cover ~70% of the earth and host rich and diverse microbial communities. These microbial communities play an integral role in global nutrient cycling and the food web. They can be both a source of disease and/or an agent of mitigation through the natural products they produce, which can have cascading impacts on community structure and ecosystem function. Despite their importance, marine sediment microbes remain woefully understudied. The goal of this dissertation was to use next generation sequencing technology and newly developed bioinformatic pipelines to gain insight into these complex communities. First, I sought to reevaluate the 1% culturability paradigm by comparing sediment microbial communities using culture-dependent and culture-independent techniques. This comparative approach not only highlighted that >1% of sediment bacteria could be cultured, but also revealed the biases associated with culture-independent methods. Thirty-nine genera were identified in culture that were not detected with culture-independent methods, including some taxa that were fairly divergent from known cultured representatives. Next, I wanted to assess connections between sediment microbial communities, the sediment metabolome and sediment characteristics across varying spatial scales. To do this, microbial communities were sampled at three spatial scales, 1 m2 quadrats, 10 m transects, and sites across a 12 km2 area. Additionally, a small molecule in situ resin capture (SMIRC) method was employed to capture the metabolome present in sediments. The results from this study indicate that microbial diversity significantly increases with spatial scale and that sediment characteristics, such as grain size and nitrate concentrations, are significantly correlated with microbial communities. The SMIRC method was able to capture natural products and revealed the vast chemical landscape of marine sediments, much of which remains unexplored. Finally, I sought to evaluate how microbial communities in marine sediments vary in relation to the surrounding benthic environment by comparing fringing and back reefs of Mo'orea, French Polynesia. Even within a small area, ~1 km2, fringing and back reef sediment communities were distinct from each other. Back reefs exhibited greater richness and diversity in the microbial communities while fringing reefs had greater metabolomic richness. Supervised correlative analyses identified connections between microbes, metabolites and environmental characteristics such as nutrient concentration. Many of the taxa identified in the network analyses belong to relatively unknown lineages, providing important insight into the role these lineages may be playing in their communities. In conclusion, the results of this dissertation provide fundamental baseline information about the microbial communities and metabolites associated with marine sediments.
