Download or read book Microbial Iron Acquisition and Organic Matter Cycling in the Marine Environment written by Lauren Manck and published by . This book was released on 2020 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a scarce but essential micronutrient for microbial growth in the marine environment, iron plays a critical role in supporting marine primary productivity and is tightly coupled to the cycling of carbon and additional macronutrients. While significant progress in recent years has been made in understanding the distribution of iron and iron-binding ligands in the marine environment, many questions remain regarding the mechanistic processes underlying these distributions. Heterotrophic bacteria serve as the primary drivers of the turnover of organic matter in the marine environment and have a significant cellular iron requirement, making them an important link between iron and carbon biogeochemical cycles. The work presented in this dissertation aims to improve our understanding of the molecular mechanisms by which heterotrophic marine bacteria acquire iron from their surroundings and the subsequent effects of their metabolic activities on both iron and carbon biogeochemical cycling. We have first developed Alteromonas macleodii ATCC 27126 as a model marine organism for the study of iron acquisition by heterotrophic bacteria. This has allowed us to characterize outer membrane TonB-dependent transporters for organically complexed forms of iron across the genus Alteromonas. This work revealed that a high diversity of iron-ligand compounds in the marine environment are potentially bioavailable. We have also utilized Alteromonas macleodii ATCC 27126 as a model organism for studying the functional role of siderophore production in iron acquisition in the marine environment. Through the insertional inactivation of the petrobactin biosynthetic pathway, we have determined that siderophore production increases the bioavailability of non-labile iron sources such as particulate minerals. Finally, in microcosm field experiments, we examined the transcriptional response of natural heterotrophic bacterial communities in the southern California Current System to iron additions demonstrating direct iron limitation of this community with consequences for downstream carbon processing. Together, this work sheds light on the role of heterotrophic bacteria at multiple points within the marine iron cycle, from the incorporation of iron into the marine environment to controlling the balance between the export and recycling of iron and macronutrients. It is our hope that this work results in an improved mechanistic understanding of marine iron biogeochemical cycling.
Download or read book The microbial ferrous wheel iron cycling in terrestrial freshwater and marine environments written by David Emerson and published by Frontiers E-books. This book was released on with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past 15 years, there has been steady growth in work relating to the microbial iron cycle. It is now well established that in anaerobic environments coupling of organic matter utilization to Fe reduction is a major pathway for anaerobic respiration. In iron-rich circumneutral environments that exist at oxic-anoxic boundaries, significant progress has been made in demonstrating that unique groups of microbes can grow either aerobically or anaerobically using Fe as a primary energy source. Likewise, in high iron acidic environments, progress has been made in the study of communities of microbes that oxidize iron, and in understanding the details of how certain of these organisms gain energy from Fe-oxidation. On the iron scarcity side, it is now appreciated that in large areas of the open ocean Fe is a key limiting nutrient; thus, a great deal of research is going into understanding the strategies microbial cells, principally phytoplankton, use to acquire iron, and how the iron cycle may impact other nutrient cycles. Finally, due to its abundance, iron has played an important role in the evolution of Earth’s primary biogeochemical cycles through time. The aim of this Research Topic is to gather contributions from scientists working in diverse disciplines who have common interests in iron cycling at the process level, and at the organismal level, both from the perspective of Fe as an energy source, or as a limiting nutrient for primary productivity in the ocean. The range of disciplines may include: geomicrobiologists, microbial ecologists, microbial physiologists, biological oceanographers, and biogeochemists. Articles can be original research, techniques, reviews, or synthesis papers. An overarching goal is to demonstrate the environmental breadth of the iron cycle, and foster understanding between different scientific communities who may not always be aware of one another’s work.
Download or read book The Chemistry of Microbiomes written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-07-19 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.
Download or read book Structure and Function of Microbial Communities Processing Dissolved Organic Matter in Marine Environments written by Hila Elifantz and published by . This book was released on 2007 with total page 127 pages. Available in PDF, EPUB and Kindle. Book excerpt: The current study added to the growing information regarding the composition of bacterial community in aquatic environments and the role of specific bacterial groups in DOM assimilation. In particular, this study was the first to unfold the relation between structure and function of the bacterial community in the Arctic Ocean, the only cold environment studied in that aspect to date. The molecular study of GH5 revealed the potential of the community for polysaccharides degradation, however, more need to be done to broaden our understanding of the mineralization of these compounds in the marine environment.
Download or read book Advances in Microbial Iron Cycling written by Lei Yan and published by Frontiers Media SA. This book was released on 2022-07-13 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Iron Cycle in Oceans written by Stéphane Blain and published by John Wiley & Sons. This book was released on 2016-12-19 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an up to date view of iron biogeochemistry in the ocean. It encompasses the description of iron speciation, the analytical methods used to measure the different iron forms in seawater and the different iron biogeochemical models.
Download or read book Biogeochemistry of Marine Dissolved Organic Matter written by Dennis A. Hansell and published by Elsevier. This book was released on 2024-07-04 with total page 870 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biogeochemistry of Marine Dissolved Organic Matter, 3rd edition is the most up-to-date revision of the fundamental reference for the biogeochemistry of marine dissolved organic matter. Since its original publication in June 2002, the science, questions, and priorities have advanced, and the editors of this essential guide, have added nine new chapters, including one on the South China Sea. An indispensable manual edited by the most distinguished experts in the field, this book is addressed to graduate students, marine scientists, and all professionals interested in advancing their knowledge of the field. Features up-to-date knowledge on DOM, including 9 new chapters Presents the only published work to synthesize recent research on dissolved organic carbon in the South China, a region receiving a great deal of attention in recent decades Offers contributions by world-class research leaders
Download or read book Aquatic Ecosystems Interactivity of Dissolved Organic Matter written by Stuart Findlay and published by Academic Press. This book was released on 2003 with total page 534 pages. Available in PDF, EPUB and Kindle. Book excerpt: Overviews of the source, supply and variability of DOM, surveys of the processes that mediate inputs to microbial food webs, and syntheses consolidating research findings provide a comprehensive review of what is known of DOM in freshwater. This book will be important to anyone interested in understanding the fundamental factors associated with DOM that control aquatic ecosystems."--BOOK JACKET.
Download or read book Carbon and Nutrient Fluxes in Continental Margins written by Kon-Kee Liu and published by Springer Science & Business Media. This book was released on 2010-02-11 with total page 757 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a product of the joint JGOFS (Joint Global Ocean Flux Study)/LOICZ (Land–Ocean Interactions in the Coastal Zone) Continental Margins Task Team which was established to facilitate continental margins research in the two projects. It contains signi cant information on the physical, biogeochemical, and ecosystems of continental margins nationally and regionally and provides a very valuable synthesis of this information and the physical, biogeochemical and ecosystem processes which occur on continental margins. The publication of this book is timely as it provides a very strong foundation for the development of the joint IMBER (Integrated Marine Biogeochemistry and Ecosystems Research)/LOICZ Science Plan and Implemen- tion Strategy for biogeochemical and ecosystems research in the continental margins and the impacts of global change on these systems. This initiative will move forward integrated biogeochemical and ecosystems research in the continental margins. We thank all the contributors to this volume and especially Kon-Kee Liu who has dedicated a great deal of time to ensuring a high-quality book is published. IMBER Scienti c Steering Committee Julie Hall LOICZ Scienti c Steering Committee Jozef Pacyna v 1 Preface In general, interfaces between the Earth’s larger material reservoirs (i. e. , the land, atmosphere, ocean, and sediments) are important in the control of the biogeoche- cal dynamics and cycling of the major bio-essential elements, including carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and silicon (Si), found in organic matter and the inorganic skeletons, shells, and tests of benthic and marine organisms.
Download or read book Marine Microbiology written by Colin Munn and published by Garland Science. This book was released on 2003-10-16 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine micro-organisms play a vital role in the maintenance of our planet, a fact which will have great bearing on our ability to respond to problems such as population increase, over-exploitation of fisheries, climate change and population. Powerful new tools, especially in molecular biology, remote sending and deep-sea exploration, have led to astonishing discoveries of the abundance and diversity of marine microbial life and its role in global ecology. New tools and an increased interest in ecological factors have caused an upsurge of interest in this field of study. The book aims to convey the fascinating discoveries and great importance of this fast moving discipline to the student. Marine Microbiology is divided into three sections: the first reviews the main features of the marine environment and key aspects of marine microbial life; the second looks at the role of marine microorganisms in ecology, and the final section considers some of the applications of this knowledge, looking into areas such as disease and biodegradation.
Download or read book The Role of Microorganisms in the Cycling of Organic Matter in Anoxic Marine Environments A Culture independent Approach Saara Suominen written by Saara Suominen and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Microbial Cycling of Marine High Molecular Weight Dissolved Organic Matter written by Oscar Abraham Sosa and published by . This book was released on 2016 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microorganisms play a central role mediating biogeochemical cycles in the ocean. Marine dissolved organic matter (DOM) – a reservoir of organic solutes and colloids derived from plankton is a major source of carbon, nutrients, and energy to microbial communities. The biological transformation and remineralization of DOM sustains marine productivity by linking the microbial food web to higher trophic levels (the microbial loop) and exerts important controls over the cycles of carbon and bioessential elements, such as nitrogen and phosphorus, in the sea. Yet insight into the underlying metabolism and reactions driving the degradation of DOM is limited partly because its exact molecular composition is difficult to constrain and appropriate microbial model systems known to decompose marine DOM are lacking. This thesis identifies marine microorganisms that can serve as model systems to study the metabolic pathways and biochemical reactions that control an important ecosystem function, DOM turnover. To accomplish this goal, bacterial isolates were obtained by enriching seawater in dilution-to-extinction culturing experiments with a natural source of DOM, specifically, the high molecular weight (HMW) fraction (>1 kDa nominal molecular weight) obtained by ultrafiltration. Because it is relatively easy to concentrate and it is fairly uniform in its chemical composition across the global ocean and other aquatic environments, HMW DOM has the potential to serve as a model growth substrate to study the biological breakdown of DOM. The phylogeny, genomes, and growth characteristics of the organisms identified through this work indicate that HMW DOM contains bioavailable substrates that may support widespread microbial populations in coastal and open-ocean environments. The availability of ecologically relevant isolates in culture can now serve to test hypothesis emerging from cultivation-independent studies pertaining the potential role of microbial groups in the decomposition of organic matter in the sea. Detailed studies of the biochemical changes exerted on DOM by selected bacterial strains will provide new insight into the processes driving the aerobic microbial food chain in the upper ocean.
Download or read book Microbial Iron Cycling on Trichodesmium Colonies written by Kelly Lynn Roe and published by . This book was released on 2012 with total page 167 pages. Available in PDF, EPUB and Kindle. Book excerpt: Iron is an important micronutrient to the colonial cyanobacterium Trichodesmium, a photosynthetic diazotroph. Trichodesmium is known to be limited by iron, but field studies of iron acquisition by this organism have been complicated by the fact that natural colonies have a large associated bacterial community. The research presented in this thesis will focus on understanding iron bioavailability to Trichodesmium and the associated heterotrophic bacteria and how this may affect iron cycling in the colony environment. The bioavailability of a selection of iron sources to Trichodesmium and two representative associated bacteria, Microscilla marina and Silicibacter TrichCH4B is investigated in Chapter 2. The representative bacteria are shown to acquire iron from a diverse selection of iron complexes while Trichodesmium is shown to access iron from only the most labile iron sources. A model of iron uptake on Trichodesmium colonies is created using Trichodesmium- and bacteria-specific iron uptake rates, and results suggest that bacteria are potentially responsible for the majority of iron uptake in a colony environment. The iron acquisition pathways used by Trichodesmium to acquire two forms of bioavailable iron, inorganic iron and ferric citrate complexes, are investigated in Chapter 3. Trichodesmium is shown to utilize two different iron acquisition pathways, extracellular reduction of inorganic iron and a semi-specific iron transport system for ferric citrate. Both mechanisms may give Trichodesmium a means to compete for iron in the colony environment. In Chapter 4, the Trichodesmium-associated Roseobacter Silicibacter TrichCH4B is shown to have an uptake system specific for the utilization of heme complexes and the functional characterization of this system is described. Further investigation and identification of heme uptake systems in the Roseobacter clade, an abundant bacterial lineage in the ocean, and the detection of heme genes in environmental samples suggest that heme utilization may be wide spread in the marine environment and may be a pathway for iron recycling in the ocean. Based on these studies of iron bioavailability and utilization, iron must be efficiently cycled in a Trichodesmium colony, a unique oceanic particle environment.
Download or read book Metal Ions in Biological Systems written by Astrid Sigel and published by CRC Press. This book was released on 1998-01-09 with total page 826 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Volume 35 covers the biological cycling of iron in oceans; the transport of iron in microorganisms, fungi, and plants; the roles and properties of siderophores; the regulation of iron transport and uptake in animals, plants, and microorganisms, and more. "
Download or read book Indicators of Iron Metabolism in Marine Microbial Genomes and Ecosystems written by Shane Lahman Hogle and published by . This book was released on 2016 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed picture of the chemical speciation of iron in seawater is required to comprehensively understand the marine iron cycle and its downstream effects on the cycles of other nutrient elements. Although much progress has been made in our understanding of iron-binding ligands in the marine environment, numerous questions remain as to their identity, structure, and biogeochemical sources and sinks. The recent proliferation of "omic" data from cultured organisms and environmental samples now allows us to address some of these chemical questions from a biologically informed perspective. The research presented in this thesis examines some of the specific molecular mechanisms and underlying genetics that marine heterotrophic bacteria use to acquire iron from the unique chemical conditions of the marine environment. We first examined and reviewed the sources, transformations, and ultimate fate of heme and hemoproteins, iron containing molecules, in seawater. We used comparative genomics to characterize trace metal acquisition strategies in the marine Roseobacter and SAR11 clades, and we examined these uptake pathways in light of marine trace metal chemistry, microbial ecology, and genome evolution. We developed a genetic system for targeted mutagenesis and insertional inactivation of a predicted heme uptake TonB dependent outer membrane transporter in a model marine bacterial strain Ruegeria sp. TM1040. In a series of iron amended incubations from the California current ecosystem, we examined the heterotrophic bacterial assemblage composition using high throughput sequencing of bacterial marker genes in conjunction with chemical speciation and algal physiology. Finally, we examined putative iron uptake pathways in a metatranscriptome from natural marine phyto- and bacterioplankton communities in the southern California current and integrated patterns in the metatranscriptomic data with biogeochemical field data. Our results have revealed genes responsible for trace metal metabolisms in marine heterotrophic bacteria and highlight heme uptake as a model heterotrophic iron assimilation pathway that is potentially important in particulate iron remineralization. In turn, we have provided additional insight to the chemical speciation of iron in seawater and have revealed potential molecular mechanisms by which heterotrophic bacteria shape the marine iron cycle.
Download or read book Iron and the Ecology of Marine Microbes written by Laure-Anne Ventouras and published by . This book was released on 2013 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Iron is a cofactor of a number biochemical reactions that are essential for life. In the marine environment, this micronutrient is a scarce resource that limits processes of global importance such as photosynthesis and nitrogen fixation. Given that marine microorganisms play a central role in modulating such biogeochemical cycles, understanding how their distribution, diversity and activity may be affected by changes in iron availability is key. This thesis explores how the availability of iron affects the ecology of marine microbial populations and communities. At the population level, I characterized the prevalence and diversity of iron acquisition strategies in specific populations of marine vibrios with distinct micro-habitat preferences. Using a combination of genomics and functional screens, I showed that siderophore-based iron acquisition is not conserved at the organismlevel but represents a stable trait at the population level. This population-level trait further appears to play a role in driving the diversification of specific vibrio populations, especially of those that are thought to prefer particles as a micro-habitat. At the community level, I measured whole microbial community responses to iron addition in microcosm experiments in different regions of the Pacific Ocean. Using metagenomics, I characterized the impact of iron availability on the microbial community structure of the Central Equatorial Pacific Ocean. This study showed that addition of iron to an iron-limited ecosystem triggers a phytoplankton bloom dominated by Pseudo-nitZschia-like diatoms, which in turn stimulate a Bacteroidetes population functionally distinct from the ambient free-living population. In the North Pacific Subtropical Gyre, I explored how iron availability impacts microbial community gene expression dynamics. Using a metatranscriptomic approach I showed that in that environment, the impact of iron was tightly connected to the supply of other limiting macronutrients, and seems to mostly affect photosynthetic organisms. This initial study paves the way for more in depth and longer-term studies to further investigate the effects of iron on the dynamics of the microbial community in the North Pacific Subtropical Gyre. Taken together data and analyses presented in this thesis demonstrate how iron availability can shape the ecology of marine microorganisms at population, community and functional levels.
