Download or read book QPCR Analysis of Functional Genes in Iron rich Microbial Mats at an Active Hydrothermal Vent System Loihi Seamount Hawaii written by Kelsey J. Jesser and published by . This book was released on 2014 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Microbial and Viral Roles in Hydrothermal Vent Iron Mat Elemental Cycling and Ecology at the Loihi Seamount written by Rebecca Vandzura and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Iron microbial mats at hydrothermal vents mediate fluxes of iron (Fe) and other elements to the oceans. These mats are formed by Zetaproteobacteria, which are the only apparent Fe-oxidizers in the mats. Most studies have focused on this dominant class, and their roles in carbon fixation and Fe biomineral formation. Iron mats host a diverse group of non-Zetaproteobacteria microorganisms, including viruses, and we do not yet know how these organisms contribute to biogeochemical cycling and interact with the Zetaproteobacteria. To address this, we sequenced and analyzed paired metagenomes and metatranscriptomes from three samples of Fe mats at Lō'ihi Seamount, Hawaii. These included a small, discrete sample of surface mat, as well as two large, bulk samples that included deeper regions of the mat. One deep mat sample was additionally used for shipboard Fe(II) and O2 addition experiments. Our results suggest that mat depth influences the diversity of the microbial community. Our shallow mat sample was almost entirely Zetaproteobacteria while the deeper mat samples had greater diversity, and were composed of taxa such as Zetaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Planctomycetes and Marinimicrobia. The shallow mat sample also had higher expression of carbon fixation genes and aerobic terminal oxidase genes; while the bulk samples had a larger number of polysaccharide degradation enzymes and higher expression of anaerobic processes. Within the deep mat samples, the Deltaproteobacteria were the second most abundant taxon. We identified an abundant novel clade of Deltaproteobacteria in an unknown order called DTB120, which contains genomic evidence for iron oxidation coupled to nitrate reduction. Overall, the mat microbes showed significant expression of genes involved in oxygen, nitrogen, carbon, and iron cycles. In addition to the microbes, we found evidence for viral contigs and complete viral genomes. CRISPR spacer identification revealed a history of infection among members of this microbial community. Together, the previously uncharacterized DTB120 and the viruses help link iron, nitrogen and carbon biogeochemistry in Lō'ihi Seamount hydrothermal vent Fe mats. This suggests that the flanking community is contributing to the chemical cycles and ecological success of the Fe mats.
Download or read book Functional Analysis of Cyc2 in Microbial Mat Communities of Mariana Arc and Back arc Hydrothermal Vents written by Christina A. Turner and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The primary production by Zetaproteobacteria at iron-rich vents of the Mariana Arc and back-arc supports high microbial diversity. In microaerophilic circumneutral pH, Zetaproteobacteria are able to produce energy by oxidizing ferrous iron (Fe2+) from the vent effluent with the presence of a key gene involved in their iron-oxidation, Cyc2, a fused cytochrome-porin. These genes are found in all Zetaproteobacteria known to date. This study combines molecular quantitative techniques with metagenomic analyses to enhance our confidence in gene quantification from environmental samples. The occurrence of cyc2 was quantified from microbial mat communities at NW Eifuku, NW Rota-1, Snail and Urashima Vents using primers designed from a composite metagenome to better understand the potential impact of Zetaproteobacteria metabolism on these iron-rich microbial communities. Based on a multiple sequence alignment and phylogenetic analysis, two distinct groups of the Zetaproteobacteria cyc2 were identified and termed Cluster 1 cyc2 and Cluster 3 cyc2 based on the nomenclature provided by Chan et al. (2018). Multidimensional scaling of Zetaproteobacteria SSU rRNA and cyc2 gene abundances showed that the presence of the two cyc2 sequence variants are strongly driven by an array of different vent fluid chemicals. We also report on the phylogenetic relationship between the two cyc2 variants and other representative FeOB, as well as the distribution of cyc2 gene abundances across the Mariana hydrothermal vent sites along the Arc and back-arc. Overall, this provides insight on the ecological and evolutionary implications of Zetaproteobacteria iron-oxidation represented at the community-level across a wide-range of geochemical parameters.
Download or read book Zeta proteobacteria Dominate the Formation of Microbial Mats in Low temperature Hydrothermal Vents at Loihi Seamount Hawaii written by Allen C. Rassa and published by . This book was released on 2008 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Complex Microbial Mat Communities Used to Assess Primer Selection for Targeted Amplicon Surveys written by Lindsey Smith and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying, in which a marker gene is selected for DNA amplification, has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. The most commonly used marker gene is the small subunit ribosomal RNA (SSU rRNA) gene, due to its ubiquity across all cellular organisms and the presence of both conserved and variable regions. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene were assessed using environmental samples from microbial mats surrounding iron-dominated hydrothermal vents. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities at Kamaʻehuakanaloa Seamount were elucidated in detail. Both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at iron-dominated hydrothermal vents.
Download or read book Bacterial Diversity and Community Structure of Lithotrophically driven Microbial Mats from the Mariana Arc and Back arc written by Kevin W. Hager and published by . This book was released on 2016 with total page 104 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Analysis of Microbial Communities in Hydrothermal Vents in Yellowstone Lake Yellowstone National Park Using 16S RDNA Functional Metabolic Genes and Enrichment Culture Methods written by Andrew M. Wier and published by . This book was released on 2006 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Geomicrobiology of Iron Oxyhydroxide Mats in Acidic Geothermal Springs of Yellowstone National Park Wyoming United States of America written by Mark Andrew Kozubal and published by . This book was released on 2010 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The microbial community structure and function in acidic, high-temperature ironoxidizing geothermal springs of Yellowstone National Park was investigated utilizing a variety of complementary approaches including microbial cultivation and characterization, geochemical analysis of aqueous and solid phases, phylogenetic and functional gene analysis, comparative genomics, and protein sequence modeling. Cultivation efforts resulted in the isolation of an Fe(II)-oxidizing chemolithotroph Metallosphaera yellowstonii MK1 T. The distribution and relative abundance of MK1-like 16S rRNA gene sequences was evaluated in 14 acidic geothermal springs containing Fe(III)-oxide microbial mats. Highly related MK1-like sequences (>99% sequence similarity) were consistently observed in Fe(III)-oxide mats across a temperature range of 55 to 80 °C. Quantitative PCR confirmed that organisms highly similar to strain MK1 comprised up to 40% of the total archaeal community of selected sites. Four additional isolates were obtained from thermophilic Fe(III) microbial mats including Sulfobacillus sp. MK2, Sulfolobus sp. MK3, Acidicaldus sp. MK5 and Crenarchaeota sp. MK4, which represents a new taxonomical lineage at the class level or higher. A draft genome has been assembled for M. yellowstonii strain MK1 and comparative studies indicate significant similarity to Metallosphaera sedula in regards to putative genes involved in iron and sulfur oxidation, carbon fixation, oxygen reduction and heavy metal resistance. Analysis of gene sequences reveal 7 heme copper oxidases (subunit I) and a variety of genes with possible importance in Fe(II) oxidation including the foxA-J gene cluster, a cbsA cytochrome b 558/566, and a novel sequence coding for a putative blue multi-copper protein (mco). Expression screens and reverse transcriptaseqPCR on samples from three ASC environments and in cultures grown autotrophically show that the fox gene cluster and mco are important when Fe(II) serves as the electron donor. Protein sequence analysis of foxC indicates a novel lysine-lysine or lysine arginine heme b binding domain and is likely the cytochrome component of a heterodimer complex with foxG as a ferredoxin subunit. Analysis of mco indicates a novel multicopper blue protein with two plastocyanin type I copper domains with only three homologous sequences found in Genbank. Both putative proteins likely play an important role in electron transport from Fe(II) to oxygen through Fox Proteins.
Download or read book Microbial Diversity and Geochemical Energy Sources of Tutum Bay Ambitle Island Papua New Guinea an Arsenic rich Shallow sea Hydrothermal System written by Nancy Hsia Akerman and published by . This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: I investigate the hydrothermal system located in Tutum Bay, Ambitle Island, Papua New Guinea, a shallow-sea system ~5 - 10 meters below sea level that is arsenic-rich. Hydrothermal vents in the bay expel fluids with arsenite (AsIII) concentrations as high as 950 [mu]g/L. To determine the role that Tutum Bay microorganisms might play in mediating As-redox reactions, three approaches were used: analyzing the geochemical environment for energy sources, characterizing the archaeal community composition of the sediments, and conducting culture-dependent As-cycling experiments. The second chapter of this dissertation discusses an energetic study of potential chemolithotrophic metabolic reactions, including As-redox reactions. Results show that under the environmental conditions present in Tutum Bay, significant amounts of energy for microbial metabolism could be gained from a number of reactions, including AsIII oxidizing reactions using oxygen and nitrate as terminal electron acceptors. In the third chapter, a 16S rRNA-based culture-independent investigation of the archaeal community structure of the As-rich sediments shows the presence of diverse uncultured archaea at sites both near and far from hydrothermal venting. The studies in these two chapters demonstrate that the Tutum Bay hydrothermal system provides an environment hospitable to metabolically and phylogenetically diverse microorganisms. Finally, in chapter four, evidence of functional genes related to both arsenate- and arsenite-redox were recovered from sediments examined via molecular screening. It was also shown that microbial consortia enriched from Tutum Bay sediments and porefluids were able to reduce arsenate (AsV) to arsenite when incubated at 30°C in an AsV-rich growth medium. These results demonstrate that As-redox microorganisms exist in shallow-sea hydrothermal environments and broaden our understanding of not only the types of microbial species that are capable of As-redox, but also the unique environmental niches in which life can exist and thrive.
Download or read book Community Structure of Benthic Microbial Mats at Hydrothermal Springs in Crater Lake Oregon written by Amanda Stromecki and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Crater Lake, Oregon is an oligotrophic freshwater caldera lake fed bythermally and chemically-enriched hydrothermal springs. These vents distinguish Crater Lake from other freshwater systems and provide a unique ecosystem for study. This study examines the microbial community structure of hydrothermal mat communities found in the bottom of Crater Lake. Small subunit rRNA gene amplicon sequencing from eight microbial mats was used to assess community structure. These findings revealed a relatively homogeneous, yet diverse bacterial community. High alpha diversity and low beta diversity indicates that these communities that are likely fueled by homogeneous and consistent hydrothermal fluids. An examination of autotrophic taxa abundance revealed the potential importance of reduced iron and sulfur inputs to the primary productivity of these mats. Chemoautotrophic potential within the mats was dominated by iron oxidation from Gallionella and Mariprofundus and by sulfur oxidation from Sulfuricurvum and Thiobacillus with an additional contribution of nitrite oxidation from Nitrospira. These data link the importance of the detected autotrophic metabolisms driven by fluids derived from benthic hydrothermal springs to Crater Lake's entire lentic ecosystem
Download or read book M ssbauer Spectroscopy of Environmental Materials and Their Industrial Utilization written by Enver Murad and published by Springer Science & Business Media. This book was released on 2011-06-28 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mössbauer Spectroscopy of Environmental Materials and their Industrial Utilization provides a description of the properties of materials formed on the earth's surface, their synthetic analogs where applicable, and the products of their modifications in the course of natural processes, such as weathering, or in industrial processing as reflected in their Mössbauer spectra. Particular emphasis is placed on the way in which these processes can be observed and elucidated through the use of Mössbauer spectroscopy. The first chapter covers the basic theory of the Mössbauer effect and Chapters 2 and 3 deal with the nuts and bolts of experimental Mössbauer spectroscopy. The principles of these first three chapters, illustrated with many case studies, are applied to different areas of interest in Chapters 4 through 12. The book is directed to a broad audience ranging from graduate students in environmental sciences or chemical engineering with little or no expertise in Mössbauer spectroscopy to researchers from other disciplines who are familiar with this technique but wish to learn more about possible applications to environmental materials and issues.
Download or read book Advances in Microbial Ecology written by Bernhard Schink and published by Springer Science & Business Media. This book was released on 2000-06-30 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume 16 of Advances in Microbial Ecology has a difficult history. Nearly halfway through its completion, Gwynfryn Jones had to resign as managing edi tor for health reasons, and he asked me to take over. I want to thank Gwyn for his dedicated work in this publication series, and wish him all the best for the future. After the change in editorship, some authors had to be encouraged on rather short notice to provide their chapters in order to make appearance of this volume possible within a reasonable period of time. Nonetheless, I think that the articles we present with this volume represent an enjoyable collection of up-to-date con tributions to microbial ecology. In my own understanding, microbial ecology com prises the elucidation of microbial activities in natural or semi natural environ ments, including physiology, biochemistry, population dynamics, and interactions with all the biotic and abiotic environmental conditions microbes encounter. This comprises studies on single organisms in defined cultures in an ecological per spective, the analysis of microbial activities in complex environments, as well as the development of concepts for the interactions of microorganisms with the world in which they live. Last but not least, microbial ecology is not an exotic science studied exclusively in remote places untouched by human beings.
Download or read book Extremophiles written by Koki Horikoshi and published by Wiley-Liss. This book was released on 1998-01-30 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text is devoted to a particular class of microbe & focuses on its ecology, systematics, physiological & molecular biology. Also included is a discussion of potentially exploitable biotechnological & industrial uses for extremophiles.
Download or read book Links Between Geological Processes Microbial Activities Evolution of Life written by Yildirim Dilek and published by Springer Science & Business Media. This book was released on 2008-07-01 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial systems in extreme environments and in the deep biosphere may be analogous to potential life on other planetary bodies and hence may be used to investigate the possibilities of extraterrestrial life. This book examines the mode and nature of links between geological processes and microbial activities and their significance for the origin and evolution of life on the Earth and possibly on other planets. This is a truly interdisciplinary science with societal relevance.
Download or read book Introduction to Geomicrobiology written by Kurt O. Konhauser and published by John Wiley & Sons. This book was released on 2009-03-12 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Geomicrobiology is a timely and comprehensive overview of how microbial life has affected Earth’s environment through time. It shows how the ubiquity of microorganisms, their high chemical reactivity, and their metabolic diversity make them a significant factor controlling the chemical composition of our planet. The following topics are covered: how microorganisms are classified, the physical constraints governing their growth, molecular approaches to studying microbial diversity, and life in extreme environments bioenergetics, microbial metabolic capabilities, and major biogeochemical pathways chemical reactivity of the cell surface, metal sorption, and the microbial role in contaminant mobility and bioremediation/biorecovery microbiological mineral formation and fossilization the function of microorganisms in mineral dissolution and oxidation, and the industrial and environmental ramifications of these processes elemental cycling in biofilms, formation of microbialites, and sediment diagenesis the events that led to the emergence of life, evolution of metabolic processes, and the diversification of the biosphere. Artwork from the book is available to instructors at www.blackwellpublishing.com/konhauser.
Download or read book Deep Subsurface Microbiology written by Andreas Teske and published by Frontiers Media SA. This book was released on 2015-07-01 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deep subsurface microbiology is a highly active and rapidly advancing research field at the interface of microbiology and the geosciences; it focuses on the detection, identification, quantification, cultivation and activity measurements of bacteria, archaea and eukaryotes that permeate the subsurface biosphere of deep marine sediments and the basaltic ocean and continental crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and – at best - incompletely understood microbial populations. In spatial extent and volume, Earth's subsurface biosphere is only rivaled by the deep sea water column. So far, no deep subsurface sediment has been found that is entirely devoid of microbial life; microbial cells and DNA remain detectable at sediment depths of more than 1 km; microbial life permeates deeply buried hydrocarbon reservoirs, and is also found several kilometers down in continental crust aquifers. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that have shaped the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical role as long-term organic carbon repository, inorganic electron and energy source, and subduction recycling engine continues to be explored by current research at the interface of microbiology, geochemistry and biosphere/geosphere evolution. This Research Topic addresses some of the central research questions about deep subsurface microbiology and biogeochemistry: phylogenetic and physiological microbial diversity in the deep subsurface; microbial activity and survival strategies in severely energy-limited subsurface habitats; microbial activity as reflected in process rates and gene expression patterns; biogeographic isolation and connectivity in deep subsurface microbial communities; the ecological standing of subsurface biospheres in comparison to the surface biosphere – an independently flourishing biosphere, or mere survivors that tolerate burial (along with organic carbon compounds), or a combination of both? Advancing these questions on Earth’s deep subsurface biosphere redefines the habitat range, environmental tolerance, activity and diversity of microbial life.
Download or read book Aquatic Geomicrobiology written by Donald E. Canfield and published by Gulf Professional Publishing. This book was released on 2005-03-31 with total page 660 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbes catalyze countless chemical reactions in nature which control the chemistry of the environment. Aquatic Geomicrobiology looks at these reactions and their effect on the aquatic environments from the perspective of the microbes involved. The volume begins with three introductory chapters outlining the basic principles of microbial systematics, microbial ecology, and chemical thermodynamics. These provide a framework for exploring the microbial control of elemental cycling in the remaining chapters. Readers will learn how microbes control the cycling of elements, the structure of the microbial ecosystems involved, and what environmental factors influence the activities of microbial populations. Also available in hardback Written by international experts in the microbial ecology and biogeochemistry of aquatic systems Includes introductory chapters on microbial systematics, principles of microbial ecology, and chemical thermodynamics Contains over 1500 references
