Download or read book Molecular Analysis of Microbial 16S RRNA McrA DsrAB and PmoA Genes from Deep sea Hydrothermal Vent and Cold Seep Sites written by and published by . This book was released on 2008 with total page 81 pages. Available in PDF, EPUB and Kindle. Book excerpt: Methane and sulfide are primary sources of energy supporting the dense macrobiological communities often found in cold seep areas and both free-living and symbiotic microorganisms depend on energy provided by the sharp gradient of sulfide and the reservoir of methane in the underlying sediments. In deep-sea hydrothermal vent areas, sulfide is typically the primary source of energy for microbial primary production. To investigate microbial populations and community structure in these areas, microbial communities from both deep-sea hydrothermal vent (Rainbow and Logatchev hydrothermal vent fields, Mid-Atlantic Ridge, Atlantic Ocean; 9°N hydrothermal vent area, East Pacific Rise, Pacific Ocean) and cold seep areas (Blake Ridge, western Atlantic Ocean; Florida Escarpment, Gulf of Mexico) were evaluated by molecular phylogenetic analysis of 16S rRNA, mcrA, dsrAB and pmoA gene sequences. Twenty-one clone libraries were obtained using DNA from friable vent chimney material (hydrothermal vent areas) and from vertically subsampled (top, middle and bottom) sediment core samples (cold seep areas), screened by RFLP and sequenced. At the Florida Escarpment, phylogenetic analysis of bacterial 16S rDNA suggests the dominance of epsilon-Proteobacteria in the top zone, the epsilon- delta- and [gamma]-Proteobacteria in the middle zone and the delta-Proteobacteria in the bottom zone of the core. Archaeal diversity was low throughout, but increased with depth. Cold seep mcrA sequences were distributed among the ANME-2c, -2d and -2e groups. Clone library dsrAB sequences grouped primarily within the orders Desulfobacteriales, Syntrophobacteriales and the gram-positive order Clostridales. Clone library pmoA sequences grouped among the Type I methanotrophs ([gamma]-proteobacteria) within the order Methylococcales. Most sequences recovered represented as-yet-uncultivated phylotypes distinct from any other cultivated or environmental clones. In addition, this investigation presents for the first time environmental mcrA sequences detected from chimney samples collected from a bare basalt, high-temperature deep-sea hydrothermal vent area that are related to ANME-2e sequences previously shown to be associated with the anaerobic oxidation of methane.

Download or read book Marine Hydrocarbon Seeps written by Andreas Teske and published by Springer Nature. This book was released on 2020-02-04 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an up-to-date overview of the microbiology, biogeochemistry, and ecology of marine hydrocarbon seeps, a globally occurring habitat for specialized microorganisms and invertebrates that depend on natural hydrocarbon seepage as a food and energy source. Prominent examples include the briny hydrocarbon seeps and mud volcanoes on the continental slope of the Gulf of Mexico and in the Mediterranean, the hydrothermally heated hydrocarbon seeps at Guaymas Basin (Mexico), and the oil and gas seeps off the coast of California and in the Gulf of Mexico. Featuring topical chapters by leading researchers in the area, the book describes geological settings, chemical characteristics of hydrocarbon seepage, hydrocarbon-dependent microbial populations, and ecosystem structure and trophic networks at hydrocarbon seeps. Further, it also discusses applied aspects such as bioremediation potential (oil-degrading microorganisms).

Download or read book A Molecular Analysis of Subsurface Microbial Communities Across a Hydrothermal Gradient in Okinawa Trough Sediments written by Leah Brandt and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Decades ago, life in the deep subseafloor was assumed to be non-existent. At thousands of meters under the surface and decoupled from the photic zone, the deep marine world is a hostile environment. However, the discovery of life thriving around deep-sea hydrothermal vent systems revolutionized our perception of the extent and tenacity of life on Earth and set in motion a movement to understand life at the seafloor and its significant in global biogeochemical and nutrient cycling. Seafloor sediments host an incredible diversity of microbial life, and much interest has sought to understand the spatial and stratigraphic extent of the biosphere, and also taxonomic and functional capacities of such resilient organisms. This dissertation represents a series of studies centered around these concepts I analyze samples from a sediment profile exposed to a hydrothermal gradient as a scaled-down proxy for how microbial life may exist and/or adapt to conditions as they become buried deeper into the subsurface.I have focused on the application of culture-independent, molecular methods to understand whether the taxonomic and functional data reflect changes through this temperature gradient in support of a more temperature-adapted microbial community. In chapter 2, I examined the microbial community composition at approximately meter intervals by analyzing the taxonomically specific 16S rRNA marker gene. We presumed the biosphere to be restricted to only the upper 15 m, based on phylotype vetting and decreased sequencing recovery below. However, we observed a significant proportion of archaeal sequences throughout the 15 m, with a particularly high abundance in the deepest 15 m horizon. An in-depth look at the taxa at 15 m indicates an appearance of an uncultured, high-temperature taxon here, and an abundance of a thermophilic, methane-oxidizing archaeon, which suggests thermophilic niche at this particular temperature/depth regime. The exciting results from Chapter 2 were the motivation for a continued metagenomics analysis of select samples in the same sediment profile for Chapter 3. Probing through total genomic DNA from six samples, I found evidence for temperature-dependent trends through the detection of genes of specific proteins involved in thermal processes, and attempted to correlate these genes with a taxonomic identity. I found that the deepest, hottest sample encompassed organisms from both thermophilic and hyperthermophilic temperature regimes. The dichotomy reflected between the existence of two temperature-specific niches implies that, due to the dynamic nature of the hydrothermal vent system, the deepest horizon may be undergoing a transition in temperature, thus, microbial community. Lastly, Chapter 4 was intended to provide a dataset from extractable RNA in order to distinguish representatives of the active microbial population from those represented from extant DNA; however, many challenges encountered in extraction and sequencing yield have restricted the dataset and ability to make reliable interpretations.Considering the current state of knowledge in the marine subsurface due to its challenges in sampling, low biomass yield, and diversity distantly related to what is known from surface life, this work herein contributes greatly to our understanding of microbial biogeography in terms of temperature constraints in marine subsurface sediments. The challenges in phylotype vetting and need for quality controls speak to the degree of complexities in performing and interpreting molecular analyses from subseafloor sediments. Moreover, I have also produced significant datasets, both 16S rRNA gene and metagenomics, that can continue to be used for future investigations and comparisons of microbial life in the marine seafloor.

Download or read book Environmental Metagenomics to Assess Microbial Community Diversity in the Deep sea Using 16S RDNA Amplification written by Mandy Hyun-Joo Kim and published by . This book was released on 2005 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Marine Microbiome and Biogeochemical Cycles in Marine Productive Areas written by Alejandro A. Murillo and published by Frontiers Media SA. This book was released on 2020-01-16 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Integrated omics Study of Deep sea Microbial Community and New Pseudoalteromonas Isolate written by Jieying Wu and published by . This book was released on 2013 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis research focuses on phylogenetic and functional studies of microbial communities in deep-sea water, an untapped reservoir of high metabolic and genetic diversity of microorganisms. The presence of photosynthetic cyanobacteria and diatoms is an interesting and unexpected discovery during a 16S ribosomal rRNA-based community structure analyses for microbial communities in the deep-sea water of the Pacific Ocean. Both RT-PCR and qRT-PCR approaches were employed to detect expression of the genes involved in photosynthesis of photoautotrophic organisms. Positive results were obtained and further proved the functional activity of these detected photosynthetic microbes in the deep-sea. Metagenomic and metatranscriptomic data was obtained, integrated, and analyzed from deep-sea microbial communities, including both prokaryotes and eukaryotes, from four different deep-sea sites ranging from the mesopelagic to the pelagic ocean. The RNA/DNA ratio was employed as an index to show the strength of metabolic activity of deep-sea microbes. These taxonomic and functional analyses of deep-sea microbial communities revealed a `defensive' life style of microbial communities living in the deep-sea water. Pseudoalteromonas sp. WG07 was subjected to transcriptomic analysis by application of RNA-Seq technology through the transcriptomic annotation using the genomes of closely related surface-water strain Pseudoalteromonas haloplanktis TAC125 and sediment strain Pseudoalteromonas sp. SM9913. The transcriptome survey and related functional analysis of WG07 revealed unique features different from TAC125 and SM9913 and provided clues as to how it adapted to its environmental niche. Also, a comparative transcriptomic analysis of WG07 revealed transcriptome changes between its exponential and stationary growing phases.

Download or read book Methods for the Study of Deep Sea Sediments Their Functioning and Biodiversity written by Roberto Danovaro and published by CRC Press. This book was released on 2009-12-21 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: For years scientists viewed the deep sea as calm, quiet, and undisturbed, with marine species existing in an ecologically stable and uniform environment. Recent discoveries have completely transformed that understanding and the deep sea is recognized as a complicated and dynamic environment with a rich diversity of marine species. Carefully designe

Download or read book 16S RRNA Gene Microarray Analysis of Microbial Communities in Ethanol stimulated Subsurface Sediment written by and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Evolutionary and Functional Genomics of Bacteria from the Cold Deep Sea written by Federico M. Lauro and published by . This book was released on 2007 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chapter 1 introduces the deep sea environment. Recent studies of sequence-independent diversity of deep-sea microbial communities are reviewed and re-analyzed. These are compared to sequence-dependent studies evidencing the need for new culturing and isolation methods for deep-sea bacteria. The chapter ends by reviewing the current state-of-the-art of deep-sea genetics and genomics and describes the general features of the genomes of piezophiles. Chapter 2 describes the development of three new vectors for use in Photobacterium profundum and other Gram-negative bacteria. The first one (pEE3) is a suicide vector for insertional inactivation of genes. The second one is a general purpose cloning vector (pFL122) based on the broad-host-range replicon RSF1010. The third one is a broad-host-range vector carrying an arabinose-inducible promoter to use for gene expression studies. Chapter 3 explores the diversity evolution of cultured piezophiles. Three novel strains of piezophilic bacteria were isolated, one of them being the first Gram-positive piezophile ever isolated. Most of the cultured piezophiles, belong only to a narrow range of phylogenetic lineages which cluster within clades of known psychrophiles. In the ensuing discussion the hypothesis that cold-adapted piezophiles might evolve from polar water psychrophiles and disseminated through deep-sea oceanic currents is presented. During the study specific ribosomal RNA features of the 16S of piezophiles were identified. These features are correlated with the pressure adaptation of the strains. Chapter 4 describes a high-throughput transposon mutagenesis approach to identify genes important for growth at low temperature and high pressure. These genes belong to a wide variety of categories which are discussed in detail. A large fraction of the mutants impaired in growth at low temperature had gene disruptions in genes for the synthesis of extracellular polysaccharides, providing the first direct evidence of the role of the cell envelope in adaptation to low temperature. Chapter 5 presents the results of the sequencing and the analysis of the genome of the shallow water strain P. profundum 3TCK. The genome is compared to that of the deep-water strain P. profundum SS9 identifying unique regions that might be conferring fitness in different habitats. Among these is a cluster of genes for motility important for swimming in high viscosity found only in the deep-water strain, a set of genes for UV resistance found only in the shallow water strain, and the specific rRNA features described in chapter 3 found only in the deep-water strain. The motility gene clusters are further characterized evidencing the role for particular flagellins and motor proteins for swimming at high pressure. The UV and ribosomal features are exchanged between the shallow- and the deep- water strains and the phenotypes of the resulting strains are characterized.

Download or read book Microbial Metabolism in the Deep Ocean written by Roberta Lynn Hansman and published by . This book was released on 2008 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt: To address the major role microorganisms play in the biogeochemical cycling of carbon and nutrients in the marine environment, the work presented in this dissertation uses a combination of geochemical and molecular biological techniques to investigate carbon and nitrogen metabolism in the planktonic microbial community of the deep ocean. A method was developed to isolate microbial DNA from the marine water column suitable for radiocarbon analysis, which was then applied to determine the sources of carbon fueling microbial production in the mesopelagic. Fresh organic matter delivered from sinking particles was confirmed as an important carbon source for free-living microbes, but the extent of autotrophic carbon fixation was also significant and variable with depth, highlighting the requirement for particle-delivered reduced nitrogen by the total microbial community in the deep ocean. Both findings stressed the importance of constraining particle-derived carbon and nitrogen flux to the deep ocean. The importance of methane as a carbon source in unique environments above cold methane seeps was examined using both stable carbon isotope measurements of microbial DNA and quantitative PCR of the gene encoding for particulate methane monooxygenase. The carbon isotope measurements showed that methane-carbon played an insignificant role in fueling planktonic microbial production in the deep water column just above methane seeps. The PCR measurements substantiated this result by showing that the methane oxidizing community represented only a small percentage of the microbial community in this environment. And finally, bacterial heterotrophic nitrate assimilation was studied and determined to increase with depth and/or nitrate concentration, but appeared to only be a possible nitrogen acquisition method for a small (> 1%) fraction of the bacterial community. Sequencing of the heterotrophic nitrate assimilation gene isolated from the marine environment further demonstrated that these genes were depth stratified. In addition both isotopic analyses and molecular biological techniques such as quantitative PCR indicated distinct differences between free-living and particle-attached microbial communities. Overall, future research efforts should be focused on expanding the current data set, constraining particle flux, and gaining a better understanding of microbial physiology, including in situ growth rates, in the subsurface marine environment.

Download or read book Microbial Ecology of Active Marine Hydrothermal Vent Deposits written by Gilberto Eugene Flores and published by . This book was released on 2011 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discovery of deep-sea hydrothermal vents in 1977 revealed an ecosystem supported by chemosynthesis with a rich diversity of invertebrates, Archaea and Bacteria. While the invertebrate vent communities are largely composed of endemic species and exist in different biogeographical provinces, the possible factors influencing the distribution patterns of free-living Archaea and Bacteria are still being explored. In particular, how differences in the geologic setting of vent fields influence microbial communities and populations associated with active vent deposits remains largely unknown. The overall goal of the studies presented in this dissertation was to examine the links between the geologic setting of hydrothermal vent fields and microorganisms associated with actively venting mineral deposits at two levels of biological organization. At the community level, bar-coded pyrosequencing of a segment of the archaeal and bacterial 16S rRNA gene was employed to characterize and compare the microbial communities associated with numerous deposits from several geochemically different vent fields. Results from these studies suggest that factors influencing end-member fluid chemistry, such as host-rock composition and degassing of magmatic volatiles, help to structure the microbial communities at the vent field scale. At the population level, targeted cultivation-dependent and -independent studies were conducted in order to expand our understanding of thermoacidophily in diverse hydrothermal environments. Results of these studies expanded the phylogenetic and physiological diversity of thermoacidophiles in deep-sea vent environments and provided clues to factors that are influencing the biogeography of an important thermoacidophilic archaeal lineage. Overall, these studies have increased our understanding of the interplay between geologic processes and microorganisms in deep-sea hydrothermal environments.

Download or read book written by and published by . This book was released on 1771 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Characterization of Microbial Associations with Methanotrophic Archaea and Sulfate reducing Bacteria Through Statistical Comparison of Nested Magneto FISH Enrichments written by and published by . This book was released on 2016 with total page 31 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Microbial Diversity in Sediments and Gas Hydrates Associated with Cold Seeps in the Gulf of Mexico written by Heath Jordan Mills and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: A molecular phylogenetic approach was used to characterize the composition of microbial communities from two gas hydrate sedimentary systems in the Gulf of Mexico. Nucleic acids were extracted from three distinct locales on surface breaching gas hydrate mounds, i.e., sediment overlaying gas hydrate, sediment/hydrate interface and sediment-free hydrate, and from three sediment depths, i.e., 0-2, 6-8 and 10-12 cm, in Beggiatoa sp. mat-associated sediments located several meters from exposed gas hydrate. Samples were collected from a research submersible (water depth 550-575 m) during two research cruises aboard the R/V Seward Johnson I and II funded by the NSF Life in Extreme Environments program. The 16S rRNA gene and 16S rRNA were amplified using PCR and reverse transcription-PCR, respectively, from DNA and RNA extracted from the total microbial community. The primers targeted microorganisms at the domain-specific, i.e., Bacteria and Archaea, and group-specific, i.e., sulfate-reducing bacteria (SRB) and putative anaerobic methane-oxidizing (ANME) archaea, level. Sequence analysis of the Bacteria clones revealed that the microbial communities were primarily dominated by Deltaproteobacteria. Other Proteobacteria classes, including Epsilon- and Gammaproteobacteria, represented a large fraction of the total microbial community isolated from the sediment overlying hydrate sample and the metabolically active fraction of the 0-2 cm sediment depth sampled from the Beggiatoa sp. mat-associated sediments. Sequence analysis indicated the majority of the archaeal clones were most closely related to Methanosarcinales, Methanomicrobiales and distinct lineages within the ANME groups. Several novel lineages were identified including a fourth ANME-2 clade, i.e., ANME-2D, and three clades with no closely related previously sequenced 16S rRNA gene clones or isolates, i.e., Unclassified Bacteria groups 1 and 2 and Unclassified Euryarchaeota. These studies represent the first 16S rRNA gene and 16S rRNA phylogenetic-based description of microbial communities extant in sediment-free gas hydrate and in methane-rich hydrate-associated and Beggiatoa sp.-associated sediments from a hydrocarbon seep region in the Gulf of Mexico.

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 Identification of Free Living and Particle Associated Microbial Communities Present in Hadal Regions of the Mariana Trench written by Jonathan Tarn and published by . This book was released on 2016 with total page 50 pages. Available in PDF, EPUB and Kindle. Book excerpt: Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.

Download or read book Ehrlich s Geomicrobiology written by Henry Lutz Ehrlich and published by CRC Press. This book was released on 2015-10-15 with total page 643 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in geomicrobiology have progressed at an accelerated pace in recent years. Ehrlich's Geomicrobiology, Sixth Edition surveys various aspects of the field, including the microbial role in elemental cycling and in the formation and degradation of minerals and fossil fuels. Unlike the fifth edition, the sixth includes many expert contributors