Download or read book Microbial Diversity Metabolic Potential and Transcriptional Activity Along the Inner Continental Shelf of the Northeast Pacific Ocean written by Anthony D. Bertagnolli and published by . This book was released on 2012 with total page 127 pages. Available in PDF, EPUB and Kindle. Book excerpt: Continental shelves located along eastern boundary currents occupy relatively small volumes of the world's oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of hypoxia and anoxia, events that are detrimental to larger macro-faunal species. Microbial communities, however, are metabolically diverse, capable of utilizing alternative electron donors and acceptors, and can withstand transient periods of low dissolved oxygen. Understanding the phylogenetic and metabolic diversity of microorganisms in these environments is important for assessing the impact hypoxic events have on local and global biogeochemistry. Several molecular ecology tools were used to answer questions about the distribution patterns and activities of microorganisms residing along the coast of Oregon in this dissertation. Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. However, substantial depth dependent changes were observed, with samples collected in the bottom boundary layer (BBL) displaying significant differences from those collected in the surface layer. Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. Thaumarchaea displayed significant depth dependent increases during the summer, and were detected at maximal frequencies during periods of hypoxia, suggesting that nitrification maybe influenced by local changes in dissolved oxygen. Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. Samples collected during the spring, prior to upwelling clustered independently of those collected during the summer, during a period of upwelling, and did not display any clear stratification. Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. Overall, these observations suggest that depth impacts microbial community diversity, metabolic potential, and transcriptional activity in shallow areas of the Northeast Pacific Ocean. The increase in lithotrophic genes and transcripts in the BBL suggests that this microbial community includes many organisms that are able to use inorganic electron donors for respiration. We speculate that the dissolved organic material in the BBL is semi-labile and not available for immediate oxidation, favoring the growth for microorganisms that are able to use alternative electron donors.

Download or read book Microbial Ecology in the North Pacific Subtropical Gyre written by Samuel T. Wilson and published by Frontiers Media SA. This book was released on 2018-11-16 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: The microbial community in the oligotrophic North Pacific Subtropical Gyre is dominated by unicellular microorganisms less than a few micrometers in size. Despite the persistent low nutrient concentrations, phytoplankton growth rates appear near maximal, sustained by the recycling of nutrients with plankton population sizes regulated by processes such as zooplankton grazing and viral lysis. Seasonal pulses of particle export to the deep sea and increases in phytoplankton abundance occur during the summer months; however, the factors that result in these imbalances in growth and loss processes are not well understood. Nonetheless, as a result of persistent fieldwork and development of sensitive methodologies, the biogeochemical and ecological dynamics occurring over timescales ranging from diel to interannual are being revealed. This Research Topic covers multiple aspects of microbial oceanography in the oligotrophic North Pacific Subtropical Gyre including identification and isolation of microorganisms, quantification of microbial biomass and turnover, metabolism and physiological activities, and microbial-mediated biogeochemical cycling. All of the papers use field data collected by either the Hawaii Ocean Time-series (HOT) program, the Center for Microbial Oceanography: Research and Education (C-MORE) or the Simons Collaboration on Ocean Processes and Ecology (SCOPE). These three programs have greatly increased our understanding of microbial ecology and biogeochemical cycling in the NPSG, in part by providing unparalleled access to the NPSG on oceanographic research vessels.

Download or read book Dimensions of Microbial Biodiversity in the North Pacific Subtropical Gyre written by Jessica A. Bryant and published by . This book was released on 2017 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microorganisms support all life in the oceans and are fundamental to maintaining a habitable biosphere on Earth. However an understanding of their taxonomic and functional distributions across space and time are just beginning to emerge and numerous niches within the marine environment are still awaiting exploration. The motivation for this thesis is to improve our understanding of distributions of microbes and their metabolic potential at Station ALOHA, a long-term study site representative of the North Pacific Subtropical Gyre (NPSG). We observed changes in diversity and community composition at Station ALOHA across time, ocean depth and on plastic debris, a new anthropogenically derived niche in the NPSG. Despite surface waters only experiencing mild seasonal variation in the abiotic environment, using near monthly picoplankton samples collected across a 2-year period at 25m depth, we observed that microbial community composition correlated with solar irradiance, thereby demonstrating seasonal trends. Ocean surface microbes are known to differ fundamentally from those found in the ocean's interior, yet the nature of the transitions from shallow to deep surface water communities is not well understood. Using a high resolution depth series across twelve time points, we observed that microbial communities partitioned into four groups that consisted of all samples above the deep chlorophyll maximum (DCM), 125m samples below the DCM, all 200 m samples and all 500, 770 and 1000m samples. Our data also revealed a sharp discontinuity in genomic traits including GC%, genome size and proteome elemental composition spanning the DCM, suggesting that nitrogen limitation was key to shaping this sharp genomic transition zone across disparate clades. In contrast, we observed that plastic debris in the NPSG forms a habitat for complex microbial assemblages that have organisms, lifestyles and metabolic pathways that are distinct and potentially less nutrient limited than picoplankton in the surrounding water column. Taken together this work helps expand our understanding of spatial and temporal distributions of microorganisms at Station ALOHA and can help direct future microbial oceanography surveys, highlighting new directions for future research.

Download or read book The Role of Macrobiota in Structuring Microbial Communities Along Rocky Shores written by and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

Download or read book Microbial Ecology in the North Pacific Subtropical Gyre written by and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The microbial community in the oligotrophic North Pacific Subtropical Gyre is dominated by unicellular microorganisms less than a few micrometers in size. Despite the persistent low nutrient concentrations, phytoplankton growth rates appear near maximal, sustained by the recycling of nutrients with plankton population sizes regulated by processes such as zooplankton grazing and viral lysis. Seasonal pulses of particle export to the deep sea and increases in phytoplankton abundance occur during the summer months; however, the factors that result in these imbalances in growth and loss processes are not well understood. Nonetheless, as a result of persistent fieldwork and development of sensitive methodologies, the biogeochemical and ecological dynamics occurring over timescales ranging from diel to interannual are being revealed. This Research Topic covers multiple aspects of microbial oceanography in the oligotrophic North Pacific Subtropical Gyre including identification and isolation of microorganisms, quantification of microbial biomass and turnover, metabolism and physiological activities, and microbial-mediated biogeochemical cycling. All of the papers use field data collected by either the Hawaii Ocean Time-series (HOT) program, the Center for Microbial Oceanography: Research and Education (C-MORE) or the Simons Collaboration on Ocean Processes and Ecology (SCOPE). These three programs have greatly increased our understanding of microbial ecology and biogeochemical cycling in the NPSG, in part by providing unparalleled access to the NPSG on oceanographic research vessels.

Download or read book Microbial Diversity in Restored Wetlands of San Francisco Bay written by and published by . This book was released on 2013 with total page 2 pages. Available in PDF, EPUB and Kindle. Book excerpt: Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils, we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.

Download or read book Molecular Signatures of Microbial Metabolism in the Marine Water Column written by Jenan J. Kharbush and published by . This book was released on 2015 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lipid biomarkers are valuable tools in studies of microbial metabolic diversity and function in both past and present marine ecosystems, but the distribution and biological sources of many of these biomarkers in the modern ocean have yet to be sufficiently defined. This dissertation examines two major classes of lipid biomarker compounds that are widely distributed in marine environments: hopanoids, biomarkers for bacteria, and intact polar diacylglycerols (IP-DAGs), potential biological tracers of recent carbon and nutrient cycling. The distribution and structural diversity of these lipid compounds is analyzed in tandem with genetic and metagenomic data, both expanding the knowledge related to the structural distribution of these lipids in the marine environment, and illuminating key aspects of the ecology of the producing organisms. This work is detailed in six chapters, consisting of an introduction, four research-oriented chapters, and concluding remarks. Chapters 2, 3, and 4 focus on the bacterial hopanoids. First, analysis of hopanoid structural diversity and abundance across oxygen gradients in the Santa Barbara Basin was complemented by a genetic survey, identifying a potential connection between hopanoid production and metabolic strategies associated with low oxygen environments. Next, this connection was further investigated using qPCR and surveys of existing metagenomes to quantify the relative abundance of groups of hopanoid producers in low oxygen regions of the Eastern North Pacific and Eastern Tropical Pacific oxygen minimum zones. Results revealed that dominant hopanoid producers in these regions are not Proteobacteria as previously hypothesized but instead are nitrite-utilizing organisms such as nitrite-oxidizing and anaerobic ammonia-oxidizing bacteria. Finally, a survey of an extensive metagenomic dataset from the Red Sea illuminated the distribution of hopanoid producers in a biogeochemically-distinct environment relative to those previously analyzed, and confirming that hopanoid producers may also play roles in marine nitrogen cycling. Chapter 5 details an exploratory investigation of the structural distribution of various classes of IP-DAGs, in the oligotrophic Tonga Trench. Results provide new insight into potential biological sources of IP-DAGs, and identify structures that may be useful as indicators of the contribution of groups of picophytoplankton to export production, or of in situ heterotrophic production at depth.

Download or read book Marine Ammonium oxidizing Bacteria written by Bess B. Ward and published by . This book was released on 1982 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Composition and Functional Potential of Hadal Microbial Communities written by Logan Peoples and published by . This book was released on 2018 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: Hadal trenches, oceanic locations deeper than 6,000 m, are one of the most enigmatic environments on Earth. Characterized by hydrostatic pressures reaching 16,000 pounds per square inch, these sites are expected to contain microbial diversity adapted to in situ conditions and distinct from that found at shallower depths. In this dissertation, we describe the composition and functional potential of microbial communities in the Mariana and Kermadec trenches, two hadal sites in the Pacific Ocean, using high-throughput 16S rRNA gene sequencing, meta- and single-cell genomics, and culture-based analyses. We show that hadopelagic microbial communities, which are distinct from those at abyssal depths, appear adapted to in situ hydrostatic pressure conditions and contain a number of putative hadal bathytypes, including members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter. Hadal sediment consortia contained many novel microbial lineages not previously identified in other datasets, especially within deeper sediment horizons. We characterized the functional potential of these sediment microbes using metagenomics and single-cell sequencing and showed that members of these communities have pathways for diverse carbon utilization and nitrogen and sulfur cycling. Mariana and Kermadec trench pelagic and sediment communities were distinct between one another, in part because of higher primary productivity in the overlying water column in the Kermadec relative to the Mariana Trench. Although trenches are geographically isolated, many abundant lineages in both the pelagic and sediment habitats were related to those found in other hadal and abyssal datasets. Comparisons of genomes from both trenches indicate some members may belong to the same species. These findings show the possibility for dispersal of microbes in the deep-ocean and the connectivity of trenches with each other and shallower sites. Finally, we look to the future of hadal exploration by describing the development of a new full-ocean depth lander and water sampler capable of maintaining high hydrostatic pressure upon recovery. Deployments in the Mariana Trench at depths exceeding 10,700 m and the collection of genomes from the hadal lineages Aquibacter and Marinimicrobia show the power of this instrumentation. This dissertation provides a deep dive into microbial community composition and functional potential within hadal trenches.

Download or read book Microbial Interactions in the North Pacific Ocean written by Phillip Jackson Gainer and published by . This book was released on 2018 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: A majority of Earth’s surface is covered by the marine ecosystem. This ecosystem is characterized by the numerical dominance of microbes, both eukaryotic and prokaryotic and their infecting viruses. As the basis of the food web in marine systems these members of the microbial community are vital to the function of the planet. Despite their noted importance, the microbial communities in many oceanic regions are largely uncharacterized due to geographic isolation, including the largest oceanic basin on the planet, the North Pacific Ocean. Basin scale studies of the North Pacific have primarily focused on characterization of abundance and diversity of bacteria and viruses. Interactions between these microbial constituents have been largely unexplored on a basin scale. As such, this body of work aims to generate hypotheses on the influence that biotic interactions have on microbial community structure and evolution on a basin scale. First, the role biotic interactions responsible for shaping virus abundances and production rates in the North Pacific Ocean were examined. We found that virus abundance and production rates correlated to bacterial taxa that are enriched in particle associated communities, indicating that particles may serve as sites of increased viral activity in the North Pacific Ocean. Secondly, we utilized network analysis to explore inferred bacterial co-occurrences within the North Pacific Basin. We found that diverse taxa participate in at least one significant co-occurrence with another microbe within this basin. Further, network topology parameters, such as high connectance and low modularity, proposed to be hallmarks of community stability differed regionally, indicating that the North Pacific Subtropical Gyre may be more robust to environmental changes. Finally, we developed an assay to screen for Synechococcus WH7803 transposon mutants that are resistant to a co-occurring cyanomyovirus, to identify genes necessary for lytic viral infection. Characterization of these genes will allow for a more holistic understanding of the interactions between this cyanobacterium and its infecting viruses in the natural environment. These findings highlight the importance of considering interactions between microbial entities in the marine system in understanding the functioning of microbial communities in the North Pacific basin.

Download or read book The Microbial Fate of Carbon in High latitude Seas Impact of the Microbial Loop on Oceanic Uptake of CO sub 2 written by and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation examines pelagic microbial processes in high-latitude seas, how they affect regional and global carbon cycling, and how they might respond to hypothesized changes in climate. Critical to these interests is the effect of cold temperature on bacterial activity. Also important is the extent to which marine biological processes in general impact the inorganic carbon cycle. The study area is the Northeast Water (NEW) Polynya, a seasonally-recurrent opening in the permanent ice situated over the northeastern Greenland continental shelf. This work was part of an international, multi-disciplinary research project studying carbon cycling in the coastal Arctic. The first chapter describes a simple model which links a complex marine food web to a simplified ocean and atmosphere. The second chapter investigates the inorganic carbon inventory of the summertime NEW Polynya surface waters to establish the effect of biological processes on the air-sea pCO[sub 2] gradient. The third and fourth chapters use a kinetic approach to examine microbial activities in the NEW Polynya as a function of temperature and dissolved organic substrate concentration, testing the so-called Pomeroy hypothesis that microbial activity is disproportionately reduced at low environmental temperatures owing to increased organic substrate requirements. Together, the suite of data collected on microbial activities, cell size, and grazing pressure suggest how unique survival strategies adopted by an active population of high-latitude bacteria may contribute to, rather than detract from, an efficient biological carbon pump.

Download or read book Investigating Marine Microbial Metabolism and Diversity of Arctic Ecosystems written by David Colatriano and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The world's oceans are essential for sustaining life on Earth and harbour a vast diversity of organisms. Marine microbes play crucial roles in global biogeochemical cycling and are at the base of marine food webs. Due to the technical difficulties associated with sampling northern marine systems, relatively little is known about the microbial community composition and metabolism of these ecosystems. In this thesis work, the community composition and metabolism of northern marine ecosystems, including the Saint Lawrence Estuary, North Water and Canada Basin were described using meta-omic techniques. In the Saint Lawrence Estuary, differences in microbial community structure, metabolic lifestyles and carbon and nitrogen processing pathways were observed between the surface and deep waters. In the North Water, two distinct microbial communities with different taxonomic compositions and differing nutrient acquisition and resource allocation strategies were identified on either side of the polar mixed layer, and a third distinct community was described in the bottom waters. Functional and taxonomic analyses of the North Water polar mixed layer communities suggest a microbial community more typically associated with waters that undergo pulses of primary production on the Canadian side, while the community on the Greenland side was more typical of waters associated with a more steady level of primary production. In the Canada Basin, metagenomics was used to construct 360 Arctic Ocean metagenome assembled genomes. The analysis of six Chloroflexi MAGs revealed their potential for terrestrial derived aromatic compound degradation and that this metabolic capacity was acquired, at least in part, by lateral gene transfer from terrestrial organisms. To facilitate the meta-omic analyses performed in this thesis, a novel method to isolate microbial community DNA and proteins from the same environmental sample preserved in RNAlater was also developed. This thesis not only describes the microbial community composition and metabolism of northern marine systems over a broad geographic range, but also adds to the growing metagenomic and metaproteomic resource-base that can be used to develop and test hypotheses about northern marine microbial systems. Additionally, this work has implications for our understanding of how climate change may affect northern marine ecosystems.

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 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 Applying Meta omics to Marine Microbial Ecophysiology written by Bethany Kolody and published by . This book was released on 2020 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phytoplankton and associated microbial communities are essential for sustaining marine ecosystems. However, the structure and function of these communities is largely driven by dynamic physical forcing (e.g. upwelling, subduction) and micro-scale interactions (e.g. viral infection, trophic interactions, symbioses) that are difficult to capture. This dissertation applies recent molecular tools to these complex systems in order to resolve the physiology of key microbial players in the context of environmental forcing and community interactions. In Chapter 1, a semi-Lagrangian drifter was deployed to capture the transcriptional dynamics of a phytoplankton community across diel cycles. Apart from fungi and archaea, all groups (dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria, prasinophytes) exhibited 24-h periodicity in some transcripts. Larger portions of the transcriptome oscillated in phototrophs. Functional groups of genes, including photosynthetic machinery, had conserved timing across diverse lineages. In addition to responding to low-iron, many taxa were also being persistently infected by viruses. Chapter 2 applied metatranscriptomics to a simulated upwelling experiment to examine the response of blooming phytoplankton to nitrogen and iron, the most common nutrients limiting marine phytoplankton growth in nature. Regulation of metabolism and light harvesting machinery changed in a conserved manner across diverse lineages. Viral activity was widespread and increased under nutrient limitation. The relative expression of NRT2 to GSII and iron starvation induced proteins (ISIP1, ISIP2, ISIP3) to the thiamin biosynthesis gene, ThiC, were identified as robust markers of diatom cellular nitrogen and iron status. Chapter 3 applied high-resolution amplicon sequencing to a ship-based transect of the South Pacific along a gradient of water ages spanning newly subducted Antarctic water to subtropical water with a residence time >1,000 years. 16S and 18S rRNA diversity analyses were performed using both DNA and cDNA reverse-transcribed from RNA, providing an estimate of the breadth of deep-ocean microbial diversity that can be attributed to active cells. Microbial communities differed across size classes and were ultimately structured by physical properties of water masses and residence time in the deep ocean. These results highlight the utility of 'omics techniques for capturing the response of marine microbes to physical dynamics and resolving relationships between key community members.

Download or read book Microbial Biogeography in the Water Column and Sediments of the Northeastern Gulf of Mexico written by Nine Lisa Henriksson and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Through their metabolic activities marine microbes are essential for marine biogeochemical cycles. Charting their spatial distribution and biogeographical patterns is important in order to increase knowledge of what drives these microbial communities. We evaluated the bacterial communities at 22 locations in the northeast Gulf of Mexico during the summer months of 2013. Surface, water column, and surface sediment samples totaled 91 communities. Metadata and physical parameters measurements were collected at each location. Seawater (~20L) was collected on Sterivex filters and stored at -80U+00B0 C until gDNA extraction and subsequent Illumina sequencing (MiSeq), targeting the 16S rRNA gene. OTU picking routines generated over 280,000 OTU's and identified>14 million sequences across the dataset. Alpha diversity estimates revealed significant distinction between water column samples (Surface and Intermediate samples) and benthic samples (Sediment, Core and WOC) in terms of richness and Chao1 diversity, with the latter group prevailing. The eight most prevalent OTU's comprised 15% of the dataset population and were predominantly located in water column samples; Synechococcus (5.29%), Alteromonas (1.6%) and Prochlorococcus (1.51%) were the only groups previously classified. In contrast, most of these highly abundant groups existed in very small numbers in the benthic samples. Significant correlation was found between environmental parameters and the water column biological community. According to primer6 BEST analysis, temperature, longitude, dissolved oxygen, fluorescence, and nitrate/nitrite exert notable influence on the northeast GoM bacterial community structure.

Download or read book Marine Microbial Biogeography written by Amy Joyce Baldwin and published by . This book was released on 2007 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt: