Poulton Nicole J.

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Poulton
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Nicole J.
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  • Article
    Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres
    (Public Library of Science, 2014-04-17) Swan, Brandon K. ; Chaffin, Mark D. ; Martinez-Garcia, Manuel ; Morrison, Hilary G. ; Field, Erin K. ; Poulton, Nicole J. ; Masland, E. Dashiell P. ; Harris, Christopher C. ; Sczyrba, Alexander ; Chain, Patrick S. G. ; Koren, Sergey ; Woyke, Tanja ; Stepanauskas, Ramunas
    Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
  • Article
    Ancestral absence of electron transport chains in Patescibacteria and DPANN
    (Frontiers Media, 2020-08-17) Beam, Jacob P. ; Becraft, Eric D. ; Brown, Julia M. ; Schulz, Frederik ; Jarett, Jessica K. ; Bezuidt, Oliver ; Poulton, Nicole J. ; Clark, Kayla ; Dunfield, Peter F. ; Ravin, Nikolai V. ; Spear, John R. ; Hedlund, Brian P. ; Kormas, Konstantinos Ar. ; Sievert, Stefan M. ; Elshahed, Mostafa S. ; Barton, Hazel A. ; Stott, Matthew B. ; Eisen, Jonathan A. ; Moser, Duane P. ; Onstott, Tullis C. ; Woyke, Tanja ; Stepanauskas, Ramunas
    Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
  • Article
    Bio-GO-SHIP: the time is right to establish global repeat sections of ocean biology
    (Frontiers Media, 2022-01-10) Clayton, Sophie A. ; Alexander, Harriet ; Graff, Jason R. ; Poulton, Nicole J. ; Thompson, Luke R. ; Benway, Heather M. ; Boss, Emmanuel S. ; Martiny, Adam C.
    In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.
  • Article
    Oceanic crustal fluid single cell genomics complements metagenomic and metatranscriptomic surveys with orders of magnitude less sample volume
    (Frontiers Media, 2022-01-24) D'Angelo, Timothy ; Goordial, Jacqueline M. ; Poulton, Nicole J. ; Seyler, Lauren M. ; Huber, Julie A. ; Stepanauskas, Ramunas ; Orcutt, Beth N.
    Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml–1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to ‘omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.
  • Thesis
    Physiological and behavioral diagnostics of nitrogen limitation for the toxic dinoflagellate Alexandrium fundyense
    (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2000-09) Poulton, Nicole J.
    One challenge in phytoplankton ecology is to measure species-specific physiological responses to changes in environmental conditions. Of particular importance in this regard are harmful algal bloom (RAB) species such as the toxic dinoflagellate Alexandrium fundyense which typically inhabit coastal regions where they are not usually dominant. Within the Gulf of Maine, environmental factors, specifically nitrogen, are likely to be a controlling factor for A. fundyense blooms. Therefore, the ability to ascertain the nutritional status of this species in field assemblages in critical to understanding its bloom dynamics. The aim of this thesis was to identify physiological and behavioral indicators or diagnostics of A. fundyense from the Gulf of Maine, and to evaluate these on natural populations in the Casco Bay region. Using a species-specific monoclonal antibody, two methods for identifying and separating A. fundyense from natural field assemblages were developed. The first used a species-specific antibody and flow cytometry to successfully detect and separate A. fundyense from co-occurring organisms, including other dinoflagellates of equivalent size. In particular the fluorescence associated with the antibody labeling was not sufficient of itself for species discrimination - natural red chlorophyll autofluorescence was also needed as a second parameter for identifying and sorting A. fundyense. A second antibody method was then investigated using immunomagnetic beads to successfully separate live A. fundyense from spiked field samples. The separated cells were then used to obtain accurate chlorophyll, protein and biomass estimates. CHN values were only accurate if the unbound magnetic beads were sieved from the sample prior to analysis. This is probably needed for carbohydrate analysis as well. Since A. fundyense usually inhabits coastal areas that are frequently limited by nitrogen, behavioral adaptations and intracellular responses to nitrogen availability are a primary consideration. It was therefore necessary to identify diagnostic indicators and behavioral adaptations of A. fundyense to nitrogen stress. Using laboratory water columns, nitrogen (N)-starved batch cultures, and N-limited, semi-continuous cultures, indicators of different N-nutritional states were identified. It was determined that low N concentrations in the surface of a mesocosm did not induce a Casco Bay A. fundyense isolate to vertically migrate to deep nutrient pools. Prolonged N-stress caused dramatic changes intracellular biochemistry, specifically chlorophyll a, carbohydrate, and protein content, as well as C:N, toxin content and composition. Ratios of different toxin derivatives were identified that increased with increasing N-stress and appear to be sensitive and robust indicators of N-status. Once indicators were developed for N-stress, variability in toxin content and composition were examined in the coastal waters of Casco Bay, Maine during an A. fundyense bloom in the spring of 1998. Over the course of the field season, toxin compositional changes did occur that were generally consistent with increasing levels of N-stress as the bloom progressed and N levels decreased. As observed in N-limited culture, large increases in some toxin ratios (e.g., GTX1,4:STX and NEO:STX) were observed during the latter portion of the field season, coinciding with low N:P ratios and undetectable levels of dissolved inorganic nitrogen. Overall, the toxin compositional trends are quite remarkable and suggest that this approach may provide valuable species-specific physiological information without the need for elaborate cell separation schemes such as flow cytometry or immunomagnetic bead sorting. Further laboratory studies are needed to better characterize the toxin response of A. fundyense isolates to environmental stresses before this suite of toxin indicators can be considered robust.