Hu Sarah K

No Thumbnail Available
Last Name
Hu
First Name
Sarah K
ORCID
0000-0002-4439-1360

Filters

2019 - 2019 1 2020 - 2022 8
5 4
9
Reset filters

Settings

Search Results

Now showing 1 - 9 of 9
  • Article
    Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight)
    (Society for Applied Microbiology, 2022-07-26) Ollison, Gerid A. ; Hu, Sarah K. ; Hopper, Julie V. ; Stewart, Brittany P. ; Smith, Jayme ; Beatty, Jennifer L. ; Rink, Laura K. ; Caron, David A.
    Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2. Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes in relative abundance dynamics of the metabolically active protistan community were followed via expressed 18S V4 rRNA genes (RNA) throughout two algal blooms during the spring of 2018 and 2019 in Santa Monica Bay (central Southern California Bight). A diatom bloom formed after wind-driven, nutrient upwelling events in both years, but different taxa dominated each year. Whereas diatoms bloomed following elevated nutrients and declined after depletion each year, a massive dinoflagellate bloom manifested under relatively low inorganic nitrogen conditions following diatom bloom senescence in 2019 but not 2018. Network analysis revealed associations between diatoms and cercozoan putative parasitic taxa and syndinean parasites during 2019 that may have influenced the demise of the diatoms, and the transition to a dinoflagellate-dominated bloom.
  • Dataset
    High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 2019
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-06) Hu, Sarah K. ; Huber, Julie ; Smith, Amy R.
    High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/828392
  • Dataset
    NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2019-07-24) Caron, David ; Hu, Sarah K
    Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California. Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014. This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/745527
  • Dataset
    Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-11) Caron, David ; Hu, Sarah K
    Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community. Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503). Sequences for BioProject PRJNA608423 will be available at NCBI on Jan 1st, 2021. These data were published in Hu et al. (2018). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/745518
  • Article
    A primer for microbiome time-series analysis
    (Frontiers Media, 2020-04-21) Coenen, Ashley R. ; Hu, Sarah K. ; Luo, Elaine ; Muratore, Daniel ; Weitz, Joshua S.
    Time-series can provide critical insights into the structure and function of microbial communities. The analysis of temporal data warrants statistical considerations, distinct from comparative microbiome studies, to address ecological questions. This primer identifies unique challenges and approaches for analyzing microbiome time-series. In doing so, we focus on (1) identifying compositionally similar samples, (2) inferring putative interactions among populations, and (3) detecting periodic signals. We connect theory, code and data via a series of hands-on modules with a motivating biological question centered on marine microbial ecology. The topics of the modules include characterizing shifts in community structure and activity, identifying expression levels with a diel periodic signal, and identifying putative interactions within a complex community. Modules are presented as self-contained, open-access, interactive tutorials in R and Matlab. Throughout, we highlight statistical considerations for dealing with autocorrelated and compositional data, with an eye to improving the robustness of inferences from microbiome time-series. In doing so, we hope that this primer helps to broaden the use of time-series analytic methods within the microbial ecology research community.
  • Article
    Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications
    (Frontiers Media, 2022-06-28) Cohen, Natalie R. ; Alexander, Harriet ; Krinos, Arianna I. ; Hu, Sarah K. ; Lampe, Robert H.
    Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.
  • Article
    Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities
    (National Academy of Sciences, 2021-02-09) Coesel, Sacha N. ; Durham, Bryndan P. ; Groussman, Ryan D. ; Hu, Sarah K. ; Caron, David A. ; Morales, Rhonda L. ; Ribalet, François ; Armbrust, E. Virginia
    The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
  • Dataset
    High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2021-01-06) Hu, Sarah K. ; Huber, Julie
    High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-2015. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/828345
  • Dataset
    Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
    (Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu, 2020-05-06) Caron, David ; Hu, Sarah K
    This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from extracted DNA and RNA. Columns represent samples, including month sampled, material (either extracted RNA or DNA), and depth (in meters); thus values in each column represent the number of sequences in that sample that belong to a given OTU (OTUs by row). Each row represents a single OTU. The last column lists the taxonomic identifier assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/748064