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7 results for “Station ALOHA”
Multiple years of Seaglider observations of hydrography, dissolved oxygen, chlorophyll a, and optical backscatter at Station ALOHA
<p><strong>File descriptions:</strong></p> <p>Seaglider missions are identified as GLIDER_MISSION<em> </em>(i.e. sg148_12 is glider 148, mission 12) and each have three files associated. For example:</p> <ol> <li><strong>sg148_12_qc_pass.xlsx</strong> contains only quality controlled (QC flags = 1) core data for an entire mission. Core data may include temperature, conductivity, salinity, potential density anomaly, calibrated dissolved oxygen concentrations, calibrated chlorophyll <em>a</em> concentrations, and the backscattering coefficient due to particles (bbp) at up to three wavelengths (470, either 650 or 660, and 700 nm) and spike flags. Bbp data is corrected with an <em>in situ</em> dark subtraction from near 200 m deep. Associated metadata (datetime, latitude, longitude, depth, dive number, and vertical profile direction) is also included.</li> <li><strong>sg148_12_alldata.nc </strong>contains all data (i.e. all QC flag levels) and associated quality control flags. In addition to core and metadata, factory-only calibrated observations (e.g. dissolved oxygen concentrations, chlorophyll <em>a</em> concentrations, and bbp) are listed. </li> <li><strong>sg148_12_qctests.nc</strong><em> </em>contains all quality control test values (pass: QC = 1, input flag: QC = 2, questionable data QC = 3, bad data: QC = 4). The maximum test QC flag value (e.g. out of range, density inversions, bioflouling, etc.) was passed to the variable QC flag (e.g chla_qcflag or salin_qcflag). . </li> </ol> <p> </p> <p><strong>Dataset description:</strong></p> <p>The SCOPE-ALOHA Seaglider dataset was designed to monitor the spatial and temporal variability of physical and biogeochemical properties around the long term sampling site Station ALOHA (22°45′N, 158°W). Seagliders are autonomous underwater vehicles that take high frequency (up to 0.2 Hz in our dataset), depth-resolved observations over several months and can be used to map large spatial features. The gliders depicted in this study were equipped with sensors to measure temperature, salinity, pressure, dissolved oxygen concentration (O2), chlorophyll a concentration (Chl a) from fluorescence (excitation/emission lambda = 470/695 nm), and the particulate backscattering coefficient (bbp) at three wavelengths (lambda = 470 nm, 700 nm, and either 650 or 660 nm depending upon mission). Vertical profiles down to at least 200 m were collected for all sensors over periods of several months per mission. This dataset comprises 18 missions between 2008 and 2023 centered on Station ALOHA, totaling over 20,000 depth profiles. Chlorophyll <em>a</em> and oxygen concentrations are calibrated with discrete observations. Particulate backscattering coefficients are corrected with an additional dark subtraction. This dataset is an improvement on the raw data files as they are quality controlled, calibrated, and corrected.</p> <p>Raw data files can be found at https://hahana.soest.hawaii.edu/seagliders/index.php.</p> <p>version notes:</p> <p>v1.0 original</p> <p>v1.1 Metaadata tab on xlsx files edited, no change to data</p> <p>v1.2 fixed error: variable qc flags added to alldata.nc files</p> <p>v1.3 Added error estimates and CF_standard_name to alldata.nc files</p> <p><strong>Methods:</strong></p> <p><em><strong>Code for all processing steps is on GitHub </strong></em><strong>(</strong><em><strong>https://github.com/cathygarcia/SeagliderDataprocessing</strong></em><strong>)</strong><em><strong>.</strong> The steps listed here are a brief summary. </em></p> <p><em>Temperature, Conductivity, Salinity, and Potential Density Anomaly</em></p> <ul> <li>Both temperature and conductivity profiles were lag corrected.</li> <li>Practical salinity was calculated using the Gibbs Seawater Toolbox (gsw_SP_from_C.m), and then converted to absolute salinity (gsw_SA_from_SP.m). </li> <li>Potential density anomaly was calculated with respect to a reference water pressure of 0 db using the Gibbs Seawater Toolbox (gsw_sigma0.m).</li> </ul> <p><em>Dissolved oxygen concentrations</em></p> <ul> <li>Raw optode phase values proceeded through a series of corrections to account for the effects of temperature, salinity, pressure, and time response in addition to sensor drift (Bittig et al., 2018, Barone et al., 2019).</li> <li> Optode phase values were converted to dissolved oxygen concentrations, and re-calibrated using discrete Winkler measurements. </li> </ul> <p><em>Chlorophyll</em> <em>a</em></p> <ul> <li>Factory-calibrated chlorophyll <em>a</em> observations were re-calibrated using discrete measurements of either HPLC chlorophyll <em>a </em>(16 missions) or fluorometric chlorophyll <em>a</em> (2 missions).</li> <li>Daytime chlorophyll <em>a</em> values are not quench corrected, and may be lower than actual values. It is recommended to use nighttime profiles near the surface. </li> <li>Additionally, a spike flag is included based on published protocol (Briggs et al., 2011).</li> </ul> <p><em>Backscattering coefficient due to particles (bbp)</em></p> <ul> <li>Factory-calibrated bbp values could have a large offset, that was not expected based on natural variability.</li> <li>A mission-specific deep dark correction (1st percentile of bbp at 190-200 m) was subtracted for each bbp dataset. Both the uncorrected and corrected data are available.</li> <li>Additionally, a spike flag is included based on published protocol (Briggs et al., 2011).</li> </ul> <p> </p>
Transcriptome assemblies of three diatom and three prymnesiophyte isolates from Station ALOHA and Kaneohe Bay
<p><strong>Culture ID/name</strong></p> <p>AT125A – Pseudo-nitzschia sp.</p> <p>AT125C – Pseudo-nitzschia sp.</p> <p>ATCH2 – Chaetoceros sp.</p> <p>Pn B2 – Pseudo-nitzschia sp.</p> <p>KB-HA01 – Chrysochromulina sp. (also called </p> <p>AL-TEMP-12 – Chrysochromulina sp. (also called </p> <p>NF-H275 – Chrysochromulina sp.<br> <br> </p> <p><strong>Growth Conditions</strong></p> <p>All cultures were grown at 27°C, 12:12 light:dark cycle, and with a light intensity of 100 µmol photons m<sup>-2</sup> sec<sup>-1</sup>. AT125C, AT125A, and Pn B2 were grown with Aquil media. ATCH2 was grown with F/20 media with the phosphate concentration modified to a final concentration of 0.5µM. KB-HA01 was grown with F/2 media and AL-TEMP-12 and NF-H275 were grown with K media. None of the cultures were axenic. All cultures were filtered in “light” and “dark” conditions and were in exponential phase when filtered. (Filter types and volumes filtered listed below.) After filtration, all filters were placed into 2mL screwcap tubes, flash frozen with liquid nitrogen, and stored at -80°C.</p> <p><strong>Growth Conditions</strong></p> <p>All cultures were grown at 27°C, 12:12 light:dark cycle, and with a light intensity of 100 µmol photons m<sup>-2</sup> sec<sup>-1</sup>. AT125C, AT125A, and Pn B2 were grown with Aquil media. ATCH2 was grown with F/20 media with the phosphate concentration modified to a final concentration of 0.5µM. KB-HA01 was grown with F/2 media and AL-TEMP-12 and NF-H275 were grown with K media. None of the cultures were axenic. All cultures were filtered in “light” and “dark” conditions and were in exponential phase when filtered. (Filter types and volumes filtered listed below.) After filtration, all filters were placed into 2mL screwcap tubes, flash frozen with liquid nitrogen, and stored at -80°C.<br> <br> [TRANSCRIPTOME SEQUENCING]<br> <br> [QC AND ASSEMBLY]<br> <br> [POST-ASSEMBLY PROCESSING]<br> Diamond v2.0.5.143 was used to blast (e-value: 1e-5) to a cross-kingdom reference sequence database (as described in Coesel et al., 2021). Diamond v2.0.5.143 was used to find the least common ancestor of each contig based upon the blast results. Contigs that were identified as bacteria, archaea, or viruses were excluded from the assemblies.<br> <br> </p>
Station ALOHA seasonal siderophore concentrations and iron uptake
<p>Seasonal total siderophore concentrations and surface (15 m) and 300 m iron uptake from Station ALOHA.</p>
Deep sea dissolved organic nitrogen and phosphorus (DON and DOP) at Station ALOHA in the North Pacific Subtropical Gyre
<p>Data on organic and inorganic nutrients in unfiltered seawater that was sampled at and around Station ALOHA, north of Oahu, Hawaii, in the North Pacific Subtropical Gyre. Seawater was collected into HDPE or polypropylene bottles and immediately frozen. Silicate, phosphate and nitrate+nitrite are determined colormetrically on a SEAL Analytical Autoanalyzer (AA3 with HR detectors), with the exception of nitrate+nitrite that is <0.5umol/L, which is analyzed by high-sensitivity chemiluminescence. Total phosphorus (TP) and total nitrogen (TN) are determined by analysis of phosphate and nitrate, respectively, after oxidation by high-intensity ultraviolet light. Total organic phosphorus and total organic nitrogen are determined by subtracting background PO4 and NO3+NO2 from TP and TN, respectively. Total organic carbon is determined by combustion on a Shimadzu TOC-V analyzer. This dataset was originally published in the following article, in which additional details and interpretations of the data can be found:</p> <p>R. K. Foreman, K. M. Björkman, C. A. Carlson, K. Opalk, D. M. Karl, (2019). Improved ultraviolet photo‐oxidation system yields estimates for deep‐sea dissolved organic nitrogen and phosphorus, Limnol. Oceanogr. Methods, <a href="https://doi.org/10.1002/lom3.10312">doi.org/10.1002/lom3.10312</a> <br> </p>
Dissolved Siderophore Concentrations Station ALOHA
<p>Dissolved (< 0.2 um) siderophore concentrations measured at Station ALOHA in different seasons.</p>
Sequencing of fractionated marine nanoparticles from Station ALOHA (HOT319)
<p>Seawater from 25m at Station ALOHA in the North Pacific Subtropical Gyre was filtered through a 0.2 µm filter and separated into extracellular vesicle-enriched and viral-like particle enriched fractions. Particle fractions were sequenced with an Oxford Nanopore R9.4.1 flowcell. Frameshifts introduced from Nanopore sequencing error were corrected using the <em>proovframe </em>algorithm (https://github.com/thackl/proovframe) and Illumina short-read sequences from the identical DNA samples.</p> <p>This dataset includes all proovframe-corrected Nanopore sequences (>1kb) from the two fractions in FASTA format, each fraction divided into multiple gzip-compressed files:</p> <p>EV_enriched_corrected_nanopore_[01-10]: reads from the extracellular vesicle-enriched fraction</p> <p>VLP_enriched_corrected_nanopore_[01-10]: reads from the viral-like particle-enriched fraction</p> <p>Additionally, we provide assembled metagenomic contigs from the cellular (>0.2µm) fraction of the same water sample in HOT319_25m_cellularfraction_assembly.fna.gz</p> <p>The original raw seqence data used to generate these datasets can be obtained from the NCBI sequence read archive (Bioproject PRJNA855972).</p>
Time and depth resolved archaea amoA genes at Station ALOHA
<p>This dataset contains amoA gene abundances from Station ALOHA, the long-term ocean field site in the subtropical North Pacific. Whole seawater samples from six discrete depths (5, 25, 45, 75, 100, 125, 150, and 175 m) were collected on near-monthly Hawaii Ocean Time-series (HOT) program cruises. Seawater was filtered onto 0.2 mm pore size Supor filters to concentrate plankton biomass. DNA from filters was subsequently extracted using a Qiagen Plant and Tissue kit, with archaeal amoA genes quantified using digital droplet PCR (ddPCR) with the EvaGreen Mastermix. Two different sets of ddPCR primers were used for gene quantification by ddPCR: one primer set targeted amoA genes deriving from members of the Thaumarchea often termed “Group A”, while the other primer set targeted amoA genes deriving from Thaumarchea termed “Group B” (Beman JM, Popp BN, Francis CA. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California. ISME J. 2008 Apr;2(4):429-41. doi: 10.1038/ismej.2007.118.). Gene lower detection limits were determined as 3x the standard deviation of no template control reactions (nuclease-free water added instead of environmental DNA). The time stamp indicates the time of sample collection (when the hydrocast went into the water) and is reported in UTC.</p>
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