http://lod.bco-dmo.org/id/dataset/930163 eng; USA utf8 dataset Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 2024-06-21 ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data ISO 19115-2:2009(E) Biological oceanographic measurements, 16S rRNA gene amplicons and metagenomes from surface seawater taken from August 2017 to June 2021 at sites within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi 2024-08-30 publication 2024-08-30 revision Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA) 2024-08-30 publication https://doi.org/10.26008/1912/bco-dmo.930163.1 Michael S. Rappé University of Hawaiʻi at Mānoa principalInvestigator Kelle C. Freel University of Hawaiʻi at Mānoa principalInvestigator A. Hiʻilei Kawelo Paepae o He'eia principalInvestigator Keliʻiahonui Kotubetey Paepae o He'eia principalInvestigator Yoshimi M. Rii He'eia National Estuarine Research Reserve principalInvestigator Kawika B. Winter He'eia National Estuarine Research Reserve principalInvestigator Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. publisher Cite this dataset as: Tucker, S. J., Rii, Y. M., Freel, K. C., Kotubetey, K., Kawelo, A. H., Winter, K. B., Rappé, M. S. (2024) Biological oceanographic measurements, 16S rRNA gene amplicons and metagenomes from surface seawater taken from August 2017 to June 2021 at sites within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-08-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.930163.1 [access date] Kāneʻohe Bay Time-series - phytoplankton and biogeochemistry Dataset Description: &lt;p&gt;The current dataset includes and expands upon the data collected from samples that were previously published in the PeerJ paper (Tucker at al., 2021). We would like to note that in this current dataset flow cytometry for all samples collected between 2017-2021 were measured using the Beckman Coulter CytoFLEX S. In the PeerJ publication of the 2017-2019 KByT dataset (see related dataset), the flow cytometry measures were conducted with the EPICS ALTRA flow cytometer. Thus intercomparison between the 2017-2019 dataset and this 2017-2021 dataset will show differences in cellular abundances reported.&amp;nbsp;&lt;/p&gt; &lt;div class=&quot;fieldset-wrapper&quot;&gt; &lt;div class=&quot;field field-name-field-dataset-description field-type-text-long field-label-hidden&quot;&gt; &lt;div class=&quot;field-items&quot;&gt; &lt;div class=&quot;field-item even&quot;&gt; &lt;p&gt;Other Grants:&lt;br /&gt; * &quot;National Science Foundation Graduate Research Fellowship Program&quot; (Grant ID 1842402, National Science Foundation)&lt;br /&gt; * &quot;NOAA Margaret A. Davidson Fellowship&quot; (Grant ID NA20NOS4200123, National Oceanic and Atmospheric Administration)&lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; Methods and Sampling: &lt;p&gt;The methods summarized below are part of the following publication, currently in review and available as a pre-print:&amp;nbsp;Tucker, S. J. &lt;em&gt;et al.&lt;/em&gt; Sharp transitions in phytoplankton communities across estuarine to open ocean waters of the tropical Pacific. (2024) doi:10.1101/2024.05.23.595464.&lt;/p&gt; &lt;p&gt;The methods employed in this study were collaboratively developed with Heʻeia Fishpond stewards and the Heʻeia National Estuarine Research Reserve (NERR; Winter et al. 2020). Sampling campaigns were conducted with permission from Paepae o Heʻeia, the stewards of Heʻeia Fishpond, and the private landowner, Kamehameha Schools.&lt;/p&gt; &lt;p&gt;At all stations, seawater samples for biogeochemical analyses and nucleic acids were collected, as were in situ measurements of seawater temperature, pH, and salinity with a YSI 6600 or ProDSS multi-parameter sonde (YSI Incorporated, Yellow Springs, OH, USA). Approximately one liter of seawater was prefiltered with 85-μm Nitex mesh and subsequently filtered through a 25-mm diameter, 0.1-μm pore-sized polyethersulfone (PES) filter membrane (Supor-100, Pall Gelman Inc., Ann Arbor, MI, USA) to collect microbial cells for DNA isolation. The filters were subsequently submerged in DNA lysis buffer (Suzuki et al. 2001; Yeo et al. 2013) and stored in −80°C until further processing.&lt;/p&gt; &lt;p&gt;Seawater subsamples for fluorometric chlorophyll a concentrations (125 mL) and photosynthetic pigments via high-performance liquid chromatography (HPLC; 2 L) were collected on 25-mm diameter GF/F glass microfiber filters (Whatman, GE Healthcare Life Sciences, Chicago, IL, USA) and stored in aluminum foil at −80°C until extraction. The collection of phytoplankton pigments on the GF/F glass microfiber filters allow for comparisons with the Hawaii Ocean Time-series data. However, because the filters have a pore size of 0.7µm, we acknowledge that most small cyanobacteria were likely missed. Chlorophyll a was extracted with 100% acetone and measured with a Turner 10-AU fluorometer (Turner Designs, Sunnyvale, CA, USA) following standard techniques (Welschmeyer 1994). Photosynthetic pigments measured via high performance liquid chromatography were extracted in 100% acetone and analyzed on a Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector, following (Mantoura and Llewellyn 1983) and modified according to (Bidigare et al. 1989).&lt;/p&gt; &lt;p&gt;For cellular enumeration, seawater was preserved in 2 mL aliquots in a final concentration of 0.95% (v:v) paraformaldehyde (Electron Microscopy Services, Hatfield, PA, USA) at −80 °C until analyzed via flow cytometry. Cellular enumeration of cyanobacterial picophytoplankton (Synechococcus and Prochlorococcus), eukaryotic picophytoplankton, and non-cyanobacterial (presumably heterotrophic) bacteria and archaea (hereafter referred to as heterotrophic bacteria) was performed on a Beckman Coulter CytoFLEX S, following the method of (Monger and Landry 1993). Inorganic nutrients were measured using a Seal Analytical AA3 HR Nutrient Autoanalyzer (detection limits: NO2− + NO3− , 0.009 µM; SiO4, 0.09 µM;&amp;nbsp; PO43 –, 0.009 µM; NH4, 0.03 µM).&amp;nbsp;&lt;/p&gt; &lt;p&gt;DNA extraction and 16S rRNA gene sequencing followed previously published methods (Tucker et al. 2021). Briefly, amplicon libraries were made from polymerase chain reactions of the 16S rRNA gene using barcoded 515F and 926R universal primers (Parada et al. 2016) and paired-end sequenced with MiSeq v2 2x250 technology (Illumina, San Diego, CA, USA). Genomic DNA from a subset of 32 of the 368 total samples collected between 2017-2021 were used for metagenomic sequencing. This included samples from four sampling events between 2017 and 2019 at 6-10 stations. Libraries were constructed from approximately 100 ng of genomic DNA using the Kappa HyperPrep Kit (Roche, Pleasanton, CA, USA) with mechanical shearing (Covaris, Woburn, MA, USA) and paired-end sequenced on a single lane of the NovaSeq 6000 SP 150 (Illumina, San Diego, CA, USA).&lt;/p&gt; Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1538628 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1538628 Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2149128 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2149128 completed Michael S. Rappé University of Hawaiʻi at Mānoa 808-372-2394 University of Hawaii at Manoa - Hawaii Institute of Marine Biology 46-007 Lilipuna Rd Kaneohe HI 96744 USA rappe@hawaii.edu pointOfContact Kelle C. Freel University of Hawaiʻi at Mānoa kfreel@hawaii.edu pointOfContact A. Hiʻilei Kawelo Paepae o He'eia hiilei@paepaeoheeia.org pointOfContact Keliʻiahonui Kotubetey Paepae o He'eia Kelii@paepaeoheeia.org pointOfContact Yoshimi M. Rii He'eia National Estuarine Research Reserve shimi@hawaii.edu pointOfContact Kawika B. Winter He'eia National Estuarine Research Reserve kawikaw@hawaii.edu pointOfContact asNeeded Dataset Version: 1 Unknown SampleID Universal_Sample_ID Metagenome Metagenome_ID Year Sampling_Order Season Month Month_abb Time Date ISO_DateTime_UTC decimal_date Day_of_year Community_Type latitude longitude Site SW_Temperature_at_site_degC Salinity_ppt Depth_m pH Prochlorococcus_cells_per_mL Synechococcus_cells_per_mL Eukaryotic_picophytoplankton_cells_per_mL Heterotrophic_bacteria_cells_per_mL chlorophyll_a_ug_per_L Phosphate_uM Silicate_uM NitrateNitrite_uM Ammonia_uM X19_butanoyloxyfucoxanthin_ng_per_L X19_hexanoyloxyfucoxanthin_ng_per_L Alloxanthin_ng_per_L Beta_Carotene_ng_per_L Alpha_Carotene_ng_per_L Chlorophyll_a_ng_per_L Chlorophyll_b_ng_per_L Chlorophyll_c_1_and_2_ng_per_L Chlorophyll_c_3_ng_per_L Chlorophyllide_ng_per_L Diadinoxanthin_ng_per_L Diatoxanthin_ng_per_L Fucoxanthin_ng_per_L Lutein_ng_per_L Neoxanthin_ng_per_L Peridinin_ng_per_L Prasinoxanthin_ng_per_L Violaxanthin_ng_per_L Zeaxanthin_ng_per_L divinyl_chlorophyll_a_ng_per_L monovinyl_chlorophyll_a_ng_per_L total_chlorophyll_a_ng_per_L biosample_accession Amplicon_bioproject_accession Amplicon_SRA_accession Amplicon_study Amplicon_library_strategy Amplicon_library_source Amplicon_library_layout Amplicon_platform Amplicon_instrument_model Amplicon_design_description Amplicon_filetype Amplicon_filename Amplicon_filename2 Metagenome_bioproject_accession Metagenome_SRA_accession Metagenome_study Metagenome_library_strategy Metagenome_library_selection Metagenome_library_layout Metagenome_platform Metagenome_instrument_model Metagenome_design_description Metagenome_filetype Metagenome_filename Metagenome_filename2 Illumina MiSeq v2 NovaSeq 6000 SP 150 Beckman Coulter CytoFLEX S Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector Seal Analytical AA3 HR Nutrient Autoanalyzer theme None, User defined sample identification sample description accession number year month of year time of day date ISO_DateTime_UTC day of month latitude longitude site water temperature at measurement depth salinity depth pH synechococcus abundance from flow cytometry picoeukaryote abundance from flow cytometry heterotrophic bacteria abundance from flow cytometry chlorophyll a phosphate Silicate (reactive silica) nitrate plus nitrite Ammonia fucoxanthin alloxanthin carotene-beta carotene-alpha chlorophyll b chlorophyll c total chlorophyllide diadinoxanthin diatoxanthin lutein neoxanthin peridinin prasinoxanthin violaxanthin zeaxanthin NCBI BioSample accession NCBI BioProject accession NCBI SRA run accession (SRR) NCBI SRA study accession (SRP) seq_descrip instrument instrument model datatype file_name featureType BCO-DMO Standard Parameters Automated DNA Sequencer Automated DNA Sequencer Flow Cytometer Fluorometer High-Performance Liquid Chromatograph Multi Parameter Portable Meter Nutrient Autoanalyzer instrument BCO-DMO Standard Instruments otherRestrictions otherRestrictions Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use. Population genomics and ecotypic divergence in the most dominant lineage of marine bacteria https://rappelab.wordpress.com/marine-bacterioplankton/population-genomics-of-sar11-marine-bacteria/ Population genomics and ecotypic divergence in the most dominant lineage of marine bacteria <p>In the upper water column of Earth's coastal and open oceans, roughly one million microscopic, single-celled bacteria inhabit each milliliter of seawater, where they play important roles in driving nutrient cycles and other processes that are vital to the habitability of these systems to other marine life. While some marine bacteria are similar to plants in that they use energy from the sun to transform the greenhouse gas carbon dioxide into living material and produce oxygen as a byproduct, other marine bacteria known as chemoheterotrophs are similar to humans and other animals in that they consume organic matter and oxygen, producing carbon dioxide as a consequence of their growth. Although they are limited in size and shape when observed under a microscope, genetic techniques such as DNA sequencing have revealed tremendous functional (i.e. what they are doing) and phylogenetic (i.e. how they are related) biodiversity in natural communities of marine bacteria. Despite this high genetic diversity, a single group of phylogenetically related chemoheterotrophic bacteria known as SAR11 can sometimes make up over 50% of the microscopic cells inhabiting seawater systems around the globe; it is considered one of the most abundant organisms on Earth and thus an important aspect of ocean ecology. While it is known that the SAR11 group consists of many distinct "types" that differ in abundance with location, depth and time, we know little about what genetically encoded features distinguish the different types, or how genetic characteristics are gained and lost within the group. The goal of this study is to use a genomics approach to understand the evolutionary processes that shape one of the most abundant groups of organisms on our planet, and to improve our theoretical understanding of the evolutionary processes that shape natural microbial biodiversity in general. This project will provide advanced, cross-disciplinary professional training for a postdoctoral scientist and a graduate student, and will increase the participation of underrepresented groups in scientific research by mentoring undergraduate students of native Hawaiian or Pacific Island ancestry in hands-on research and training. Results will be incorporated into a new university course offering on comparative genomics and microbial evolution. A culture collection of marine microorganisms will also be expanded and maintained, providing a valuable resource for other marine scientists.</p> <p>This project will take advantage of recent advances in DNA sequencing technology and a high throughput extinction culturing approach in order to investigate the evolutionary characteristics of genomes from sympatric populations of the globally important SAR11 marine bacterial lineage. The major objectives of this project are to understand the forces that shape genomic diversity in large bacterial populations such as SAR11, and to determine the nature by which this diversity is reflected in functional differences between populations, as inferred from genomics. SAR11 cells will be isolated from similar ecosystems in the tropical North and South Pacific, as well as the coastal ocean of the subpolar North Pacific, in order to investigate the effect of geographic distance versus habitat similarity on the population genetics of free-living, planktonic marine bacteria. By opening a unique genomic window that encompasses SAR11 lineages of varying degrees of genetic divergence simultaneously, this study will facilitate the investigation of evolutionary dynamics that spans a continuum between macro- and microevolutionary processes. Quantitative information regarding the mechanisms by which genetic diversity is generated, propagated, and removed from native SAR11 populations will also help efforts to model the fate of SAR11 and other large marine bacterioplankton populations in the face of predicted climate-induced changes to the global ocean.</p> Pelagibacteromics largerWorkCitation project Illuminating the physiology, cellular characteristics, and ecogenomics of the first cultivated strain of the SAR86 lineage https://osprey.bco-dmo.org/project/866771 Illuminating the physiology, cellular characteristics, and ecogenomics of the first cultivated strain of the SAR86 lineage <p><em>NSF Award Abstract:</em><br /> Since their initial discovery nearly 30 years ago, a group of marine bacteria known as SAR86 has come to be recognized as one of the main groups of microorganisms inhabiting the global surface ocean, where they can make up 20% or more of the planktonic cells that live in seawater. SAR86 cells appear to employ a heterotrophic lifestyle wherein the energy for cellular growth and metabolism is derived from organic compounds, and oxygen is converted to carbon dioxide via aerobic respiration. This basal metabolism appears to be supplemented by harvesting energy from sunlight using a unique light-harvesting system based on a protein known as proteorhodopsin. Despite its global prevalence and thus importance to understanding Earth’s major elemental cycles, a major factor that limits understanding of SAR86 marine bacteria is the lack of cultured isolates, such that even the most basic cellular features and metabolic traits are unknown. This study leverages the first isolated strain from the SAR86 lineage in a set of experiments designed to characterize basic aspects of SAR86 cells and to link metabolic traits with specific genetic features of SAR86. Collectively, these experiments are increasing understanding of one of the global-ocean’s most abundant microbial inhabitants. This project also supports the maintenance and public dissemination of a culture collection of marine microorganisms at the University of Hawaiʻi, the development of an educational module that focuses on the ecology of marine microbes inhabiting coastal Hawaiʻi, and the collaboration of the research team with community education partners on a new 3-D virtual reality rendering of the research laboratory and institute. One postdoctoral researcher, one graduate student, and multiple undergraduates are being trained in engaging, cutting-edge research, including the exposure of undergraduate students of native Hawaiian and Pacific Island ancestry to hands-on research and training.</p> <p>The project uses living cultures and the closed, annotated genome of the first isolated strain of the enigmatic SAR86 clade, HIMB1674, in a set of experiments to provide fundamental information on the cellular and physiological characteristics of SAR86 cells and connect specific metabolic features to genes and pathways encoded by the genome. The project links the genome of HIMB1674 to publicly available genomes and metagenomes from around the globe and integrates SAR86 eco-genomics into a time-series study that spans a steep coastal to open-ocean environmental gradient in the tropical Pacific Ocean. The experiments offer a combination of dry-lab informatic analyses, wet-lab experimentation with cultures, and a field program that uniquely illuminates the systems biology of SAR86 marine bacteria. The three main goals of this project are to 1) use SAR86 strain HIMB1674 to quantify basic cellular characteristics and investigate specific metabolic features predicted from its genome, 3) use the complete genome sequence of strain HIMB1674 as an anchor to investigate the eco-evolutionary characteristics of the SAR86 lineage, and 3) perform experiments designed to isolate additional SAR86 strains.</p> <p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p> SAR86 HIMB1674 largerWorkCitation project eng; USA oceans -157.83585 -157.7663 21.43582 21.526 2017-08-23 2021-06-21 From projects that focused on the following 2 locations: 1. Moorea, Oahu, and Gulf of Alaska 2. Coastal Hawai’i in the tropical North Pacific Ocean 0 BCO-DMO catalogue of parameters from Biological oceanographic measurements, 16S rRNA gene amplicons and metagenomes from surface seawater taken from August 2017 to June 2021 at sites within and adjacent to Kāneʻohe Bay, Oʻahu, Hawaiʻi Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact http://lod.bco-dmo.org/id/dataset-parameter/931570.rdf Name: SampleID Units: unitless Description: <p>Sample ID. Sample ID is composed of the station ID abbreviation and a uniqe sample ID #. In most cases a month abbreviation is also included.</p> http://lod.bco-dmo.org/id/dataset-parameter/931571.rdf Name: Universal_Sample_ID Units: unitless Description: <p>Universal Sample ID. Universal Sample ID is used to connect multiple sample types within the Kāneʻohe Bay Time-series. It is composed of the Project ID &quot;KBT&quot;, the date (mm.dd.yyyy), and Station ID.</p> http://lod.bco-dmo.org/id/dataset-parameter/931572.rdf Name: Metagenome Units: unitless Description: <p>Metagenome associated</p> http://lod.bco-dmo.org/id/dataset-parameter/931573.rdf Name: Metagenome_ID Units: unitless Description: <p>Metagenome ID</p> http://lod.bco-dmo.org/id/dataset-parameter/931574.rdf Name: Year Units: unitless Description: <p>Year of sampling.</p> http://lod.bco-dmo.org/id/dataset-parameter/931575.rdf Name: Sampling_Order Units: unitless Description: <p>Order of sampling events from 1 to 36.</p> http://lod.bco-dmo.org/id/dataset-parameter/931576.rdf Name: Season Units: unitless Description: <p>Season as defined by analyses included in associated paper.</p> http://lod.bco-dmo.org/id/dataset-parameter/931577.rdf Name: Month Units: unitless Description: <p>Month of sampling.</p> http://lod.bco-dmo.org/id/dataset-parameter/931578.rdf Name: Month_abb Units: unitless Description: <p>Abbreviation of month of sampling.</p> http://lod.bco-dmo.org/id/dataset-parameter/931579.rdf Name: Time Units: hh:mm Description: <p>Local time (Hawaiʻi Standard Time) of sampling surface seawater.</p> http://lod.bco-dmo.org/id/dataset-parameter/931580.rdf Name: Date Units: unitless Description: <p>Collection date.</p> http://lod.bco-dmo.org/id/dataset-parameter/931581.rdf Name: ISO_DateTime_UTC Units: unitless Description: <p>Date Time of surface seawater sampling in ISO format. UTC timezone</p> http://lod.bco-dmo.org/id/dataset-parameter/931582.rdf Name: decimal_date Units: unitless Description: <p>Decimal date of sampling collection day.</p> http://lod.bco-dmo.org/id/dataset-parameter/931583.rdf Name: Day_of_year Units: unitless Description: <p>Day of the year of sample collection.</p> http://lod.bco-dmo.org/id/dataset-parameter/931584.rdf Name: Community_Type Units: unitless Description: <p>Environment description, local. Defined by analyses included in associated publication.</p> http://lod.bco-dmo.org/id/dataset-parameter/931585.rdf Name: latitude Units: Decimal Degrees Description: <p>Latitiude of sample collection site.</p> http://lod.bco-dmo.org/id/dataset-parameter/931586.rdf Name: longitude Units: Decimal Degrees Description: <p>Longitude of sample collection site.</p> http://lod.bco-dmo.org/id/dataset-parameter/931587.rdf Name: Site Units: unitless Description: <p>Site ID for collection.</p> http://lod.bco-dmo.org/id/dataset-parameter/931588.rdf Name: SW_Temperature_at_site_degC Units: degrees Celsius Description: <p>Temperature of surface seawater in situ.</p> http://lod.bco-dmo.org/id/dataset-parameter/931589.rdf Name: Salinity_ppt Units: ppt Description: <p>Salinity of surface seawater in situ.</p> http://lod.bco-dmo.org/id/dataset-parameter/931590.rdf Name: Depth_m Units: meters Description: <p>Depth of sample collection.</p> http://lod.bco-dmo.org/id/dataset-parameter/931591.rdf Name: pH Units: no unit Description: <p>pH of surface seawater in situ.</p> http://lod.bco-dmo.org/id/dataset-parameter/931592.rdf Name: Prochlorococcus_cells_per_mL Units: cells per mL Description: <p>Surface seawater cellular abundances of Prochlorocococcus cells counted on CytoFLEX S flow cytometer.</p> http://lod.bco-dmo.org/id/dataset-parameter/931593.rdf Name: Synechococcus_cells_per_mL Units: cells per mL Description: <p>Surface seawater cellular abundances of Synechococcus cells counted on CytoFLEX S flow cytometer.</p> http://lod.bco-dmo.org/id/dataset-parameter/931594.rdf Name: Eukaryotic_picophytoplankton_cells_per_mL Units: cells per mL Description: <p>Surface seawater cellular abundances of photosynthetic picoeukaryotes counted on CytoFLEX S flow cytometer.</p> http://lod.bco-dmo.org/id/dataset-parameter/931595.rdf Name: Heterotrophic_bacteria_cells_per_mL Units: cells per mL Description: <p>Surface seawater cellular abundances of non-cyanobacterial (presumably heterotrophic) bacteria and archaea (referred to as heterotrophic bacteria) counted on CytoFLEX S flow cytometer.</p> http://lod.bco-dmo.org/id/dataset-parameter/931596.rdf Name: chlorophyll_a_ug_per_L Units: micrograms per Liter Description: <p>Extracted chlorophyll a concentrations from surface seawater.</p> http://lod.bco-dmo.org/id/dataset-parameter/931597.rdf Name: Phosphate_uM Units: µM Description: <p>Inorganic nutrients. Concentrations of phosphate in surface sewater sample (PO43 –).</p> http://lod.bco-dmo.org/id/dataset-parameter/931598.rdf Name: Silicate_uM Units: µM Description: <p>Inorganic nutrients. Concentrations of silicate in surface sewater sample (SiO4 ).</p> http://lod.bco-dmo.org/id/dataset-parameter/931599.rdf Name: NitrateNitrite_uM Units: µM Description: <p>Inorganic nutrients. Concentrations of nitrate+nitrite in surface sewater sample (NO2− + NO3− ).</p> http://lod.bco-dmo.org/id/dataset-parameter/931600.rdf Name: Ammonia_uM Units: µM Description: <p>Inorganic nutrients. Concentrations of ammonia in surface sewater sample (NH4).</p> http://lod.bco-dmo.org/id/dataset-parameter/931601.rdf Name: X19_butanoyloxyfucoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment 19&#039;-But-Fucoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931602.rdf Name: X19_hexanoyloxyfucoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment 19&#039;-Hex-Fucoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931603.rdf Name: Alloxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Alloxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931604.rdf Name: Beta_Carotene_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Beta Carotene measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931605.rdf Name: Alpha_Carotene_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Alpha Carotene measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931606.rdf Name: Chlorophyll_a_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Chlorophyll a measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931607.rdf Name: Chlorophyll_b_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Chlorophyll b measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931608.rdf Name: Chlorophyll_c_1_and_2_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Chlorophyll c 1&amp;2 measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931609.rdf Name: Chlorophyll_c_3_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Chlorophyll c 3 measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931610.rdf Name: Chlorophyllide_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Chlorophyllide measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931611.rdf Name: Diadinoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Diadinoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931612.rdf Name: Diatoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Diatoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931613.rdf Name: Fucoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Fucoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931614.rdf Name: Lutein_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Lutein measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931615.rdf Name: Neoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Neoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931616.rdf Name: Peridinin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Peridinin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931617.rdf Name: Prasinoxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Prasinoxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931618.rdf Name: Violaxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Violaxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931619.rdf Name: Zeaxanthin_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment Zeaxanthin measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931620.rdf Name: divinyl_chlorophyll_a_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment divinyl chlorophyll a measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931621.rdf Name: monovinyl_chlorophyll_a_ng_per_L Units: ng per L Description: <p>Photosynthetic pigment monovinyl chlorophyll a measured via high performance liquid chromatography</p> http://lod.bco-dmo.org/id/dataset-parameter/931622.rdf Name: total_chlorophyll_a_ng_per_L Units: ng per L Description: <p>Photosynthetic pigments measured via high performance liquid chromatography (sum of monovinyl and divininyl chlorophyll a).</p> http://lod.bco-dmo.org/id/dataset-parameter/931623.rdf Name: biosample_accession Units: unitless Description: <p>NCBI Bioproject Accession for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931624.rdf Name: Amplicon_bioproject_accession Units: unitless Description: <p>NCBI Biosample Accession.</p> http://lod.bco-dmo.org/id/dataset-parameter/931625.rdf Name: Amplicon_SRA_accession Units: unitless Description: <p>NCBI SRA Accession for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931626.rdf Name: Amplicon_study Units: unitless Description: <p>NCBI Study ID for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931627.rdf Name: Amplicon_library_strategy Units: unitless Description: <p>Sequencing library type for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931628.rdf Name: Amplicon_library_source Units: unitless Description: <p>Source of sequencing library for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931629.rdf Name: Amplicon_library_layout Units: unitless Description: <p>Single or paired end sequencing reads for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931630.rdf Name: Amplicon_platform Units: unitless Description: <p>Platform used for library creation for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931631.rdf Name: Amplicon_instrument_model Units: unitless Description: <p>Sequencer model for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931632.rdf Name: Amplicon_design_description Units: unitless Description: <p>Description of ampicon library.</p> http://lod.bco-dmo.org/id/dataset-parameter/931633.rdf Name: Amplicon_filetype Units: unitless Description: <p>File type for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931634.rdf Name: Amplicon_filename Units: unitless Description: <p>Forward reads file name for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931635.rdf Name: Amplicon_filename2 Units: unitless Description: <p>Reverse reads file name for amplicon data.</p> http://lod.bco-dmo.org/id/dataset-parameter/931636.rdf Name: Metagenome_bioproject_accession Units: unitless Description: <p>NCBI Biosample Accession.</p> http://lod.bco-dmo.org/id/dataset-parameter/931637.rdf Name: Metagenome_SRA_accession Units: unitless Description: <p>NCBI SRA Accession for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931638.rdf Name: Metagenome_study Units: unitless Description: <p>NCBI Study ID for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931639.rdf Name: Metagenome_library_strategy Units: unitless Description: <p>Sequencing library type for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931640.rdf Name: Metagenome_library_selection Units: unitless Description: <p>Selection used for sequencing library for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931641.rdf Name: Metagenome_library_layout Units: unitless Description: <p>Single or paired end sequencing reads for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931642.rdf Name: Metagenome_platform Units: unitless Description: <p>Platform used for library creation for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931643.rdf Name: Metagenome_instrument_model Units: unitless Description: <p>Sequencer model for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931644.rdf Name: Metagenome_design_description Units: unitless Description: <p>Description of metagenome library.</p> http://lod.bco-dmo.org/id/dataset-parameter/931645.rdf Name: Metagenome_filetype Units: unitless Description: <p>File type for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931646.rdf Name: Metagenome_filename Units: unitless Description: <p>Forward reads file name for metagenomes.</p> http://lod.bco-dmo.org/id/dataset-parameter/931647.rdf Name: Metagenome_filename2 Units: unitless Description: <p>Reverse reads file name for metagenomes.</p> GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact 219012 https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/55c1a8e6-e482-40af-8af4-0093f575d816/content download https://doi.org/10.26008/1912/bco-dmo.930163.1 download onLine dataset &lt;p&gt;The methods summarized below are part of the following publication, currently in review and available as a pre-print:&amp;nbsp;Tucker, S. J. &lt;em&gt;et al.&lt;/em&gt; Sharp transitions in phytoplankton communities across estuarine to open ocean waters of the tropical Pacific. (2024) doi:10.1101/2024.05.23.595464.&lt;/p&gt; &lt;p&gt;The methods employed in this study were collaboratively developed with Heʻeia Fishpond stewards and the Heʻeia National Estuarine Research Reserve (NERR; Winter et al. 2020). Sampling campaigns were conducted with permission from Paepae o Heʻeia, the stewards of Heʻeia Fishpond, and the private landowner, Kamehameha Schools.&lt;/p&gt; &lt;p&gt;At all stations, seawater samples for biogeochemical analyses and nucleic acids were collected, as were in situ measurements of seawater temperature, pH, and salinity with a YSI 6600 or ProDSS multi-parameter sonde (YSI Incorporated, Yellow Springs, OH, USA). Approximately one liter of seawater was prefiltered with 85-μm Nitex mesh and subsequently filtered through a 25-mm diameter, 0.1-μm pore-sized polyethersulfone (PES) filter membrane (Supor-100, Pall Gelman Inc., Ann Arbor, MI, USA) to collect microbial cells for DNA isolation. The filters were subsequently submerged in DNA lysis buffer (Suzuki et al. 2001; Yeo et al. 2013) and stored in −80°C until further processing.&lt;/p&gt; &lt;p&gt;Seawater subsamples for fluorometric chlorophyll a concentrations (125 mL) and photosynthetic pigments via high-performance liquid chromatography (HPLC; 2 L) were collected on 25-mm diameter GF/F glass microfiber filters (Whatman, GE Healthcare Life Sciences, Chicago, IL, USA) and stored in aluminum foil at −80°C until extraction. The collection of phytoplankton pigments on the GF/F glass microfiber filters allow for comparisons with the Hawaii Ocean Time-series data. However, because the filters have a pore size of 0.7µm, we acknowledge that most small cyanobacteria were likely missed. Chlorophyll a was extracted with 100% acetone and measured with a Turner 10-AU fluorometer (Turner Designs, Sunnyvale, CA, USA) following standard techniques (Welschmeyer 1994). Photosynthetic pigments measured via high performance liquid chromatography were extracted in 100% acetone and analyzed on a Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector, following (Mantoura and Llewellyn 1983) and modified according to (Bidigare et al. 1989).&lt;/p&gt; &lt;p&gt;For cellular enumeration, seawater was preserved in 2 mL aliquots in a final concentration of 0.95% (v:v) paraformaldehyde (Electron Microscopy Services, Hatfield, PA, USA) at −80 °C until analyzed via flow cytometry. Cellular enumeration of cyanobacterial picophytoplankton (Synechococcus and Prochlorococcus), eukaryotic picophytoplankton, and non-cyanobacterial (presumably heterotrophic) bacteria and archaea (hereafter referred to as heterotrophic bacteria) was performed on a Beckman Coulter CytoFLEX S, following the method of (Monger and Landry 1993). Inorganic nutrients were measured using a Seal Analytical AA3 HR Nutrient Autoanalyzer (detection limits: NO2− + NO3− , 0.009 µM; SiO4, 0.09 µM;&amp;nbsp; PO43 –, 0.009 µM; NH4, 0.03 µM).&amp;nbsp;&lt;/p&gt; &lt;p&gt;DNA extraction and 16S rRNA gene sequencing followed previously published methods (Tucker et al. 2021). Briefly, amplicon libraries were made from polymerase chain reactions of the 16S rRNA gene using barcoded 515F and 926R universal primers (Parada et al. 2016) and paired-end sequenced with MiSeq v2 2x250 technology (Illumina, San Diego, CA, USA). Genomic DNA from a subset of 32 of the 368 total samples collected between 2017-2021 were used for metagenomic sequencing. This included samples from four sampling events between 2017 and 2019 at 6-10 stations. Libraries were constructed from approximately 100 ng of genomic DNA using the Kappa HyperPrep Kit (Roche, Pleasanton, CA, USA) with mechanical shearing (Covaris, Woburn, MA, USA) and paired-end sequenced on a single lane of the NovaSeq 6000 SP 150 (Illumina, San Diego, CA, USA).&lt;/p&gt; Specified by the Principal Investigator(s) asNeeded 7.x-1.1 Biological and Chemical Oceanography Data Management Office (BCO-DMO) Unavailable 508-289-2009 WHOI MS#36 Woods Hole MA 02543 USA info@bco-dmo.org http://www.bco-dmo.org Monday - Friday 8:00am - 5:00pm For questions regarding this resource, please contact BCO-DMO via the email address provided. pointOfContact Illumina MiSeq v2 Illumina MiSeq v2 PI Supplied Instrument Name: Illumina MiSeq v2 PI Supplied Instrument Description:Amplicon sequencing Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. NovaSeq 6000 SP 150 NovaSeq 6000 SP 150 PI Supplied Instrument Name: NovaSeq 6000 SP 150 PI Supplied Instrument Description:Metagenome sequencing Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. Beckman Coulter CytoFLEX S Beckman Coulter CytoFLEX S PI Supplied Instrument Name: Beckman Coulter CytoFLEX S Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/ Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) PI Supplied Instrument Name: Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) PI Supplied Instrument Description:Chlorophyll a measurements Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/ Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector PI Supplied Instrument Name: Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector PI Supplied Instrument Description:Photosynthetic pigments measured via high performance liquid chromatography: Waters 2690 separations module equipped with a C18 column and full spectrum photodiode array detector, Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/ PI Supplied Instrument Name: PI Supplied Instrument Description:In situ measurements: YSI 6,600 sonde or ProDSS multi-parameter sonde (YSI Incorporated, Yellow Springs, OH, USA) Instrument Name: Multi Parameter Portable Meter Instrument Short Name: Instrument Description: An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held. Seal Analytical AA3 HR Nutrient Autoanalyzer Seal Analytical AA3 HR Nutrient Autoanalyzer PI Supplied Instrument Name: Seal Analytical AA3 HR Nutrient Autoanalyzer PI Supplied Instrument Description:Inorganic nutrients: Seal Analytical AA3 HR Nutrient Autoanalyzer (detection limits: NO2− + NO3− , 0.009 µM; SiO4, 0.09 µM;  PO43 –, 0.009 µM; NH4, 0.03 µM) Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/