http://lod.bco-dmo.org/id/dataset/963210
eng; USA
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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
2025-05-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021
2025-05-30
publication
2025-05-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-10
publication
https://doi.org/10.26008/1912/bco-dmo.963210.1
A. Murat Eren
University of Chicago
principalInvestigator
Kelle C. Freel
University of Hawaiʻi at Mānoa
principalInvestigator
Jessika Fuessel
University of Chicago
principalInvestigator
Michael S. Rappé
University of Hawaiʻi at Mānoa
principalInvestigator
Sarah J. Tucker
University of Hawaiʻi at Mānoa
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., Fuessel, J., Freel, K. C., Rappé, M. S., Eren, A. M. (2025) Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.963210.1 [access date]
Dataset Description: <p>Related Data:<br />
<br />
NCBI Project ID&nbsp;<a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1201851" target="_blank">PRJNA1201851</a>&nbsp;offers access to all raw data for short-read and long-read metagenomes, as well as metatranscriptomes and transfer RNA (tRNA) transcripts.<br />
<br />
doi:<a href="http://doi.org/10.6084/m9.figshare.28784717" target="_blank">10.6084/m9.figshare.28784717</a> serves anvi’o contigs-db files for the individual co-assemblies of short-read (SR) as well as long-read (LR) sequencing of metagenomes. Please note that an anvi’o contigs-db includes gene calls, functional annotations, HMM hits, and other information about each contig, and you can always use the program anvi-export-contigs to get a FASTA file for sequences.&nbsp;<br />
<br />
doi:<a href="http://doi.org/10.6084/m9.figshare.28784762" target="_blank">10.6084/m9.figshare.28784762</a> serves FASTA files for metagenome-assembled genomes (MAGs) we have reconstructed from short-read and long-read sequencing of the metagenomes. They are the outputs of quite a preliminary effort, thus secondary attempts to recover genomes from the co-assemblies are most welcome (and very much encouraged). Please see the Supplementary Table for taxonomic annotation and completion/redundancy estimates of the MAGs.<br />
<br />
doi:<a href="http://doi.org/10.6084/m9.figshare.28784765" target="_blank">10.6084/m9.figshare.28784765</a>. The EcoPhylo output that describes the phylogeography of ribosomal protein L14 (https://anvio.org/help/main/workflows/ecophylo/).<br />
<br />
See more about related data and code at&nbsp;https://merenlab.org/data/hads/</p> Methods and Sampling: <p>The methods characterized below are part of the following publication, currently in prep: Tucker SJ, Fuessel J, Freel KC, Kiefl E, Freel EB, Ramfelt O, Sullivan CE, Gajigan AP, Mochimaru H, Souza MR, Quinn M, Ratum C, Tran LL, Miller SE, Trigodet F, Lolans K, Morrison HG, Fallon B, Huettel B, Pan T, Rappé MS, Eren AM. A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA (tRNA) transcripts.&nbsp;</p>
<p>Hawaiʻi Diel Sampling (HaDS) collection and processing:&nbsp;</p>
<p>We sampled surface seawater from August 18, 2021 9:00 AM to August 20, 2021 9:00 AM Hawaiʻi Standard Time (HST), from a depth of ~0.25 m at station HP1 within coastal Kāneʻohe Bay, Oʻahu, Hawaiʻi, and station STO1 in the adjacent offshore.&nbsp; Sampling took place every 1.5 hours for 48 hours and yielded 33 sampling events at each site. We collected seawater samples for flow cytometry, fluorometric chlorophyll a concentrations, and nucleic acids, and recorded in situ measurements of seawater temperature, pH, and salinity with a YSI 6600 or YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA) and and in situ measurements of Photosynthetic Photon Flux Fluence Rate (PPFFR) with a LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA).&nbsp;</p>
<p>Roughly 10-20L of seawater was first pre-filtered through an 85-μm Nitex mesh and then ~4 (HP1) or ~9 (STO1) L of seawater was filtered through 0.2-μm pore-sized polyethersulfone (PES) Sterivex cartridge filters (MilliporeSigma, Burlington, MA, USA) to collect microbial cells for nucleic acids isolation. RNAlater (Invitrogen, Waltham, MA, United States) was immediately added to the Sterivex filters and stored the samples at −80 °C until further processing.</p>
<p>Seawater subsamples (125 mL) were collected on 25-mm diameter GF/F glass microfiber filters (Whatman, GE Healthcare Life Sciences, Chicago, IL, USA) and the filters were stored in aluminum foil at −80 °C until analysis of fluorometric chlorophyll a concentrations. Chlorophyll a was extracted in 100% acetone and the concentration determined with a Turner 10-AU fluorometer (Turner Designs, Sunnyvale, CA, USA), according to standard techniques (Welschmeyer 1994). Seawater aliquots (2 mL) in a final concentration of 0.95% (v:v) paraformaldehyde (Electron Microscopy Services, Hatfield, PA, USA) were collected and stored at&nbsp; −80 °C for cellular enumeration. Abundances of heterotrophic bacteria, photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus were enumerated by the SOEST Flow Cytometry Facility on a Beckman Coulter CytoFLEX S, following the method of Monger and Landry (1993).&nbsp; Dissolved inorganic nutrients were measured by the SOEST Laboratory for Analytical Biogeochemistry (S-LAB) on a Seal Analytical AA3 HR Nutrient Autoanalyzer, while concentrations of dissolved organic carbon and total nitrogen were measured by the S-LAB on a Shimadzu High-Temperature TOC-L Combustion Analyzer.</p>
<p>DNA extraction, preparation, and sequencing for short-read metagenomics:</p>
<p>Co-extraction of RNA and DNA was adapted from previously published protocols (Donaldson et al. 2020) and was used to extract DNA from Sterivex cartridge filters for short-read metagenomic sequencing.&nbsp;Cells suspended in the RNAlater within the Sterivex filter cartridges were collected by attaching a 10 mL air-filled clean syringe to the Sterivex cartridge and pushing the liquid into a nuclease-free 1 mL centrifuge vial. After centrifugation for 15 min at 4 °C at 13,000 rpm, we discarded the supernatant and kept the cell pellet on ice for further processing. The cartridge was opened holding the filter with a sterilized PVC pipe cutter and the cylinder with the PES membrane removed. Using a sterilized scalpel, the filter membrane was removed from the barrel. We cut the filter into ~6-8 small pieces in a sterile petri dish and transferred the pieces to a Lysing Matrix E (MP Biomedicals, Irvine, CA, USA) vial and added 450 µL Buffer A, 210 µL 20% SDS and 500 µL phenol:chloroform:IAA 125:24:1 pH 8. (50 mL Buffer A: 2 mL 5 M NaCl, 2 mL 0.5 M EDTA, 46 mL dH2O, all solutions were molecular grade and nuclease-free). Using in 50 µl Buffer A, we resuspended the cell pellet obtained from RNAlater and vortexed vigorously for 30 sec followed by a quick centrifugation step in a microcentrifuge and transferred the solution to the Lysing Matrix E vial. The cells were lysed with a Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA) on setting 6 for 30 sec followed by two min on ice followed by another lysing cycle with the same settings. The vials were centrifuged for 3 min at 4 °C at 13,000 rpm and the upper aqueous phase removed to a fresh, nuclease-free 1.5 mL centrifuge vial. Following the addition of 500 µL phenol:chloroform:IAA, we repeated the centrifugation step. After transferring the aqueous phase to a new centrifuge vial, we added 3 M sodium acetate at 1/10th of the transferred volume and mixed the solution by inversion. Following the addition of 500 µL ice-cold pure ethanol, we placed the samples in the freezer at -20 °C overnight.&nbsp;</p>
<p>The next day, samples were thawed and centrifuged at 13,000 rpm at 4 °C for 20 min, and the supernatant was carefully decanted to retain the nucleic acid pellet. We washed the pellet with 500 µL 70% ethanol at 4 °C and vortexed shortly followed by centrifugation at 13,000 rpm at 4 °C for 10 min. We decanted the liquid carefully and air-dried the pellet for 15 min. We added 100 µL of nuclease-free dH2O to the pellet and vortexed the pellet for 20 min with a Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA) and a Vortex adapter 24 (Qiagen, Hilden, Germany). We purified the DNA with the DNA Clean &amp; Concentrator-100 (Zymo Research, Irvine, CA, USA) and eluted in a final volume of 30 µL.&nbsp;</p>
<p>Following shearing of DNA to 400 bp on a Covaris S220 focused-ultrasonicator system, DNA was cleaned and concentrated with AMPure XP beads (Beckman Coulter, Brea, CA, USA) and metagenomic sequencing libraries prepared using the Ovation Ultralow System V2 with indexed sequencing adapters (Tecan Genomics, Männedorf, Switzerland). Final libraries were pooled at equimolar amounts and size-selected the library using a BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA) targeting the 468–572 bp region. DNA concentration was evaluated using the Qubit dsDNA high-sensitivity (HS) assays (Thermo Fisher Scientific) and the purity estimated with a NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific) before library preparation. We quantified the short-read metagenomic libraries using real-time PCR using KAPA library quantification reagents (Roche 07960204001) prior to sequencing. We paired-end sequenced the final pool on a NextSeq 500/550 High Output v2.5 using the 300 cycles kit (Illumina, San Diego, CA, USA). The Keck Sequencing Facility at the Marine Biological Laboratory in Woods Hole, MA, USA carried out the short-read metagenomic library preparation and sequencing.&nbsp;</p>
<p>Nucleic acid extraction, preparation, and sequencing for long-read metagenomics and metatranscriptomics:&nbsp;</p>
<p>The filters were first removed from the Sterivex cartridge as described above, and cut into small pieces to transfer them to 2 mL ZR BashingBead lysis tubes with 0.1 &amp; 0.5 mm beads (Zymo Research Europe, Germany) for subsequent cell disruption with a Qiagen TissueLyser (3 min. at 25 Hz). Next, DNA and total RNA were isolated from the same starting material using the ZymoBIOMICS DNA/RNA Miniprep Kit (Zymo Research Europe, Germany), with an additional DNase I treatment of the extracted RNA.&nbsp;</p>
<p>DNA directly served as input for a barcoded DNA library preparation without prior fragmentation. DNA was quality-controlled using HS Qubit assays (Thermo, Waltham, USA) and pulse-field capillary electrophoresis (Agilent FEMTOpulse). We prepared HiFi SMRTbell libraries (PacBio, Menlo Park, CA, USA) for long-read DNA sequencing following manufacturer protocols using the Ultra Low DNA Input approach and sequenced the libraries on a PacBio Revio device. For demultiplexing, adapter trimming, and deduplication of the sequencing data we relied on the PacBio SMRTlink software suite.</p>
<p>RNAseq libraries were prepared with the Universal Prokaryotic RNA-Seq Prokaryotic Any Deplete Kit by Tecan Genomics, including the proprietary adapter addition step of the kit and dual 8-mer barcode indexing. RNA was evaluated quality using HS Qubit assays (Thermo, Waltham, USA) and a PicoChip (Agilent Bioanalyzer) for total RNA. The libraries were paired-end sequenced on an Illumina NextSeq2000. The MPI Cologne Genomics Center conducted nucleic acid extraction, library preparation, and sequencing for long-read metagenomics and metatranscriptomics.</p>
<p>RNA extraction, preparation, and transfer RNA sequencing:&nbsp;</p>
<p>We prepared the following solutions: 1) marine microbe lysis solution: 40 mM EDTA, 50 mM TRIS and 0,75 M sucrose final concentration, 2) lysozyme stock solution: 100 mg/mL in TE buffer pH 8, RNAse free, and 3) Lysis solution 670 µL per sample: 600 µL marine microbe lysis solution, 67 µL lysozyme stock solution, 0.2 µL SUPERase (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA, 20 U/μL). For each Sterivex cartridge, we collected and pelleted cells that were suspended in RNAlater following the same steps described above and then resuspended the pellet with 70 µL of lysis solution. We removed the filter from the Sterivex cartridge using the steps described above, cut the filter into small pieces using a clean scalpel, and transferred the filter pieces to a 14 mL culture tube containing 600 µL of lysis solution. We then added the lysis solution with the resuspended cell pellet to the corresponding 14 mL tube with the filter pieces, and vortexed vigorously for 2 min. The samples were incubated in a 37 °C water bath for 45-60 min with gentle agitation of the samples every 10 min. Next, we added 7.4 µL of proteinase K (800 U/mL, New England Biolabs, Ipswich, MA, USA) and 74 µL of 10% SDS for a final concentration of 1%. The sample was placed in a 37 °C water bath for 2 h with gentle agitation every 10 min. Samples were stored at -80 °C until extraction.&nbsp;</p>
<p>The samples were thawed on ice. Next, we transferred the lysate to Lysing Matrix C tubes (MP Biomedicals, Santa Ana, CA, USA), which contain 1 mm silica lysing beads. We added 400 µL of 0.3 M NaOAc/HOAc, 10 mM EDTA, pH4.8 and an equal volume of acetate-saturated phenol/chloroform and vortexed briefly. The samples were placed in a reciprocating bead beater for 2-min at maximum intensity, pausing between 1 min intervals followed by centrifugation at 13,000 x g for 15 min at 4 °C. The aqueous phase was transferred to a fresh Lysing Matrix C tube and the phenol/chloroform extraction steps repeated. To precipitate the RNA, we added 1 v of 100 % isopropanol, vortexed each sample thoroughly, and incubated them overnight at -20 °C. The sample was centrifuged at 4 °C for 15 min at 13,000 x g, the supernatant discarded, and the pellet washed with 1 mL of chilled 75% ethanol. Following centrifugation for 5 min at 13,000 x g at 4 °C and removal of the ethanol, we let the RNA pellet air dry for 10 min at room temperature and then redissolved it in 30 µL of an acid-elution buffer (10 mM NaOAc/1 mM EDTA, pH 4.8). The sample was cleaned with the Zymo Research Oligo Clean &amp; Concentrate, and eluted in RNAse-free water. Finally, we added an equivalent amount of acid-elution buffer to each extract to reach a final concentration of 5 mM NaOac/0.05 mM EDTA, pH 4.8. We evaluated the quality and quantity of the RNA used in the tRNA libraries using a Qubit RNA HS assay (ThermoFisher Scientific, USA) and a Nanodrop Microvolume Spectrophotometer (ThermoFisher Scientific, USA). Previously published protocols for transfer RNA library preparation (MSR-seq; Watkins et al., 2022) were followed with paired-end multiplexed small RNA sequencing conducted on an Illumina NovaSeq 6000. Subsequently, we demultiplexed sequence data with custom scripts.</p>
<p>Kāneʻohe Bay Time-series (KByT) collection and processing:</p>
<p>To contextualize the diel data, we deeply sequenced four metagenomes collected at stations HP1 and STO1 on December 23, 2020 and May 24, 2021. These sampling events were part of the routine Kāneʻohe Bay Time-series sampling and processing of nucleic acids and other associated biogeochemical parameters followed previously published protocols (Tucker et al. 2021, 2025). Briefly, approximately one L of seawater collected from ~2m depth at HP1 and STO1 was prefiltered using an 85 μm Nitex mesh and subsequently collected on a 25-mm diameter 0.1-μm pore-sized polyethersulfone (PES) membrane for nucleic acids (Supor-100, Pall Gelman Inc., Ann Arbor, MI, USA). The filters were submerged in DNA lysis buffer (Suzuki et al., 2001) and stored at −80 °C until extraction. Genomic DNA was extracted using a Qiagen Blood and Tissue Kit (Qiagen Inc., Valencia, CA, USA) with modifications (Becker, Brandon &amp; Rappé, 2007). All other processing of subsamples follow the protocols described above. The short-read metagenomic library preparation and sequencing protocols for these 4 deeply sequenced samples are the same as those used for the diel short-read metagenomes.<br />
<br />
Deployment description:<br />
<br />
Small boat operations between the Hawaiʻi Institute of Marine Biology, coastal station HP1, and offshore station STO1 were conducted every 1.5 hours for 48 hours between 18 August 2021 and 20 August 2021. Small boat operations conducted through routine Kāneʻohe Bay Time-series (KByT) sampling yielded two additional sampling events at station HP1 and station STO1 on 23 December 2020 and 24 May 2021.</p>
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
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2019589 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2019589
Funding provided by Simons Foundation (Simons) Award Number: 933515
Funding provided by Simons Foundation (Simons) Award Number: LS-FMME-00989028
completed
A. Murat Eren
University of Chicago
meren@hifmb.de
pointOfContact
Kelle C. Freel
University of Hawaiʻi at Mānoa
kfreel@hawaii.edu
pointOfContact
Jessika Fuessel
University of Chicago
ju.fuessel@gmail.com
pointOfContact
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
Sarah J. Tucker
University of Hawaiʻi at Mānoa
stucker@mbl.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
HADS_Universal_Sample_ID
NCBI_BioProject
BioSample_accession
sampleID_MTX
sampleID_TRNA
sampleID_MGX
sampleID_HMW
Station
Date
Time_sampled
ISO_DateTime_UTC
lat
lon
Temp
Salinity
Depth
pH
PPFFR
PRO_mL
SYN_mL
PEUK_mL
HBACT_mL
chla
Phosphate_uM
Silicate_uM
NitrateNitrite_uM
Ammonia_uM
DOC_uM
TN_uM
MGX_SRA_accession
MGX_filename
MGX_filename2
MTX_SRA_accession
MTX_filename
MTX_filename2
TRNA_SRA_accession
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HMW_SRA_accession
HMW_filename
Agilent FEMTOpulse
Qubit (Thermo, Waltham, USA)
Illumina NextSeq 500/550 High Output v2.5
Illumina NextSeq2000
Illumina NovaSeq 6000
PacBio Revio device
PicoChip (Agilent Bioanalyzer)
Beckman Coulter CytoFLEX S
Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA)
Qiagen TissueLyser
LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA)
YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA)
Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA)
Vortex adapter 24 (Qiagen, Hilden, Germany)
Seal Analytical AA3 HR Nutrient Autoanalyzer
BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA)
Shimadzu High-Temperature TOC-L Combustion Analyzer
NanoDrop Spectrophotometer (Thermo Fisher Scientific)
Covaris S220 focused-ultrasonicator system
YSI 6600 (YSI Incorporated, Yellow Springs, OH, USA)
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
station
date_local
time_local
ISO_DateTime_UTC
latitude
longitude
water temperature at measurement depth
salinity
depth
pH
photosynthetic photon flux fluence rate (PPFFR)
prochlorococcus abundance
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
Ammonium
dissolved organic Carbon
total alkalinity (TA)
NCBI SRA run accession (SRR)
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Agilent Femto Pulse System
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Automated DNA Sequencer
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no_bcodmo_term
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Sage Science BluePippin DNA size selection device
Shimadzu TOC-L Analyzer
Thermo Scientific NanoDrop spectrophotometer
Turner Designs Fluorometer 10-AU
ultrasonic cell disrupter (sonicator)
YSI Sonde 6-Series
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.
Center for Chemical Currencies of a Microbial Planet
https://ccomp-stc.org/
Center for Chemical Currencies of a Microbial Planet
Functions carried out by microscopic inhabitants of the surface ocean affect every aspect of life on our planet, regardless of distance from the coast. Ocean phytoplankton are responsible for half of the photosynthesis on Earth, the first step in a complex system that annually withdraws 50 billion metric tons of carbon from the atmosphere to sustain their growth. Of this, 25 billion metric tons participate in a rapid cycle in which biologically reactive material is released into seawater and converted back into carbon dioxide by marine bacteria within hours to days. The chemical-microbe network at the heart of this fast cycle remains poorly constrained; consequently, its primary currencies and controls remain elusive; its sensitivities to changing ocean conditions are unknown; and its responses to future climate scenarios are not predictable. The Center for Chemical Currencies of a Microbial Planet (C-CoMP) integrates research, education and knowledge transfer activities to develop a mechanistic understanding of surface ocean carbon flux within the context of a changing ocean and through increased participation in ocean sciences. C-CoMP supports science teams that merge biology, chemistry, modeling, and informatics to close long-standing knowledge gaps in the identities and dynamics of organic molecules that serve as the currencies of elemental transfer between the ocean and atmosphere. C-CoMP fosters education, outreach, and knowledge transfer activities that engage students of all ages, broaden participation in the next generation of ocean scientists, and extend novel open-science approaches into complementary academic and industrial communities. The Center framework is critical to this mission, uniquely facilitating an open exchange of experimental and computational science, methodological and conceptual challenges, and collaborations that establish integrated science and education partnerships. With expanded participation in ocean science research and ocean literacy across the US society, the next generation of ocean scientists will better reflect the diverse US population.
Climate-carbon feedbacks on the marine carbon reservoir are major uncertainties for future climate projections, and the trajectory and rate of ocean changes depend directly on microbial responses to temperature increases, ocean acidification, and other perturbations driven by climate change. C-CoMP research closes an urgent knowledge gap in the mechanisms driving carbon flow between ocean and atmosphere, with global implications for predictive climate models. The Center supports interdisciplinary science teams following open and reproducible science practices to address: (1) the chemical currencies of surface ocean carbon flux; (2) the structure and regulation of the chemical-microbe network that mediates this flux; and (3) sensitivity of the network and its feedbacks on climate. C-CoMP leverages emerging tools and technologies to tackle critical challenges in these themes, in synergy with existing ocean programs and consistent with NSF’s Big Ideas. C-CoMP education and outreach activities seek to overcome barriers to ocean literacy and diversify participation in ocean research. The Center is developing (1) initiatives to expand ocean literacy in K-12 and the broader public, (2) ocean sciences undergraduate curricula and research opportunities that provide multiple entry points into research experiences, (3) post-baccalaureate programs to transition undergraduates into graduate education and careers in ocean science, and (4) interdisciplinary graduate student and postdoctoral programs that prepare the next generation of ocean scientists. The C-CoMP team includes education faculty who evaluate the impacts of education and outreach activities and export successful STEM initiatives to the education community. C-CoMP is revolutionizing the technologies for studying chemical transformations in microbial systems to build understanding of the outsized impact of microbes on elemental cycles. Open science, cross-disciplinary collaborations, community engagement, and inclusive practices foster strategic advances in critical science problems and STEM initiatives. C-CoMP science, education, and knowledge-transfer themes are efficiently addressed through a sustained network of scientists addressing critical research challenges while broadening the workforce that will tackle multi-disciplinary problems with academic, industrial and policy partners.
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.
The Program's Data Management Plan (DMP) is available as a PDF document.
C-CoMP
largerWorkCitation
program
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
From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments
https://merenlab.org/data/hads
From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments
<p>Physiological responses of marine microorganisms to environmental conditions are key drivers of both the ecology and evolution of microbial communities and the biogeochemistry of the world's oceans. Marine bacteria respond to fluctuating environmental conditions with both transcriptional and translation regulation. While the study of transcriptional regulation in marine microbial communities has gained traction through the application of metatranscriptomics, still relatively little is understood about how marine microbial populations utilize translational regulation to shape protein synthesis.</p>
<p>Translational regulation through transfer RNAs (tRNAs) allows cells to regulate gene expression beyond transcription and yield proteins that are not encoded by the genome. Due to the central role of tRNAs in protein synthesis, the characterization of tRNA modifications and tRNA abundances offer direct insights into translational processes. However, molecular and computational challenges have limited the capacity to conduct investigations of tRNAs in naturally occurring microbial habitats. Here we apply high-throughput sequencing of tRNAs collected from surface ocean marine microbial communities to observe epi-changes in translational regulation in response to changing ocean conditions. These metaepitranscriptomic data are collected in tandem with metagenomic and metatranscriptomic data as well as measures of the physical, chemical, and biological ocean conditions. Through this integrated dataset, we aim to develop new computational approaches to analyze high-throughput transfer RNA sequencing data and use these approaches to gain new insights into the ecology and environmental responses of major marine populations.</p>
C-CoMP Diel Multi 'Omics
largerWorkCitation
project
eng; USA
oceans
-157.80331
-157.7663
21.43688
21.4829
2020-12-23
2021-08-20
From projects that focused on the following 2 locations: 1. Coastal Hawai’i in the tropical North Pacific Ocean 2. Surface ocean tropical Pacific
0
BCO-DMO catalogue of parameters from Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021
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/963334.rdf
Name: HADS_Universal_Sample_ID
Units: unitless
Description: <p>Universal Sample ID. Universal Sample ID is used to connect multiple sample types within the Hawai_i Diel Sampling (HaDS). It is composed of the Project ID "HADS", the date of sampling (yyyymmdd), the sampling hour, and the sampling station.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963335.rdf
Name: NCBI_BioProject
Units: unitless
Description: <p>NCBI BioProject Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963336.rdf
Name: BioSample_accession
Units: unitless
Description: <p>NCBI Biosample Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963337.rdf
Name: sampleID_MTX
Units: unitless
Description: <p>MTX Sample ID. MTX Sample ID has similar components of the univeral sample ID plus the sample type (mtx for metatranscriptomics) and the sample number that is unique only among MTX samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963338.rdf
Name: sampleID_TRNA
Units: unitless
Description: <p>TRNA Sample ID. TRNA Sample ID has similar components of the univeral sample ID plus the sample type (TRNA for transfer RNA sequencing) and the sample number that is unique only among TRNA samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963339.rdf
Name: sampleID_MGX
Units: unitless
Description: <p>MGX Sample ID. MGX Sample ID has similar components of the univeral sample ID plus the sample type (MGX for short-read metagenomics) and the sample number that is unique only among MGX samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963340.rdf
Name: sampleID_HMW
Units: unitless
Description: <p>HMW Sample ID. HMW Sample ID has similar components of the univeral sample ID plus the sample type (HMW for long-read metagenomics that uses high-molecular weight DNA) and the sample number that is unique only among HMW samples.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963341.rdf
Name: Station
Units: unitless
Description: <p>Station ID for collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963342.rdf
Name: Date
Units: unitless
Description: <p>Collection date (ISO 8601 format)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963343.rdf
Name: Time_sampled
Units: hh:mm
Description: <p>Local time (Hawaiii Standard Time) of sampling surface seawater.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963344.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>DateTime with timezone (ISO 8601 format) for sampling surface seawater (UTC time zone)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963345.rdf
Name: lat
Units: Decimal Degrees
Description: <p>Latitiude of sample collection site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963346.rdf
Name: lon
Units: Decimal Degrees
Description: <p>Longitude of sample collection site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963347.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperature of surface seawater in situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963348.rdf
Name: Salinity
Units: ppt
Description: <p>Salinity of surface seawater in situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963349.rdf
Name: Depth
Units: meters
Description: <p>Depth of sample collection.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963350.rdf
Name: pH
Units: pH scale
Description: <p>pH of surface seawater in situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963351.rdf
Name: PPFFR
Units: Micromoles of photons per square meter per second (umol/m2/s)
Description: <p>Photosynthetic Photon Flux Fluence Rate in situ.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963352.rdf
Name: PRO_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/963353.rdf
Name: SYN_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/963354.rdf
Name: PEUK_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/963355.rdf
Name: HBACT_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/963356.rdf
Name: chla
Units: micrograms per Liter
Description: <p>Extracted chlorophyll a concentrations from surface seawater.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963357.rdf
Name: Phosphate_uM
Units: micromolar (uM)
Description: <p>Inorganic nutrients. Concentrations of phosphate in surface seawater sample (PO43-).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963358.rdf
Name: Silicate_uM
Units: micromolar (uM)
Description: <p>Inorganic nutrients. Concentrations of silicate in surface seawater sample (SiO4 ).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963359.rdf
Name: NitrateNitrite_uM
Units: micromolar (uM)
Description: <p>Inorganic nutrients. Concentrations of nitrate+nitrite in surface seawater sample (NO2- + NO3- ).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963360.rdf
Name: Ammonia_uM
Units: micromolar (uM)
Description: <p>Inorganic nutrients. Concentrations of ammonia in surface seawater sample (NH4).</p>
http://lod.bco-dmo.org/id/dataset-parameter/963361.rdf
Name: DOC_uM
Units: micromolar (uM)
Description: <p>Dissolved organic carbon. Concentrations of dissolved organic carbon in surface seawater sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963362.rdf
Name: TN_uM
Units: micromolar (uM)
Description: <p>Total Nitrogen. Concentrations of total nitrogen in surface seawater sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963363.rdf
Name: MGX_SRA_accession
Units: unitless
Description: <p>Short-read metagenome NCBI Sequence Read Archive Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963364.rdf
Name: MGX_filename
Units: unitless
Description: <p>Short-read metagenome R1 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963365.rdf
Name: MGX_filename2
Units: unitless
Description: <p>Short-read metagenome R2 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963366.rdf
Name: MTX_SRA_accession
Units: unitless
Description: <p>Metatranscriptome NCBI Sequence Read Archive Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963367.rdf
Name: MTX_filename
Units: unitless
Description: <p>Metatranscriptome R1 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963368.rdf
Name: MTX_filename2
Units: unitless
Description: <p>Metatranscriptome R2 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963369.rdf
Name: TRNA_SRA_accession
Units: unitless
Description: <p>tRNA-seq NCBI Sequence Read Archive Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963370.rdf
Name: TRNA_filename
Units: unitless
Description: <p>tRNA R1 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963371.rdf
Name: TRNA_filename2
Units: unitless
Description: <p>tRNA R2 file name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963372.rdf
Name: HMW_SRA_accession
Units: unitless
Description: <p>Long-read metagenomics NCBI Sequence Read Archive Accession.</p>
http://lod.bco-dmo.org/id/dataset-parameter/963373.rdf
Name: HMW_filename
Units: unitless
Description: <p>Long-read metagenomics file name.</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
41543
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/60333095-54b6-4d74-8eb7-5744bce3d5dd/content
download
https://doi.org/10.26008/1912/bco-dmo.963210.1
download
onLine
dataset
<p>The methods characterized below are part of the following publication, currently in prep: Tucker SJ, Fuessel J, Freel KC, Kiefl E, Freel EB, Ramfelt O, Sullivan CE, Gajigan AP, Mochimaru H, Souza MR, Quinn M, Ratum C, Tran LL, Miller SE, Trigodet F, Lolans K, Morrison HG, Fallon B, Huettel B, Pan T, Rappé MS, Eren AM. A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA (tRNA) transcripts.&nbsp;</p>
<p>Hawaiʻi Diel Sampling (HaDS) collection and processing:&nbsp;</p>
<p>We sampled surface seawater from August 18, 2021 9:00 AM to August 20, 2021 9:00 AM Hawaiʻi Standard Time (HST), from a depth of ~0.25 m at station HP1 within coastal Kāneʻohe Bay, Oʻahu, Hawaiʻi, and station STO1 in the adjacent offshore.&nbsp; Sampling took place every 1.5 hours for 48 hours and yielded 33 sampling events at each site. We collected seawater samples for flow cytometry, fluorometric chlorophyll a concentrations, and nucleic acids, and recorded in situ measurements of seawater temperature, pH, and salinity with a YSI 6600 or YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA) and and in situ measurements of Photosynthetic Photon Flux Fluence Rate (PPFFR) with a LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA).&nbsp;</p>
<p>Roughly 10-20L of seawater was first pre-filtered through an 85-μm Nitex mesh and then ~4 (HP1) or ~9 (STO1) L of seawater was filtered through 0.2-μm pore-sized polyethersulfone (PES) Sterivex cartridge filters (MilliporeSigma, Burlington, MA, USA) to collect microbial cells for nucleic acids isolation. RNAlater (Invitrogen, Waltham, MA, United States) was immediately added to the Sterivex filters and stored the samples at −80 °C until further processing.</p>
<p>Seawater subsamples (125 mL) were collected on 25-mm diameter GF/F glass microfiber filters (Whatman, GE Healthcare Life Sciences, Chicago, IL, USA) and the filters were stored in aluminum foil at −80 °C until analysis of fluorometric chlorophyll a concentrations. Chlorophyll a was extracted in 100% acetone and the concentration determined with a Turner 10-AU fluorometer (Turner Designs, Sunnyvale, CA, USA), according to standard techniques (Welschmeyer 1994). Seawater aliquots (2 mL) in a final concentration of 0.95% (v:v) paraformaldehyde (Electron Microscopy Services, Hatfield, PA, USA) were collected and stored at&nbsp; −80 °C for cellular enumeration. Abundances of heterotrophic bacteria, photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus were enumerated by the SOEST Flow Cytometry Facility on a Beckman Coulter CytoFLEX S, following the method of Monger and Landry (1993).&nbsp; Dissolved inorganic nutrients were measured by the SOEST Laboratory for Analytical Biogeochemistry (S-LAB) on a Seal Analytical AA3 HR Nutrient Autoanalyzer, while concentrations of dissolved organic carbon and total nitrogen were measured by the S-LAB on a Shimadzu High-Temperature TOC-L Combustion Analyzer.</p>
<p>DNA extraction, preparation, and sequencing for short-read metagenomics:</p>
<p>Co-extraction of RNA and DNA was adapted from previously published protocols (Donaldson et al. 2020) and was used to extract DNA from Sterivex cartridge filters for short-read metagenomic sequencing.&nbsp;Cells suspended in the RNAlater within the Sterivex filter cartridges were collected by attaching a 10 mL air-filled clean syringe to the Sterivex cartridge and pushing the liquid into a nuclease-free 1 mL centrifuge vial. After centrifugation for 15 min at 4 °C at 13,000 rpm, we discarded the supernatant and kept the cell pellet on ice for further processing. The cartridge was opened holding the filter with a sterilized PVC pipe cutter and the cylinder with the PES membrane removed. Using a sterilized scalpel, the filter membrane was removed from the barrel. We cut the filter into ~6-8 small pieces in a sterile petri dish and transferred the pieces to a Lysing Matrix E (MP Biomedicals, Irvine, CA, USA) vial and added 450 µL Buffer A, 210 µL 20% SDS and 500 µL phenol:chloroform:IAA 125:24:1 pH 8. (50 mL Buffer A: 2 mL 5 M NaCl, 2 mL 0.5 M EDTA, 46 mL dH2O, all solutions were molecular grade and nuclease-free). Using in 50 µl Buffer A, we resuspended the cell pellet obtained from RNAlater and vortexed vigorously for 30 sec followed by a quick centrifugation step in a microcentrifuge and transferred the solution to the Lysing Matrix E vial. The cells were lysed with a Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA) on setting 6 for 30 sec followed by two min on ice followed by another lysing cycle with the same settings. The vials were centrifuged for 3 min at 4 °C at 13,000 rpm and the upper aqueous phase removed to a fresh, nuclease-free 1.5 mL centrifuge vial. Following the addition of 500 µL phenol:chloroform:IAA, we repeated the centrifugation step. After transferring the aqueous phase to a new centrifuge vial, we added 3 M sodium acetate at 1/10th of the transferred volume and mixed the solution by inversion. Following the addition of 500 µL ice-cold pure ethanol, we placed the samples in the freezer at -20 °C overnight.&nbsp;</p>
<p>The next day, samples were thawed and centrifuged at 13,000 rpm at 4 °C for 20 min, and the supernatant was carefully decanted to retain the nucleic acid pellet. We washed the pellet with 500 µL 70% ethanol at 4 °C and vortexed shortly followed by centrifugation at 13,000 rpm at 4 °C for 10 min. We decanted the liquid carefully and air-dried the pellet for 15 min. We added 100 µL of nuclease-free dH2O to the pellet and vortexed the pellet for 20 min with a Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA) and a Vortex adapter 24 (Qiagen, Hilden, Germany). We purified the DNA with the DNA Clean &amp; Concentrator-100 (Zymo Research, Irvine, CA, USA) and eluted in a final volume of 30 µL.&nbsp;</p>
<p>Following shearing of DNA to 400 bp on a Covaris S220 focused-ultrasonicator system, DNA was cleaned and concentrated with AMPure XP beads (Beckman Coulter, Brea, CA, USA) and metagenomic sequencing libraries prepared using the Ovation Ultralow System V2 with indexed sequencing adapters (Tecan Genomics, Männedorf, Switzerland). Final libraries were pooled at equimolar amounts and size-selected the library using a BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA) targeting the 468–572 bp region. DNA concentration was evaluated using the Qubit dsDNA high-sensitivity (HS) assays (Thermo Fisher Scientific) and the purity estimated with a NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific) before library preparation. We quantified the short-read metagenomic libraries using real-time PCR using KAPA library quantification reagents (Roche 07960204001) prior to sequencing. We paired-end sequenced the final pool on a NextSeq 500/550 High Output v2.5 using the 300 cycles kit (Illumina, San Diego, CA, USA). The Keck Sequencing Facility at the Marine Biological Laboratory in Woods Hole, MA, USA carried out the short-read metagenomic library preparation and sequencing.&nbsp;</p>
<p>Nucleic acid extraction, preparation, and sequencing for long-read metagenomics and metatranscriptomics:&nbsp;</p>
<p>The filters were first removed from the Sterivex cartridge as described above, and cut into small pieces to transfer them to 2 mL ZR BashingBead lysis tubes with 0.1 &amp; 0.5 mm beads (Zymo Research Europe, Germany) for subsequent cell disruption with a Qiagen TissueLyser (3 min. at 25 Hz). Next, DNA and total RNA were isolated from the same starting material using the ZymoBIOMICS DNA/RNA Miniprep Kit (Zymo Research Europe, Germany), with an additional DNase I treatment of the extracted RNA.&nbsp;</p>
<p>DNA directly served as input for a barcoded DNA library preparation without prior fragmentation. DNA was quality-controlled using HS Qubit assays (Thermo, Waltham, USA) and pulse-field capillary electrophoresis (Agilent FEMTOpulse). We prepared HiFi SMRTbell libraries (PacBio, Menlo Park, CA, USA) for long-read DNA sequencing following manufacturer protocols using the Ultra Low DNA Input approach and sequenced the libraries on a PacBio Revio device. For demultiplexing, adapter trimming, and deduplication of the sequencing data we relied on the PacBio SMRTlink software suite.</p>
<p>RNAseq libraries were prepared with the Universal Prokaryotic RNA-Seq Prokaryotic Any Deplete Kit by Tecan Genomics, including the proprietary adapter addition step of the kit and dual 8-mer barcode indexing. RNA was evaluated quality using HS Qubit assays (Thermo, Waltham, USA) and a PicoChip (Agilent Bioanalyzer) for total RNA. The libraries were paired-end sequenced on an Illumina NextSeq2000. The MPI Cologne Genomics Center conducted nucleic acid extraction, library preparation, and sequencing for long-read metagenomics and metatranscriptomics.</p>
<p>RNA extraction, preparation, and transfer RNA sequencing:&nbsp;</p>
<p>We prepared the following solutions: 1) marine microbe lysis solution: 40 mM EDTA, 50 mM TRIS and 0,75 M sucrose final concentration, 2) lysozyme stock solution: 100 mg/mL in TE buffer pH 8, RNAse free, and 3) Lysis solution 670 µL per sample: 600 µL marine microbe lysis solution, 67 µL lysozyme stock solution, 0.2 µL SUPERase (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA, 20 U/μL). For each Sterivex cartridge, we collected and pelleted cells that were suspended in RNAlater following the same steps described above and then resuspended the pellet with 70 µL of lysis solution. We removed the filter from the Sterivex cartridge using the steps described above, cut the filter into small pieces using a clean scalpel, and transferred the filter pieces to a 14 mL culture tube containing 600 µL of lysis solution. We then added the lysis solution with the resuspended cell pellet to the corresponding 14 mL tube with the filter pieces, and vortexed vigorously for 2 min. The samples were incubated in a 37 °C water bath for 45-60 min with gentle agitation of the samples every 10 min. Next, we added 7.4 µL of proteinase K (800 U/mL, New England Biolabs, Ipswich, MA, USA) and 74 µL of 10% SDS for a final concentration of 1%. The sample was placed in a 37 °C water bath for 2 h with gentle agitation every 10 min. Samples were stored at -80 °C until extraction.&nbsp;</p>
<p>The samples were thawed on ice. Next, we transferred the lysate to Lysing Matrix C tubes (MP Biomedicals, Santa Ana, CA, USA), which contain 1 mm silica lysing beads. We added 400 µL of 0.3 M NaOAc/HOAc, 10 mM EDTA, pH4.8 and an equal volume of acetate-saturated phenol/chloroform and vortexed briefly. The samples were placed in a reciprocating bead beater for 2-min at maximum intensity, pausing between 1 min intervals followed by centrifugation at 13,000 x g for 15 min at 4 °C. The aqueous phase was transferred to a fresh Lysing Matrix C tube and the phenol/chloroform extraction steps repeated. To precipitate the RNA, we added 1 v of 100 % isopropanol, vortexed each sample thoroughly, and incubated them overnight at -20 °C. The sample was centrifuged at 4 °C for 15 min at 13,000 x g, the supernatant discarded, and the pellet washed with 1 mL of chilled 75% ethanol. Following centrifugation for 5 min at 13,000 x g at 4 °C and removal of the ethanol, we let the RNA pellet air dry for 10 min at room temperature and then redissolved it in 30 µL of an acid-elution buffer (10 mM NaOAc/1 mM EDTA, pH 4.8). The sample was cleaned with the Zymo Research Oligo Clean &amp; Concentrate, and eluted in RNAse-free water. Finally, we added an equivalent amount of acid-elution buffer to each extract to reach a final concentration of 5 mM NaOac/0.05 mM EDTA, pH 4.8. We evaluated the quality and quantity of the RNA used in the tRNA libraries using a Qubit RNA HS assay (ThermoFisher Scientific, USA) and a Nanodrop Microvolume Spectrophotometer (ThermoFisher Scientific, USA). Previously published protocols for transfer RNA library preparation (MSR-seq; Watkins et al., 2022) were followed with paired-end multiplexed small RNA sequencing conducted on an Illumina NovaSeq 6000. Subsequently, we demultiplexed sequence data with custom scripts.</p>
<p>Kāneʻohe Bay Time-series (KByT) collection and processing:</p>
<p>To contextualize the diel data, we deeply sequenced four metagenomes collected at stations HP1 and STO1 on December 23, 2020 and May 24, 2021. These sampling events were part of the routine Kāneʻohe Bay Time-series sampling and processing of nucleic acids and other associated biogeochemical parameters followed previously published protocols (Tucker et al. 2021, 2025). Briefly, approximately one L of seawater collected from ~2m depth at HP1 and STO1 was prefiltered using an 85 μm Nitex mesh and subsequently collected on a 25-mm diameter 0.1-μm pore-sized polyethersulfone (PES) membrane for nucleic acids (Supor-100, Pall Gelman Inc., Ann Arbor, MI, USA). The filters were submerged in DNA lysis buffer (Suzuki et al., 2001) and stored at −80 °C until extraction. Genomic DNA was extracted using a Qiagen Blood and Tissue Kit (Qiagen Inc., Valencia, CA, USA) with modifications (Becker, Brandon &amp; Rappé, 2007). All other processing of subsamples follow the protocols described above. The short-read metagenomic library preparation and sequencing protocols for these 4 deeply sequenced samples are the same as those used for the diel short-read metagenomes.<br />
<br />
Deployment description:<br />
<br />
Small boat operations between the Hawaiʻi Institute of Marine Biology, coastal station HP1, and offshore station STO1 were conducted every 1.5 hours for 48 hours between 18 August 2021 and 20 August 2021. Small boat operations conducted through routine Kāneʻohe Bay Time-series (KByT) sampling yielded two additional sampling events at station HP1 and station STO1 on 23 December 2020 and 24 May 2021.</p>
Specified by the Principal Investigator(s)
* Table within submitted file "final_submission_may22205_bco_dmo_Tucker.txt" was imported into the BCO-DMO data system for this dataset. Values "NA" imported as missing data values. Table will appear as Data File: 963210_v1_biogeochem-and-sampling-info-hads.csv (along with other download format options).
Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Date converted to ISO 8601 format
* ISO DateTime with timezone (UTC) column added in ISO 8601 format. (from local time provided in HST)
* lat_lon combined column *e.g. "21.4829 N 157.7663 W" split into lat and lon in decimal degrees lat "21.4829", lon "-157.7663" for improved geospatial readiness.
* For sample HADS_20210819_H2100_STO1, converted Time_sampled "21.25" to 21:25 to match the format of the column.
Specified by BCO-DMO Data Managers
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
Agilent FEMTOpulse
Agilent FEMTOpulse
PI Supplied Instrument Name: Agilent FEMTOpulse PI Supplied Instrument Description:quality control of DNA libraries Instrument Name: Agilent Femto Pulse System Instrument Short Name: Instrument Description: Femto Pulse System. Parallel capillary electrophoresis instrument for analysis of nucleic acids. Compatible with the Femto Pulse 12-capillary array.
The Agilent Femto Pulse System offers an excellent solution for analyzing high molecular weight DNA samples with high accuracy. Utilizing pulsed-field electrophoresis technology, this system delivers precise quantification and qualification of DNA samples up to 165 kb, crucial for evaluating the quality of long-read sequencing libraries and predicting the average read length in long-read NGS.
In comparison to other non-denaturing gel-based analytical instruments, the Femto Pulse System stands out by achieving significantly higher sensitivity for nucleic acid smears and fragments. This capability enables the detection of low-abundance samples, making it an ideal instrument for highly sensitive analysis of RNA or cfDNA samples.
(from https://www.agilent.com/en/product/automated-electrophoresis/femto-pulse-systems/femto-pulse-system/femto-pulse-system-365750)
Qubit (Thermo, Waltham, USA)
Qubit (Thermo, Waltham, USA)
PI Supplied Instrument Name: Qubit (Thermo, Waltham, USA) PI Supplied Instrument Description:quantify DNA and RNA 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.
Illumina NextSeq 500/550 High Output v2.5
Illumina NextSeq 500/550 High Output v2.5
PI Supplied Instrument Name: Illumina NextSeq 500/550 High Output v2.5 PI Supplied Instrument Description:sequencing of omic libraries 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.
Illumina NextSeq2000
Illumina NextSeq2000
PI Supplied Instrument Name: Illumina NextSeq2000 PI Supplied Instrument Description:sequencing of omic libraries 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.
Illumina NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:sequencing of omic libraries 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.
PacBio Revio device
PacBio Revio device
PI Supplied Instrument Name: PacBio Revio device PI Supplied Instrument Description:sequencing of omic libraries 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.
PicoChip (Agilent Bioanalyzer)
PicoChip (Agilent Bioanalyzer)
PI Supplied Instrument Name: PicoChip (Agilent Bioanalyzer) PI Supplied Instrument Description:quality and quantity assessment of RNA Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument Description: A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
Beckman Coulter CytoFLEX S
Beckman Coulter CytoFLEX S
PI Supplied Instrument Name: Beckman Coulter CytoFLEX S PI Supplied Instrument Description:cellular enumeration of Prochlorococcus, Synechococcus, heterotrophic bacteria, and photosynthetic picoeukaryotes 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/
Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA)
Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA)
PI Supplied Instrument Name: Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA) PI Supplied Instrument Description:Bead Ruptor Elite (OMNI International, Kennesaw, GA, USA)- bead beating for cell lysis Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Qiagen TissueLyser
Qiagen TissueLyser
PI Supplied Instrument Name: Qiagen TissueLyser PI Supplied Instrument Description:cell lysis Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA)
LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA)
PI Supplied Instrument Name: LI-193 Underwater Spherical Quantum Sensor and LI-250A Light Meter (LI-COR Environmental, Lincoln, NE, USA) PI Supplied Instrument Description:in situ measurements of Photosynthetic Photon Flux Fluence Rate Instrument Name: Light Meter Instrument Short Name:Light Meter Instrument Description: Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)
YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA)
YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA)
PI Supplied Instrument Name: YSI EcoSense EC300 (YSI Incorporated, Yellow Springs, OH, USA) PI Supplied Instrument Description:in situ seawater measurements 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.
Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA)
Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA)
PI Supplied Instrument Name: Vortex-Genie 2 (Scientific Industries, Bohemia, NY, USA) PI Supplied Instrument Description:vortexing samples Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
Vortex adapter 24 (Qiagen, Hilden, Germany)
Vortex adapter 24 (Qiagen, Hilden, Germany)
PI Supplied Instrument Name: Vortex adapter 24 (Qiagen, Hilden, Germany) PI Supplied Instrument Description:vortexing samples Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
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:measured concentrations of inorganic nutrients 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/
BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA)
BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA)
PI Supplied Instrument Name: BluePippin 1.5% agarose gel cassette (Sage Science, Beverly, MA, USA) PI Supplied Instrument Description:size-selection of omics libraries Instrument Name: Sage Science BluePippin DNA size selection device Instrument Short Name:BluePippin Instrument Description: An automated DNA size selection instrument, with pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. The instrument is used to automatically extract DNA fragments of a user selected size for downstream technologies such as miRNA isolation, DNA sequencing, RNA-seq, genotyping, DNA sequencing, ChIP-seq, and Long-read sequencing. The instrument uses electrophoresis along with laser detection or other imaging technology to determine when to start collecting DNA based on size ranges entered by the user. Once the DNA is no longer in the desired size range, collection ceases. The instrument has electrophoresis voltage options: 25V, 100V or 150V constant, or 100V pulsed field. The optical detection wavelength is 470 nm excitation, and 525 nm emission. The instrument can run up to 5 samples/gel cassettes at a time, with no possibility of cross contamination.
Shimadzu High-Temperature TOC-L Combustion Analyzer
Shimadzu High-Temperature TOC-L Combustion Analyzer
PI Supplied Instrument Name: Shimadzu High-Temperature TOC-L Combustion Analyzer PI Supplied Instrument Description:Measured the concentration of dissolved organic carbon and total nitrogen Instrument Name: Shimadzu TOC-L Analyzer Instrument Short Name:Shimadzu TOC-L Instrument Description: A Shimadzu TOC-L Analyzer measures DOC by high temperature combustion method.
Developed by Shimadzu, the 680 degree C combustion catalytic oxidation method is now used worldwide. One of its most important features is the capacity to efficiently oxidize hard-to-decompose organic compounds, including insoluble and macromolecular organic compounds. The 680 degree C combustion catalytic oxidation method has been adopted for the TOC-L series.
http://www.shimadzu.com/an/toc/lab/toc-l2.html Community Standard Description: http://onto.nerc.ac.uk/CAST/124.html
NanoDrop Spectrophotometer (Thermo Fisher Scientific)
NanoDrop Spectrophotometer (Thermo Fisher Scientific)
PI Supplied Instrument Name: NanoDrop Spectrophotometer (Thermo Fisher Scientific) PI Supplied Instrument Description:measure DNA purity Instrument Name: Thermo Scientific NanoDrop spectrophotometer Instrument Short Name:NanoDrop spectrophotometer Instrument Description: Thermo Scientific NanoDrop spectrophotometers provide microvolume quantification and purity assessments of DNA, RNA, and protein samples. NanoDrop spectrophotometers work on the principle of ultraviolet-visible spectrum (UV-Vis) absorbance. The range consists of the NanoDrop One/OneC UV-Vis Spectrophotometers, NanoDrop Eight UV-Vis Spectrophotometer and NanoDrop Lite Plus UV Spectrophotometer.
PI Supplied Instrument Name: PI Supplied Instrument Description:chlorophyll a extractions Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/
Covaris S220 focused-ultrasonicator system
Covaris S220 focused-ultrasonicator system
PI Supplied Instrument Name: Covaris S220 focused-ultrasonicator system PI Supplied Instrument Description:mechanical shearing of genomic DNA Instrument Name: ultrasonic cell disrupter (sonicator) Instrument Short Name: Instrument Description: Instrument that applies sound energy to agitate particles in a sample.
YSI 6600 (YSI Incorporated, Yellow Springs, OH, USA)
YSI 6600 (YSI Incorporated, Yellow Springs, OH, USA)
PI Supplied Instrument Name: YSI 6600 (YSI Incorporated, Yellow Springs, OH, USA) PI Supplied Instrument Description:In situ seawater measurements Instrument Name: YSI Sonde 6-Series Instrument Short Name:YSI Sonde 6-Series Instrument Description: YSI 6-Series water quality sondes and sensors are instruments for environmental monitoring and long-term deployments. YSI datasondes accept multiple water quality sensors (i.e., they are multiparameter sondes). Sondes can measure temperature, conductivity, dissolved oxygen, depth, turbidity, and other water quality parameters. The 6-Series includes several models. More from YSI. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0737/