Dataset: Kāneʻohe Bay Time-series - microbial community

Name: Flow cytometry, 16S rRNA gene amplicons, chlorophyll a, and surface seawater measurements taken between August 2017 to June 2019 Kāneʻohe Bay, Oʻahu, Hawaiʻi
Published: 2024-08-30
Keywords: SAR11, microbial oceanography, marine bacteria, Pelagibacterales, Biogeography, time-series dataset, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.930084.1

Spatial Extent: N:21.526 E:-157.7663 S:21.43635 W:-157.83585

Kāneʻohe Bay, Oʻahu, Hawaiʻi and adjacent offshore waters, 21° 28′ N, 157° 48′ W, depth 2m

Temporal Extent: 2017-08-23 - 2019-06-14

Project:

Population genomics and ecotypic divergence in the most dominant lineage of marine bacteria (Pelagibacteromics)

Principal Investigator:

Michael S. Rappé (University of Hawaiʻi at Mānoa, HIMB)

Scientist:

Kelle C. Freel (University of Hawaiʻi at Mānoa, HIMB)

Yoshimi M. Rii (University of Hawaiʻi at Mānoa, HIMB)

Student:

Elizabeth A. Monaghan (University of Hawaiʻi at Mānoa, HIMB)

Oscar Ramfelt (University of Hawaiʻi at Mānoa, HIMB)

Clarisse E.S. Sullivan (University of Hawaiʻi at Mānoa, HIMB)

Sarah J. Tucker (University of Hawaiʻi at Mānoa, HIMB)

Contact:

Sarah J. Tucker (University of Hawaiʻi at Mānoa, HIMB)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-08-30

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Flow cytometry, 16S rRNA gene amplicons, chlorophyll a, and surface seawater measurements taken between August 2017 to June 2019 Kāneʻohe Bay, Oʻahu, Hawaiʻi

Abstract:

These data include temperature, pH, salinity, chlorophyll a concentrations, cellular abundances of Prochlorococcus, Synechococcus, photosynthetic picoeukaryotes, and heterotrophic bacteria, and 16S ribosomal RNA gene amplicon libraries from 200 surface seawater samples collected as part of the Kāneʻohe Bay Time-series (KByT). Near-monthly sampling of surface seawater was conducted between August 2017 to June 2019 at 10 sites within coastal waters of Kāneʻohe Bay, Oʻahu, Hawaiʻi and in the adjacent offshore. Instruments used were a YSI 6,600 sonde, a Turner 10AU fluorometer, an EPICS ALTRA flow cytometer, and an Illumina MiSeq v2 platform. These data characterize the partitioning of microbial communities across sharp physiochemical gradients in surface seawaters connecting nearshore and offshore waters in the tropical Pacific. This study provides evidence for the ecological differentiation of SAR11 marine bacteria across nearshore to offshore waters in the tropical Pacific and further increases our understanding of how SAR11 genetic diversity partitions into distinct ecological units. Data were collected by Sarah J. Tucker, Kelle C. Freel, Elizabeth A. Monaghan, Clarisse E. S. Sullivan, Oscar Ramfelt, Yoshimi M. Rii, and Michael S. Rappé.

Expand/Collapse All

Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-08-30	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.930084.1	2024-08-30

Description

Other Grants:
* "National Science Foundation Graduate Research Fellowship Program" (Grant ID 1842402, National Science Foundation)
* "NOAA Margaret A. Davidson Fellowship" (Grant ID NA20NOS4200123, National Oceanic and Atmospheric Administration)

Methods & Sampling

Methods and sampling are reported in Tucker et al., (2021)

Sample collection and environmental parameters

Between August 2017 and June 2019, seawater was collected from a depth of 2 m at 10 sites in and around Kāneʻohe Bay, Oʻahu, Hawaiʻi, on a near-monthly basis (20 sampling events over 23 months). At each station, seawater samples for biogeochemical analyses and nucleic acids were collected, and in situ measurements of seawater temperature, pH, and salinity were made with a YSI 6,600 sonde (YSI Incorporated, Yellow Springs, OH, USA). Approximately one L of seawater 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; Yeo et al., 2013) and stored at −80 °C until extraction.

Subsamples for chlorophyll a were collected by filtering 125 mL of seawater onto 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 in 100% acetone and subsequent measurement of fluorescence with a Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA) followed standard techniques (Welschmeyer, 1994). Seawater for cellular enumeration was preserved in two-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 (marine Synechococcus and Prochlorococcus), eukaryotic picophytoplankton, and non-cyanobacterial (presumably heterotrophic) bacteria and archaea (hereafter referred to as heterotrophic bacteria) was performed on an EPICS ALTRA flow cytometer (Beckman Coulter Inc., Brea, CA, USA), following the method of Monger and Landry (Monger & Landry, 1993).

Data Processing Description

DNA extraction and sequencing

Genomic DNA was extracted using a Qiagen Blood and Tissue Kit (Qiagen Inc., Valencia, CA, USA) with modifications (Becker, Brandon & Rappé, 2007). For each sample, 16S rRNA gene fragments were amplified by polymerase chain reaction using a dual-index sequencing strategy where barcoded universal primers 515-Y-F and 926R (Parada, Needham & Fuhrman, 2016) are complete with Illumina sequencing adapters, barcode, and index. The 25 µL reactions included 13 µL H2O, 0.5 µL each of forward and reverse primer at 0.2 µm final concentration, one µL gDNA (0.5 ng), and 10 µL 1 × 5PRIME Hot Master Mix (0.5 U Taq DNA polymerase, 45 mm KCl, 2.5 mm Mg2+, 200 μm dNTPs) (Quantabio, Beverly, MA, USA). PCR conditions included an initial denaturation at 95 °C for 2 min followed by 30 cycles of 95 °C for 45 s, 50 °C for 45 s, and 68 °C for 90 s, and a final 5 min extension at 68 °C. PCR products were inspected on a 1.5% agarose gel and quantified using the Qubit dsDNA HS Kit (Qubit 2.0, Life Technologies, Foster City, CA, USA). PCR products were normalized to 240 ng each, pooled, and purified using the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). Pooled libraries were then sequenced on an Illumina MiSeq v2 250 bp paired-end run at the Oregon State University Center for Genome Research & Biocomputing.

BCO-DMO Processing

* No data value NA set to blank
* Split latitude and longitude value into own column.

Data Files

File
930084_v1_microbial.csv (Comma Separated Values (.csv), 99.92 KB) MD5:6d3b2670bb5a9dbf8964393ae2249678 Primary data file for dataset ID 930084, version 1

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1538628

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq v2

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Flow Cytometer

Supplied Name: EPICS ALTRA flow cytometer (Beckman Coulter Inc., Brea, CA, USA

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic 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)

Turner Designs Fluorometer 10-AU

Supplied Name: Turner 10AU fluorometer (Turner Designs, Sunnyvale, CA, USA)

Supplied Description:

Instrument Type

Generic Name: Turner Designs Fluorometer 10-AU

Acronym: Turner Fluorometer 10-AU

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/

Generic 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)

YSI Sonde 6-Series

Supplied Name: YSI 6,600 sonde (YSI Incorporated, Yellow Springs, OH, USA)

Supplied Description:

Instrument Type

Generic Name: YSI Sonde 6-Series

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0737/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_ID	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.	unitless	sample
collection_date	Collection date. Format: %Y-%m-%d	unitless	date
depth	Depth of sample collection.	m	depth
env_broad_scale	Environment description, broad.	unitless	sample_descrip
env_local_scale	Environment description, local. Defined by analyses included in associated publication.	unitless	sample_descrip
env_medium	Source of sample.	unitless	sample_descrip
geo_loc_name	Geographic location of sampling.	unitless	region
latitude	Station latitude, south is negative	decimal degrees	lat
longitude	Station longitude, west is negative	decimal degrees	lon
Site_name	Site ID for collection.	unitless	site
chlorophyll_a_ug_per_L	Extracted chlorophyll a concentrations from surface seawater.	micrograms per Liter	chl_a
ph	pH of surface seawater in situ.	no unit	pH
salinity	Salinity of surface seawater in situ.	ppt	sal
Seawater_temperature	Temperature of surface seawater in situ.	degrees Celsius (°C)	temp
Prochlorococcus_cells_per_mL	Surface seawater cellular abundances of Prochlorocococcus cells counted on EPICS ALTRA flow cytometer.	cells per mL	coccus_p
Synechococcus_cells_per_mL	Surface seawater cellular abundances of Synechococcus cells counted on EPICS ALTRA flow cytometer.	cells per mL	coccus_s
Heterotrophic_bacteria_cells_per_mL	Surface seawater cellular abundances of non-cyanobacterial (presumably heterotrophic) bacteria and archaea (referred to as heterotrophic bacteria) counted on EPICS ALTRA flow cytometer.	cells per mL	cell_concentration
Eukaryotic_picophytoplankton_cells_per_mL	Surface seawater cellular abundances of photosynthetic picoeukaryotes counted on EPICS ALTRA flow cytometer.	cells per mL	pico_euks
Universal_Sample_ID	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 "KBT", the date (mm.dd.yyyy), and Station ID.	unitless	sample
SRA_accession	NCBI SRA Accession for amplicon data.	unitless	SRA_run
study	NCBI Study ID.	unitless	SRA_study
bioproject_accession	NCBI Bioproject Accession for amplicon data.	unitless	BioProject
biosample_accession	NCBI Biosample Accession.	unitless	BioSample
library_ID	Unique barcode sample identifier for amplicon sequencing.	unitless	sample
library_strategy	Sequencing library type.	unitless	seq_descrip
library_source	Source of sequencing library.	unitless	seq_descrip
library_selection	Mode of library creation.	unitless	seq_descrip
library_layout	Single or paired end sequencing reads.	unitless	seq_descrip
platform	Platform used for library creation.	unitless	instrument
instrument_model	Sequencer model.	unitless	inst_model
design_description	Description of ampicon library.	unitless	seq_descrip
filetype	File type.	unitless	datatype
filename	Forward reads file name.	unitless	file_name
filename2	Reverse reads file name.	unitless	file_name