http://lod.bco-dmo.org/id/dataset/892971
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
2023-03-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Seawater microbial communities within coral reef seawater change over six years in response to disturbance
2023-03-30
publication
2023-03-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-04-04
publication
https://doi.org/10.26008/1912/bco-dmo.892971.1
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Joel Llopiz
Woods Hole Oceanographic Institution
principalInvestigator
T. Aran Mooney
Woods Hole Oceanographic Institution
principalInvestigator
Laura Gray
Woods Hole Oceanographic Institution
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: Becker, C. C., Weber, L., Llopiz, J., Mooney, T. A., Apprill, A. (2023) Seawater microbial communities within coral reef seawater change over six years in response to disturbance. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.892971.1 [access date]
USVI Time-series Dataset Description: Methods and Sampling: <p><strong>Sampling locations and dates:</strong><br />
Reefs on the southern shore of St. John, United States Virgin Islands (USVI) were targeted for 11 opportunistic sampling events over six years from June 2016 to June 2022. The reefs included (from west to east) Dittlif, Cocoloba, Joel’s Shoal, Europa, Yawzi, Tektite, Booby Rock, and Ram Head, all of which are within the bounds of Virgin Islands National Park, except for Dittlif. The research operations were coastal, predominantly land-based, lasting 1-3 weeks, with seawater sampling and diver-based reef surveys deployed from a power boat. Reef collections included surveys for benthic composition, small volumes of seawater for inorganic and organic nutrients and microbial abundances, larger volumes for microbial biomass and chlorophyll, and CTD casts for temperature and salinity. All collections occurred during daylight hours. Dates of seawater sampling events included June 10-12, 2016, October 28-29, 2016, March 25-28, 2017, July 26-30, 2017, November 27-30, 2017 (occurred aboard R/V Walton Smith), April 11-13, 2018, November 5-9, 2018 (occurred aboard R/V Walton Smith), August 6-10, 2020, January 17-24, 2021, October 20-25, 2021, and June 24-29, 2022.</p>
<p>These sampling points surround two major stressors to St. John, USVI reefs: two category 5 hurricanes, Irma and Maria, which impacted the reefs in September, 2017, and stony coral tissue loss disease, a multi-species disease outbreak that began emerging around St. John, USVI between January-June, 2020. As of August 2020, the disease just began affecting all reefs in the study area, except Europa and Cocoloba. All reefs were impacted by the next sampling in January 2021.</p>
<p><strong>Field collections:</strong><br />
Surveys were conducted via SCUBA. Point intercept benthic reef surveys were conducted to understand the percent cover of organisms and substrates on each reef. Surveys proceeded using four to six 10-meter (m) long transects, with the underlying biological reef organisms or substrate recorded every 10 centimeters (cm). Transects were collected yearly prior to the 2017 hurricane, then were collected at each field sampling event. Following the emergence of stony coral tissue loss disease in 2020, roving diver surveys to quantify that disease were conducted in January and October 2021. Disease surveys lasted thirty minutes within a 100 m² plot and the diver counted all apparently healthy and diseased coral colonies and recorded species level, when possible. At the conclusion of the survey, the area surveyed within the plot was estimated.</p>
<p>At each reef, measurements of temperature (ºC) and salinity (psu) were conducted using a CastAway CTD (SonTek, Xylem, San Diego, CA, USA). Next, small volumes of water were collected from both surface and approximately within 1 m of reef depth (referred to as "benthic" depth) for organic nutrients, inorganic nutrients, and microbial cell abundances. Seawater for total organic carbon (TOC) and total nitrogen (TN) was collected into 40-milliliter (ml) combusted borosilicate glass vials. Seawater for inorganic nutrients (phosphate, ammonium, silicate, nitrite plus nitrate), was collected in acid-clean 30 ml HDPE bottles (Nalgene, ThermoFisher Scientific, Waltham, MA, USA). Bottles for all collections were triple-rinsed with seawater prior to collection. Following collection, organic nutrient samples were fixed with 75 microliters (μl) phosphoric acid and stored at room temperature until analysis. A 1.4 ml aliquot from the inorganic nutrient collection was placed into a cryovial for flow cytometry-based analysis for microbial cell abundances, then fixed with paraformaldehyde (1% final concentration, Electron Microscopy Sciences) in the dark for 20 minutes, then frozen in a liquid nitrogen dry shipper and stored at -80º Celsius (C) until analysis. Bottles for inorganic nutrient analysis were kept frozen at -20ºC until analysis. Inorganic and organic nutrients and microbial cell abundances were collected in biological duplicates for the June and October 2016 sampling events, but not for further events. Duplicates from those events were averaged for comparison to all other timepoints, which were sampled in singlicate.</p>
<p>Seawater for microbial biomass and chlorophyll analysis was collected from surface and benthic depths at each reef. For all benthic seawater collections prior to 2019, a groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA) was used. Beginning in August 2020, an 8L diver-operated Niskin bottle was used to enable more accurate collection of water directly over the reef habitat. Seawater (4L) for chlorophyll (benthic depth only) and for microbial biomass was collected into acid-clean or bleach-clean, then triple seawater-rinsed Platy® water tank bags (Platypus, Cascade Designs, Seattle, WA, USA) or LDPE Nalgene bottles. Samples were kept in a cooler on ice until filtration within 6 hours of collection. Seawater was filtered for both microbial biomass and chlorophyll via peristalsis using a Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA) through acid-clean or 10% bleached silicone tubing (L/S, platinum-cured, #96410-24 size, Cole-Parmer) and a 25-millimeter (mm) filter holder (Swinnex-25, Millipore Corporation) with either a 0.2-micrometer (μm) Supor filter (Pall, Port Washington, New York, USA) or GF/F filter. Seawater was filtered 2 liters at a time for technical duplicates. In some cases, the 0.2 μm filter would clog, so less than the 2 liters were filtered. In those cases, the amount filtered was recorded. Prior to November 2018, the 4L chlorophyll sample was filtered through a single GF/F filter. For consistency with other environmental variables (nutrients and microbial abundances), any technical duplicates of chlorophyll (post-2018) were averaged to yield one variable for environmental analyses. All filters were placed in cryovials and frozen in a liquid nitrogen dry shipper and stored at -80ºC upon return to the Woods Hole Oceanographic Institution until analysis.</p>
<p><strong>Laboratory processing:</strong><br />
Samples for organic nutrients were analyzed on a Shimadzu TOC-VCSH TOC analyzer (Hansell and Carlson, 2001), using a TNM-1 module to generate non-purgeable total organic carbon (TOC) and total nitrogen (TN). The inorganic nutrient samples were analyzed at Oregon State University as described previously (Becker et al., 2020), and used a Technicon AutoAnalyzer II (SEAL Analytical) and Alpkem RFA 300 Rapid Flow Analyzer to generate concentrations of ammonium, phosphate, silicate, nitrite, and nitrate plus nitrite. The microbial abundance samples were analyzed as described in Becker et al. (2020) at the University of Hawaii SOEST Flow Cytometry Facility. The facility used a Beckman-Coulter Altra flow cytometer (Beckman Coulter Life Sciences). The seawater samples were stained with Hoechst 33342 DNA stain and excited with 488 nm and UV wavelengths (Campbell and Vaulot, 1993; Monger and Landry, 1993). Signals were collected and then processed in FlowJo software (Tree Star) to generate populations and abundances (cells per milliliter) of Prochlorococcus, Synechococcus, eukaryotic phytoplankton ("picoeukaryotes"), and non-pigmented bacteria and archaea. Non-pigmented bacteria and archaea are mostly heterotrophic and referred to as "heterotrophic microbes" in this study (Monger and Landry, 1993; Marie et al., 1997).</p>
<p>Chlorophyll was extracted with 90% acetone using standard methods (JGOFS, 1996). Briefly, filters were thawed and placed individually in 5 ml of 90% acetone and capped. If the filter was dark, 10 ml of acetone was used. After a 24-hour extraction in the dark at 4°C, the tubes were vortexed and centrifuged and ~3 ml of solvent was measured on an AquaFluor fluorometer at 664 nanometer (nm) (Turner Designs handheld 800446) fitted with a red-sensitive photomultiplier. Before and after analysis, blanks including air, 90% acetone, and a black standard were run. After each measurement, samples were acidified with two drops of 10% hydrochloric acid, and re-measured to assess phaeopigment concentration. Readings volume-corrected and concentrations generated with a standard curve. Chlorophyll from June and October 2016 was assessed using high-performance liquid chromatography.</p>
<p>DNA extraction of duplicate 0.22 μm filters proceeded as described previously (Becker et al., 2020) using a method that combines physical and chemical lysis with column purification (Santoro et al., 2010). In addition to the seawater filters, DNA from 14 blank filters was extracted as a DNA extraction control. Briefly, the filters were subjected to chemical lysis with a sucrose-EDTA and 10% SDS lysis buffer and physical lysis with a 15 bead-beating step. The DNeasy Blood and Tissue Kit (Qiagen) was then used to purify the lysate. Resulting DNA was diluted 1:100 in UV-sterile PCR-grade water in preparation for PCR. Single, barcoded PCR reactions per sample were run to amplify the small subunit (SSU) ribosomal RNA (rRNA) gene of bacteria and archaea using primers 515F and 806R (Apprill et al., 2015; Parada et al., 2016). In addition to samples, genomic DNA from Microbial Mock Community B (even, low concentration), v5.1L, for 16S rRNA Gene Sequencing, HM-782D, was used as a sequencing control and PCR-grade water was used as a negative PCR control. PCR reactions (50 μl) contained the following: 2 μl DNA template, 0.5 μl of GoTaq DNA Polymerase (Promega), 1 μl each of forward and reverse primers at 10 μM, 1 μl of 10 mM deoxynucleoside triphosphate (dNTP) mix (Promega), 5 μl MgCl2, 10 μl GoTaq 5X colorless flexi buffer (Promega), and 29.5 μl nuclease-free water. Reactions proceeded with: 95°C for 2 minutes; 28 cycles of 95°C for 20 seconds, 55°C for 15 seconds, and 72°C for 5 minutes; and finally 72°C for 10 minutes before holding at 4ºC. PCR products were all purified with the QIAquick 96 PCR purification kit (Qiagen) or MinElute PCR Purification Kit (Qiagen). Concentrations of purified barcoded PCR products were measured with the Qubit 2.0 fluorometer. Each barcoded sample was diluted to 1 nanogram per microliter (ng/μl) and pooled. Samples were sequenced across four runs to maximize read output per sample on an Illumina MiSeq 2 x 250 bp sequencing at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign or the BioMicro center at Massachusetts Institute of Technology. All resulting fastq files were downloaded and used for further analysis. Fastq files were also uploaded to the NCBI sequence read archive under BioProject accession number PRJNA936592.</p>
<p><strong>Known Issues/Problems:</strong><br />
In some cases, data are missing. This is noted as either "not collected", which indicates that the sample does not exist, or "not applicable" meaning the data were not relevant to the sampling design.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536782 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536782
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA19OAR4320074
completed
Amy Apprill
Woods Hole Oceanographic Institution
508-289-2649
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4
Woods Hole
MA
02543
USA
aapprill@whoi.edu
pointOfContact
Joel Llopiz
Woods Hole Oceanographic Institution
508-289-3845
266 Woods Hole Rd. Redfield 212 (MS# 33)
Woods Hole
MA
02543
USA
jllopiz@whoi.edu
pointOfContact
T. Aran Mooney
Woods Hole Oceanographic Institution
508-289-3714
Biology Department MRF Mail Stop 50
Woods Hole
MA
02543
USA
amooney@whoi.edu
pointOfContact
Laura Gray
Woods Hole Oceanographic Institution
508-289-2981; 301-602-1540
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, Mailstop 4
Woods Hole
MA
02543
USA
laura.gray@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
BioProject_accession
BioSample_accession
collection_date
depth_m
geo_loc_name
latitude
longitude
site
depthtype
Replicate
Library
Sequences
yearmonth
prehurricane
disease
disturbance
temp_C
salinity
npoc_um
tn_um
po4_um
no2no3_um
silicate_um
no2_um
nh4_um
Chl_ug_per_l
Phaeo_ug_per_l
pro_per_ml
syn_per_ml
peuk_per_ml
hbact_per_ml
BleachCoral
CCA
CYAN
DiseasedCoral
HardCoral
Macroalgae
Other
Ramicrusta
SoftCoral
Sponge
Substrate
TurfAlgae
Alpkem RFA 300 Rapid Flow Analyzer
Illumina MiSeq
Beckman-Coulter Altra flow cytometer
AquaFluor fluorometer at 664 nm (Turner Designs handheld 800446) fitted with a red sensitive photomultiplier
Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA)
groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA)
Shimadzu TOC-VCSH total organic carbon analyzer using a TNM-1 module
CastAway CTD (SonTek, Xylem, San Diego, CA, USA)
Technicon AutoAnalyzer II (SEAL Analytical)
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
date
depth
site
latitude
longitude
sample description
replicate
count
site description
water temperature at measurement depth
salinity
total organic Carbon
Nitrogen
reactive phosphorus (PO4)
nitrate plus nitrite
Silicate, Si(OH)4, silicic acid
Nitrite
Ammonium
chlorophyll a
total phaeopigment
abundance
relative abundance
featureType
BCO-DMO Standard Parameters
Alpkem RFA300
Automated DNA Sequencer
Flow Cytometer
Fluorometer
Pump
Pump
Shimadzu TOC-V Analyzer
SonTek CastAway-CTD
Technicon AutoAnalyzer II
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.
Coral Chorus: The Role of Soundscapes in Coral Reef Larval Recruitment and Biodiversity
https://osprey.bco-dmo.org/project/659919
Coral Chorus: The Role of Soundscapes in Coral Reef Larval Recruitment and Biodiversity
<p><em>NSF Award Abstract:</em><br />
Coral reef ecosystems host some of the highest biodiversity of life per unit area on Earth and harbor about one-quarter to one-third of all marine animals. Reef-associated animals are a major source of protein for millions of people, and reefs offer shoreline protection and provide a significant source of tourism revenue, especially in developing countries. Factors that influence supply and settlement of young (larval) fish, coral, and associated animals can have large impacts on reef ecosystem and population structure, and learning more about these can help improve understanding of how to maintain the benefits provided by coral reefs. This study will lead to a detailed, mechanistic understanding of how young larvae use natural sounds to orient toward, locate, and select preferred settlement habitat. The approach will combine detailed field measurements and experiments to isolate key soundscape variables that impact coral reef larvae. </p>
<p>For marine communities, such as those on coral reefs, factors influencing larval supply and settlement can have major impacts on community structure and population replenishment. There are now some indications that sound plays an important role in attracting larvae to suitable settlement habitat. There is little understanding of what soundscape habitat information is available to larvae and how differences and variability in sound can influence settlement. This project will include comprehensive experiments, environmental measurements, and modeling with the goal of understanding the role of sound in influencing larval recruitment and local biodiversity. The investigators will measure in situ settlement of larval fish and coral in relation to different soundscapes and habitat conditions in a marine protected area using traditional larval sampling methods, moored acoustic recorders, and a suite of environmental observations. Controlled and calibrated environmental playback experiments will isolate soundscape components and determine specific and fundamental acoustic cues larvae use to orient and settle. The spatial and temporal variability of soundscape cues and components across reef habitats will be established. Finally, the project will determine the relevant ranges of sound plumes that larvae may encounter through direct measurements of the sound fields of multiple reefs.</p>
Coral Chorus
largerWorkCitation
project
eng; USA
oceans
-70.6731
-64.7048
18.297
41.5265
2016-06-10
2022-06-29
0
BCO-DMO catalogue of parameters from Seawater microbial communities within coral reef seawater change over six years in response to disturbance
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/893005.rdf
Name: sample_name
Units: unitless
Description: <p>Generic name of a sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893006.rdf
Name: BioProject_accession
Units: unitless
Description: <p>Project accession number for the NCBI Sequence Read Archive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893007.rdf
Name: BioSample_accession
Units: unitless
Description: <p>Accession number for a specific sample in the NCBI Sequence Read Archive</p>
http://lod.bco-dmo.org/id/dataset-parameter/893008.rdf
Name: collection_date
Units: unitless
Description: <p>Date of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/893009.rdf
Name: depth_m
Units: meters (m)
Description: <p>Depth of reef</p>
http://lod.bco-dmo.org/id/dataset-parameter/893010.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Broad location of the collection as Country: State</p>
http://lod.bco-dmo.org/id/dataset-parameter/893011.rdf
Name: latitude
Units: decimal degrees
Description: <p>Station latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/893012.rdf
Name: longitude
Units: decimal degrees
Description: <p>Station longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/893013.rdf
Name: site
Units: unitless
Description: <p>Name of the reef or location sampled. For laboratory controls sampled in an artificial environment, we specified either control or mock.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893014.rdf
Name: depthtype
Units: unitless
Description: <p>qualitative description of whether the water sample was collected at the surface waters or within 1 meter of the reef benthos, or benthic depth.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893015.rdf
Name: Replicate
Units: unitless
Description: <p>Replicate for technical duplicates of seawater samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/893016.rdf
Name: Library
Units: unitless
Description: <p>ID of sequencing library in which the sample was run.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893017.rdf
Name: Sequences
Units: number of reads
Description: <p>number of DNA sequences in each sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893018.rdf
Name: yearmonth
Units: unitless
Description: <p>year and month in which a sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/893019.rdf
Name: prehurricane
Units: unitless
Description: <p>yes or no referring to whether a sample was collected prior to the hurricane or not</p>
http://lod.bco-dmo.org/id/dataset-parameter/893020.rdf
Name: disease
Units: unitless
Description: <p>yes or no referring to whether there was or was not active stony coral tissue loss disease on the reef when it was sampled.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893021.rdf
Name: disturbance
Units: unitless
Description: <p>most recent major reef disturbance, either hurricane or disease. Historic refers to general collective disturbances to the reefs prior to 2017 hurricanes.</p>
http://lod.bco-dmo.org/id/dataset-parameter/893022.rdf
Name: temp_C
Units: degrees Celsius
Description: <p>Temperature of seawater taken from CastAway CTD (SonTek)</p>
http://lod.bco-dmo.org/id/dataset-parameter/893023.rdf
Name: salinity
Units: practical salinity units
Description: <p>Salinity taken from the CastAway CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/893024.rdf
Name: npoc_um
Units: micromolar (uM)
Description: <p>Non-purgeable organic carbon, referred to as total organic carbon, in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893025.rdf
Name: tn_um
Units: micromolar (uM)
Description: <p>Total nitrogen, which includes organic and inorganic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/893026.rdf
Name: po4_um
Units: micromolar (uM)
Description: <p>Phosphate in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893027.rdf
Name: no2no3_um
Units: micromolar (uM)
Description: <p>Nitrite plus nitrate concentrations in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893028.rdf
Name: silicate_um
Units: micromolar (uM)
Description: <p>Silicate concentrations in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893029.rdf
Name: no2_um
Units: micromolar (uM)
Description: <p>Nitrite concentrations in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893030.rdf
Name: nh4_um
Units: micromolar (uM)
Description: <p>Ammonium concentrations in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893031.rdf
Name: Chl_ug_per_l
Units: micrograms per liter (ug/L)
Description: <p>Amount of chlorophyll-a in the reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893032.rdf
Name: Phaeo_ug_per_l
Units: micrograms per liter (ug/L)
Description: <p>Amount of phaeophytin in the reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893033.rdf
Name: pro_per_ml
Units: cells per milliliter
Description: <p>Number of prochlorococcus cyanobacteria cells per milliliter in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893034.rdf
Name: syn_per_ml
Units: cells per milliliter
Description: <p>Number of Synechococcus cyanobacteria cells per milliliter in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893035.rdf
Name: peuk_per_ml
Units: cells per milliliter
Description: <p>Number of photosynthetic picoeukaryote cells per milliliter in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893036.rdf
Name: hbact_per_ml
Units: cells per milliliter
Description: <p>Number of unpigmented bacteria and archaea, also referred to as heterotrophic microbes, cells per milliliter in reef seawater</p>
http://lod.bco-dmo.org/id/dataset-parameter/893037.rdf
Name: BleachCoral
Units: relative abundance
Description: <p>bleached coral cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893038.rdf
Name: CCA
Units: relative abundance
Description: <p>crustose coralline algae cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893039.rdf
Name: CYAN
Units: relative abundance
Description: <p>filamentous cyanobacterial mat cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893040.rdf
Name: DiseasedCoral
Units: relative abundance
Description: <p>diseased coral cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893041.rdf
Name: HardCoral
Units: relative abundance
Description: <p>hard, or stony, coral cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893042.rdf
Name: Macroalgae
Units: relative abundance
Description: <p>macroalgal cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893043.rdf
Name: Other
Units: relative abundance
Description: <p>other cover including millepora and hydroids, zoanthids, and other invertebrates, dead coral, and eelgrass in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893044.rdf
Name: Ramicrusta
Units: relative abundance
Description: <p>Invasive Ramicrusta textilis encrusting alga cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893045.rdf
Name: SoftCoral
Units: relative abundance
Description: <p>Soft coral cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893046.rdf
Name: Sponge
Units: relative abundance
Description: <p>sponge cover in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893047.rdf
Name: Substrate
Units: relative abundance
Description: <p>Substrate includes sand, pavement, and rubble in the reef habitat</p>
http://lod.bco-dmo.org/id/dataset-parameter/893048.rdf
Name: TurfAlgae
Units: relative abundance
Description: <p>turf algal cover in the reef habitat</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
161533
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/788b8aeb-15e8-4ae6-9885-ba9bd986c954/content
download
https://doi.org/10.26008/1912/bco-dmo.892971.1
download
onLine
dataset
<p><strong>Sampling locations and dates:</strong><br />
Reefs on the southern shore of St. John, United States Virgin Islands (USVI) were targeted for 11 opportunistic sampling events over six years from June 2016 to June 2022. The reefs included (from west to east) Dittlif, Cocoloba, Joel’s Shoal, Europa, Yawzi, Tektite, Booby Rock, and Ram Head, all of which are within the bounds of Virgin Islands National Park, except for Dittlif. The research operations were coastal, predominantly land-based, lasting 1-3 weeks, with seawater sampling and diver-based reef surveys deployed from a power boat. Reef collections included surveys for benthic composition, small volumes of seawater for inorganic and organic nutrients and microbial abundances, larger volumes for microbial biomass and chlorophyll, and CTD casts for temperature and salinity. All collections occurred during daylight hours. Dates of seawater sampling events included June 10-12, 2016, October 28-29, 2016, March 25-28, 2017, July 26-30, 2017, November 27-30, 2017 (occurred aboard R/V Walton Smith), April 11-13, 2018, November 5-9, 2018 (occurred aboard R/V Walton Smith), August 6-10, 2020, January 17-24, 2021, October 20-25, 2021, and June 24-29, 2022.</p>
<p>These sampling points surround two major stressors to St. John, USVI reefs: two category 5 hurricanes, Irma and Maria, which impacted the reefs in September, 2017, and stony coral tissue loss disease, a multi-species disease outbreak that began emerging around St. John, USVI between January-June, 2020. As of August 2020, the disease just began affecting all reefs in the study area, except Europa and Cocoloba. All reefs were impacted by the next sampling in January 2021.</p>
<p><strong>Field collections:</strong><br />
Surveys were conducted via SCUBA. Point intercept benthic reef surveys were conducted to understand the percent cover of organisms and substrates on each reef. Surveys proceeded using four to six 10-meter (m) long transects, with the underlying biological reef organisms or substrate recorded every 10 centimeters (cm). Transects were collected yearly prior to the 2017 hurricane, then were collected at each field sampling event. Following the emergence of stony coral tissue loss disease in 2020, roving diver surveys to quantify that disease were conducted in January and October 2021. Disease surveys lasted thirty minutes within a 100 m² plot and the diver counted all apparently healthy and diseased coral colonies and recorded species level, when possible. At the conclusion of the survey, the area surveyed within the plot was estimated.</p>
<p>At each reef, measurements of temperature (ºC) and salinity (psu) were conducted using a CastAway CTD (SonTek, Xylem, San Diego, CA, USA). Next, small volumes of water were collected from both surface and approximately within 1 m of reef depth (referred to as "benthic" depth) for organic nutrients, inorganic nutrients, and microbial cell abundances. Seawater for total organic carbon (TOC) and total nitrogen (TN) was collected into 40-milliliter (ml) combusted borosilicate glass vials. Seawater for inorganic nutrients (phosphate, ammonium, silicate, nitrite plus nitrate), was collected in acid-clean 30 ml HDPE bottles (Nalgene, ThermoFisher Scientific, Waltham, MA, USA). Bottles for all collections were triple-rinsed with seawater prior to collection. Following collection, organic nutrient samples were fixed with 75 microliters (μl) phosphoric acid and stored at room temperature until analysis. A 1.4 ml aliquot from the inorganic nutrient collection was placed into a cryovial for flow cytometry-based analysis for microbial cell abundances, then fixed with paraformaldehyde (1% final concentration, Electron Microscopy Sciences) in the dark for 20 minutes, then frozen in a liquid nitrogen dry shipper and stored at -80º Celsius (C) until analysis. Bottles for inorganic nutrient analysis were kept frozen at -20ºC until analysis. Inorganic and organic nutrients and microbial cell abundances were collected in biological duplicates for the June and October 2016 sampling events, but not for further events. Duplicates from those events were averaged for comparison to all other timepoints, which were sampled in singlicate.</p>
<p>Seawater for microbial biomass and chlorophyll analysis was collected from surface and benthic depths at each reef. For all benthic seawater collections prior to 2019, a groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA) was used. Beginning in August 2020, an 8L diver-operated Niskin bottle was used to enable more accurate collection of water directly over the reef habitat. Seawater (4L) for chlorophyll (benthic depth only) and for microbial biomass was collected into acid-clean or bleach-clean, then triple seawater-rinsed Platy® water tank bags (Platypus, Cascade Designs, Seattle, WA, USA) or LDPE Nalgene bottles. Samples were kept in a cooler on ice until filtration within 6 hours of collection. Seawater was filtered for both microbial biomass and chlorophyll via peristalsis using a Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA) through acid-clean or 10% bleached silicone tubing (L/S, platinum-cured, #96410-24 size, Cole-Parmer) and a 25-millimeter (mm) filter holder (Swinnex-25, Millipore Corporation) with either a 0.2-micrometer (μm) Supor filter (Pall, Port Washington, New York, USA) or GF/F filter. Seawater was filtered 2 liters at a time for technical duplicates. In some cases, the 0.2 μm filter would clog, so less than the 2 liters were filtered. In those cases, the amount filtered was recorded. Prior to November 2018, the 4L chlorophyll sample was filtered through a single GF/F filter. For consistency with other environmental variables (nutrients and microbial abundances), any technical duplicates of chlorophyll (post-2018) were averaged to yield one variable for environmental analyses. All filters were placed in cryovials and frozen in a liquid nitrogen dry shipper and stored at -80ºC upon return to the Woods Hole Oceanographic Institution until analysis.</p>
<p><strong>Laboratory processing:</strong><br />
Samples for organic nutrients were analyzed on a Shimadzu TOC-VCSH TOC analyzer (Hansell and Carlson, 2001), using a TNM-1 module to generate non-purgeable total organic carbon (TOC) and total nitrogen (TN). The inorganic nutrient samples were analyzed at Oregon State University as described previously (Becker et al., 2020), and used a Technicon AutoAnalyzer II (SEAL Analytical) and Alpkem RFA 300 Rapid Flow Analyzer to generate concentrations of ammonium, phosphate, silicate, nitrite, and nitrate plus nitrite. The microbial abundance samples were analyzed as described in Becker et al. (2020) at the University of Hawaii SOEST Flow Cytometry Facility. The facility used a Beckman-Coulter Altra flow cytometer (Beckman Coulter Life Sciences). The seawater samples were stained with Hoechst 33342 DNA stain and excited with 488 nm and UV wavelengths (Campbell and Vaulot, 1993; Monger and Landry, 1993). Signals were collected and then processed in FlowJo software (Tree Star) to generate populations and abundances (cells per milliliter) of Prochlorococcus, Synechococcus, eukaryotic phytoplankton ("picoeukaryotes"), and non-pigmented bacteria and archaea. Non-pigmented bacteria and archaea are mostly heterotrophic and referred to as "heterotrophic microbes" in this study (Monger and Landry, 1993; Marie et al., 1997).</p>
<p>Chlorophyll was extracted with 90% acetone using standard methods (JGOFS, 1996). Briefly, filters were thawed and placed individually in 5 ml of 90% acetone and capped. If the filter was dark, 10 ml of acetone was used. After a 24-hour extraction in the dark at 4°C, the tubes were vortexed and centrifuged and ~3 ml of solvent was measured on an AquaFluor fluorometer at 664 nanometer (nm) (Turner Designs handheld 800446) fitted with a red-sensitive photomultiplier. Before and after analysis, blanks including air, 90% acetone, and a black standard were run. After each measurement, samples were acidified with two drops of 10% hydrochloric acid, and re-measured to assess phaeopigment concentration. Readings volume-corrected and concentrations generated with a standard curve. Chlorophyll from June and October 2016 was assessed using high-performance liquid chromatography.</p>
<p>DNA extraction of duplicate 0.22 μm filters proceeded as described previously (Becker et al., 2020) using a method that combines physical and chemical lysis with column purification (Santoro et al., 2010). In addition to the seawater filters, DNA from 14 blank filters was extracted as a DNA extraction control. Briefly, the filters were subjected to chemical lysis with a sucrose-EDTA and 10% SDS lysis buffer and physical lysis with a 15 bead-beating step. The DNeasy Blood and Tissue Kit (Qiagen) was then used to purify the lysate. Resulting DNA was diluted 1:100 in UV-sterile PCR-grade water in preparation for PCR. Single, barcoded PCR reactions per sample were run to amplify the small subunit (SSU) ribosomal RNA (rRNA) gene of bacteria and archaea using primers 515F and 806R (Apprill et al., 2015; Parada et al., 2016). In addition to samples, genomic DNA from Microbial Mock Community B (even, low concentration), v5.1L, for 16S rRNA Gene Sequencing, HM-782D, was used as a sequencing control and PCR-grade water was used as a negative PCR control. PCR reactions (50 μl) contained the following: 2 μl DNA template, 0.5 μl of GoTaq DNA Polymerase (Promega), 1 μl each of forward and reverse primers at 10 μM, 1 μl of 10 mM deoxynucleoside triphosphate (dNTP) mix (Promega), 5 μl MgCl2, 10 μl GoTaq 5X colorless flexi buffer (Promega), and 29.5 μl nuclease-free water. Reactions proceeded with: 95°C for 2 minutes; 28 cycles of 95°C for 20 seconds, 55°C for 15 seconds, and 72°C for 5 minutes; and finally 72°C for 10 minutes before holding at 4ºC. PCR products were all purified with the QIAquick 96 PCR purification kit (Qiagen) or MinElute PCR Purification Kit (Qiagen). Concentrations of purified barcoded PCR products were measured with the Qubit 2.0 fluorometer. Each barcoded sample was diluted to 1 nanogram per microliter (ng/μl) and pooled. Samples were sequenced across four runs to maximize read output per sample on an Illumina MiSeq 2 x 250 bp sequencing at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign or the BioMicro center at Massachusetts Institute of Technology. All resulting fastq files were downloaded and used for further analysis. Fastq files were also uploaded to the NCBI sequence read archive under BioProject accession number PRJNA936592.</p>
<p><strong>Known Issues/Problems:</strong><br />
In some cases, data are missing. This is noted as either "not collected", which indicates that the sample does not exist, or "not applicable" meaning the data were not relevant to the sampling design.</p>
Specified by the Principal Investigator(s)
<p><strong>Environmental data processing:</strong><br />
Data from point-intercept benthic survey transects were grouped into different benthic categories, including bleached coral, crustose coralline algae (CCA), cyanobacterial mats (CYAN), diseased coral, hard coral, macroalgae, ramicrusta, soft coral, sponge, substrate (a combination of rubble, pavement, sand, and rock), turf algae, and other (a combination of millepora and hydroids, zoanthids, and other invertebrates, dead coral, and eelgrass). Counts of each category were transformed to a percent and averaged over the 4-6 transects per reef at each timepoint. Those values were used for data analyses. Data from the disease surveys were used to generate disease prevalence on reefs in January 2021 and October 2021 by dividing the number of coral colonies afflicted by stony coral tissue loss disease by the total number of colonies identified.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- converted data from Excel format to csv.</p>
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
Alpkem RFA 300 Rapid Flow Analyzer
Alpkem RFA 300 Rapid Flow Analyzer
PI Supplied Instrument Name: Alpkem RFA 300 Rapid Flow Analyzer Instrument Name: Alpkem RFA300 Instrument Short Name:Alpkem RFA300 Instrument Description: A rapid flow analyser (RFA) that may be used to measure nutrient concentrations in seawater. It is an air-segmented, continuous flow instrument comprising a sampler, a peristaltic pump which simultaneously pumps samples, reagents and air bubbles through the system, analytical cartridge, heating bath, colorimeter, data station, and printer. The RFA-300 was a precursor to the smaller Alpkem RFA/2 (also RFA II or RFA-2). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0414/
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq 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 Altra flow cytometer
Beckman-Coulter Altra flow cytometer
PI Supplied Instrument Name: Beckman-Coulter Altra flow cytometer 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/
AquaFluor fluorometer at 664 nm (Turner Designs handheld 800446) fitted with a red sensitive photomultiplier
AquaFluor fluorometer at 664 nm (Turner Designs handheld 800446) fitted with a red sensitive photomultiplier
PI Supplied Instrument Name: AquaFluor fluorometer at 664 nm (Turner Designs handheld 800446) fitted with a red sensitive photomultiplier 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/
Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA)
Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA)
PI Supplied Instrument Name: Masterflex L/S peristaltic pump (Cole-Parmer, Vernon Hills, IL, USA) Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA)
groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA)
PI Supplied Instrument Name: groundwater pump (Mini-Monsoon 12V, Proactive Environmental Products, Bradenton, Florida, USA) Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
Shimadzu TOC-VCSH total organic carbon analyzer using a TNM-1 module
Shimadzu TOC-VCSH total organic carbon analyzer using a TNM-1 module
PI Supplied Instrument Name: Shimadzu TOC-VCSH total organic carbon analyzer using a TNM-1 module Instrument Name: Shimadzu TOC-V Analyzer Instrument Short Name:Shimadzu TOC-V Instrument Description: A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method. Community Standard Description: http://onto.nerc.ac.uk/CAST/124
CastAway CTD (SonTek, Xylem, San Diego, CA, USA)
CastAway CTD (SonTek, Xylem, San Diego, CA, USA)
PI Supplied Instrument Name: CastAway CTD (SonTek, Xylem, San Diego, CA, USA) Instrument Name: SonTek CastAway-CTD Instrument Short Name:CastAway-CTD Instrument Description: The Sontek CastAway-CTD (manufactured by Xylem) is a handheld castable instrument that provides instantaneous profiles of temperature, salinity, and sound speed. Each cast is referenced with both time and location using its built-in GPS receiver. The CastAway software displays profiles of the casts in addition to mapping the locations of the data collection points. The CastAway-CTD has a 5 Hz response and sampling rate, accurate to 0.1 (PSS-78), 0.05° Celsius.
Conductivity range is 0 to 100,000 µS/cm.
Temperature range is -5° to 45° Celsius.
Pressure range is 0 to 100 decibars.
Further specs and information can be found on the manufacturer's website: https://www.xylem.com/en-us/brands/wtw/wtw-products/castaway-ctd/
Technicon AutoAnalyzer II (SEAL Analytical)
Technicon AutoAnalyzer II (SEAL Analytical)
PI Supplied Instrument Name: Technicon AutoAnalyzer II (SEAL Analytical) Instrument Name: Technicon AutoAnalyzer II Instrument Short Name: Instrument Description: A rapid flow analyzer that may be used to measure nutrient concentrations in seawater. It is a continuous segmented flow instrument consisting of a sampler, peristaltic pump, analytical cartridge, heating bath, and colorimeter. See more information about this instrument from the manufacturer. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0291/