http://lod.bco-dmo.org/id/dataset/907866
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
2023-09-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Seawater nutrient/metabolite and flow cytometry metadata - Picoplankton incubation experiment 2020
2023-09-07
publication
2023-09-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-10-04
publication
https://doi.org/10.26008/1912/bco-dmo.907866.1
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Cole G. Easson
Middle Tennessee State University
principalInvestigator
Cara L. Fiore
Appalachian State University
principalInvestigator
Alicia M. Reigel
Appalachian State University
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: Reigel, A. M., Apprill, A., Fiore, C. L., Easson, C. G. (2023) Seawater nutrient/metabolite and flow cytometry metadata - Picoplankton incubation experiment 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-09-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.907866.1 [access date]
Methods and Sampling: <p><strong>Collection Media and inoculum:</strong></p>
<p>Sponge exhalent water and reef sea water, for use as media in the incubation experiment, were collected on 9-December-2020 from Looe Key Reef Sanctuary Preservation Area (24.54605, -81.40610) in the Florida Keys National Marine Sanctuary (FKNMS). Sponge exhalent water was collected from each of 4 individuals of two sponge species,&nbsp;<em>Niphates digitatalis</em>&nbsp;and&nbsp;<em>Xestospongia muta</em>. Exhalent water collection was completed by scuba divers using a three-way valve with one valve attached to a ~8cm piece of PharMed L/S 25 tubing (Masterflex® L/S® Precision Pump Tubing, Radnor, PA, USA) that was placed into the excurrent osculum of the sponge to collect exhalent water, a second valve attached to a syringe to create suction and pull in exhalent water, and the final valve attached to ~8cm piece of Teflon tubing that further attaches to the stainless-steel fitting on a 1 L FlexFoil PLUS bag (SKC, Eighty Four, PA, USA) for final exhalent water storage. Exhalent water was pulled into the syringe at a rate of ~2ml min<sup>-1</sup>, below the estimated pumping rate of both sponge species. Two bags (~1L) were filled per sponge and all sponges were located within 4 meters of one another at ~8m depth. Upon return to the boat all bags were sealed and placed in an ice-filled cooler until further processing in the lab (~2 hrs).&nbsp;</p>
<p>Reef surface water, for use as both reef metabolome media and picoplankton inoculum during the incubation experiment, was collected in 6 acid-washed 2 L Nalgene© HDPE bottles (Thermo Fisher Scientific, Waltham, MA, USA) from ~1 m below the surface just above the reef at Looe Key. Metabolome bottles were immediately placed in a cooler filled with ice until return to the lab (~1 hr). The reef picoplankton inoculum was kept in the dark at ambient seawater temperature.</p>
<p><strong>Picoplankton incubation experimental setup: </strong></p>
<p>The 48-hour experiment included two treatments, reef (i.e., control) and sponge metabolome, that were sampled at 0 hours, 24 hours, and 48 hours (T<sub>0</sub>, T<sub>24</sub>, T<sub>48</sub>, respectively). Surface seawater (6 L) for picoplankton inoculum was filtered through three 1.6 µm, 47 mm pre-combusted GF/A filter to remove larger eukaryotic plankton and particular matter. Filters were housed in a 47 mm acid-washed in-line PFA filter holder (Advantec, Cole-Parmer, Vernon Hills, IL, USA). Filtering was completed via peristalsis (MasterFlex L/S pump and pump heads, Cole-Parmer, Vernon Hills, IL, USA). Samples were filtered slowly (50 ml min<sup>-1</sup>) to avoid bursting of microbial cells on the filter membrane and filters were changed every 2 L. PharMed L/S 25 (Masterflex® L/S® Precision Pump Tubing, Radnor, PA, USA) acid-washed tubing was used for all filtration. The sponge and reef metabolome media (6 L each) were both passed through 0.22 µm, 47 mm polytetrafluoroethylene (PTFE) filters (Omnipore, EMD Millipore Corporation, Billerica, MA, USA) using the same process detailed above. Sponge metabolome media consisted of a 3:1 ratio of filtered sponge exhalent water (1:1 exhalent water from&nbsp;<em>X. muta</em>&nbsp;and&nbsp;<em>N. digitalis</em>) to 0.22 µm filtered sea water.</p>
<p>Following filtering, two 20 L food grade containers were used, one per treatment, to pool the filtered inoculum with the filtered media. Pooling was done to ensure consistent starting mixtures for each incubation bottle. Following initial (T<sub>0</sub>) sampling as detailed below, pooled treatments were evenly distributed into four 2 L Nalgene© bottles per treatment for an approximate ratio of 1:2 filtered picoplankton inoculum to filtered media. All incubation bottles were kept in a dark incubator at 26ºC for the duration of the 48-hr experiment and only removed for picoplankton community sampling at T<sub>24</sub>. Water chemistry and cell abundance was assessed for both the sponge and reef metabolome treatments at the start (T<sub>0</sub>) and end (T<sub>48</sub>) of the incubation experiment. Samples were also taken at T<sub>24</sub>, but they were only used to obtain cell abundance.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924540 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924540
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1923962 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1923962
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
Cole G. Easson
Middle Tennessee State University
615-898-5822
1672 Greenland Drive SCI 2044
Murfreesboro
TN
37132
USA
Cole.Easson@mtsu.edu
pointOfContact
Cara L. Fiore
Appalachian State University
828-262-7548
572 Rivers St
Boone
NC
28607
USA
fiorec@appstate.edu
pointOfContact
Alicia M. Reigel
Appalachian State University
Lexington
VA
USA
areigel@wlu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
Sampling_Date
Experimental_Sampling_Time
Incubation_Treatment
Ultra_Violet_Humic_like
Marine_Humic_like
Visible_Humic_like
Tryptophan_like
Tyrosine_like
Phenylalanine_like
Fulvic_Acid_like
Phosphate
Total_Inorganic_Nitrogen
Silicate
Nitrite
Nitrate
Ammonium
Picoplankton_Cell_Concentration
NPOC
TN
Fucose
Rhamnose
Arabinose
Galactose
Glucose
Xylose_Mannose
Fructose
anthranilate
phenylalanine
inosine
adenosine
4_methyl_2_oxopentanoic_acid
4_aminobenzoic_acid
tyrosine
S_5_adenosyl_L_homocysteine
desthiobiotin
pantothenic_acid
glutathione_oxidized
tryptophan
n_acetyl_muramic_acid
4_hydroxybenzoic_acid
riboflavin
chorismate
3_3_dimethyl_2oxobutanoic_acid
5_hydroxy_L_tryptophan
Alpkem RFA 300 colorimetric autoanalyzer, Alpkem, Kranj, Slovenia
Bio-Rad ZE5, Hercules, California, USA
Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp
DIONEX ICS3000 system, Thermo Fisher Scientific
Shimadzu TOC-L analyzer
Absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA
Technicon Auto Analyzer II, SEAL Analytical Inc., Mequon, Wisconsin, USA
theme
None, User defined
sample identification
date
incubation time or duration
treatment
wave statistics
reactive phosphorus (PO4)
nitrate plus nitrite
Silicate, Si(OH)4, silicic acid
Nitrite
Nitrate
Ammonium
cell_concentration
dissolved organic Carbon
Nitrogen
monosaccharide
metabolite
featureType
BCO-DMO Standard Parameters
Alpkem RFA300
Flow Cytometer
Fluorometer
Ion Chromatograph
Shimadzu TOC-L Analyzer
Spectrophotometer
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.
Collaborative Research: The Influence of Sponge Holobiont Metabolism on Coral Reef Dissolved Organic Matter and Reef Microorganisms
https://osprey.bco-dmo.org/project/822468
Collaborative Research: The Influence of Sponge Holobiont Metabolism on Coral Reef Dissolved Organic Matter and Reef Microorganisms
<p><em>NSF Award Abstract:</em><br />
The seawater around coral reefs is typically low in nutrients, yet coral reefs are teeming with life and are often compared to oases in a desert. Life exists in these 'marine deserts' in large part, due to symbiotic associations between single-celled microbes and invertebrates such as corals and sponges. The concentration and type of dissolved organic matter (DOM), a complex pool of organic nutrients such as amino acids, vitamins, and other diverse compounds, also affects the health of coral reefs. The composition of DOM on coral reefs is linked to both the composition of free-living microbes in the seawater and to the nutrition of filter-feeding organisms, such as corals and sponges. However, the factors that influence the composition of DOM on coral reefs and the consequences of how it changes are not well understood. Recent work suggests that sponges could have a significant impact on the composition of reef dissolved organic nutrients, depending on sponge species due to differences in filtration capacity and in their symbiotic microbial communities. This project characterizes how diverse sponge species process DOM on coral reefs and determines the impacts of this processing on the free-living microbial community. Seawater is collected from sponges (pre- and post- sponge filtration) on coral reefs in the relatively pristine region of Curacao, and incubation experiments measure the impact of sponge filtration on the growth of the free-living microbial community. The organic nutrients of seawater samples are analyzed using cutting-edge techniques to distinguish the types of nutrients that are processed by sponges. The incubation experiments, using free-living microbes collected from the coral reef, quantify the impact of sponge filtration on the growth and composition of this community. This project provides fundamental understanding of how sponges contribute to the base of the coral reef food web. As the human-driven impacts continue to alter the composition of organisms on reefs, this understanding is necessary to predict changes to reef microbial food webs and is thus essential for scientists, reef managers, and policy decision makers. This project trains undergraduate students and a postdoctoral scholar and contributes to undergraduate and K-12 education through development of sponge-centric lessons that focus on local U.S. east coast aquatic environments as well as coral reef ecosystems.</p>
<p>Sponges vary in their capacity to filter seawater and in their associated microbial communities, leading to diverse metabolic strategies that often coexist in one habitat. While it is well-established that sponges are important in processing dissolved organic matter (DOM), an important reservoir of reduced carbon compounds, and transferring this energy to benthic food webs, there has been limited work to understand the consequences of sponge processing on the composition of coral reef DOM and on pelagic food webs. Specifically, while studies have shown that exudates of corals and algae select for specific groups of picoplankton (autotrophic and heterotrophic, respectively), similar data for sponges are required to understand the multiple factors that shape the composition of DOM and of the picoplankton community on coral reefs. Thus, this project is aimed at addressing a major knowledge gap of the role of sponge-derived DOM (sponge exometabolome) in coral reef biogeochemistry. An in situ sampling design targeting prominent Caribbean sponges and picoplankton incubation experiments is coupled to address both the composition of sponge exometabolomes and delineate shifts in the picoplankton community derived from sponge exometabolomes. Molecular-level changes to seawater DOM by sponge processing and the impact of these changes on the overall coral reef DOM profile is assessed with two DOM analysis techniques: a commonly used fluorometry technique (fDOM analysis) and with high-resolution mass spectrometry (LC-MS/MS). Additionally, microbiome and functional gene profiling, growth metrics, and nutrient analyses are employed to assess changes in the picoplankton community in response to sponge exometabolomes. Advanced data analysis techniques then synthesize data generated by each approach to provide novel insight on a poorly uncharacterized biogeochemical pathway on coral reefs. The work outlined here represents entirely novel information on the impact of sponge metabolism on the composition of DOM, sheds light on biologically important molecules involved in benthic-pelagic coupling, and importantly, generates data using standardized methods, thus facilitating comparison to previous and future DOM datasets.</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>
Sponge Holobiont DOM
largerWorkCitation
project
eng; USA
oceans
-81.4061
-81.4061
24.54605
24.54605
2020-12-13
2020-12-15
Caribbean Sea
0
BCO-DMO catalogue of parameters from Seawater nutrient/metabolite and flow cytometry metadata - Picoplankton incubation experiment 2020
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/910596.rdf
Name: SampleID
Units: unitless
Description: <p>Unique sample indentity</p>
http://lod.bco-dmo.org/id/dataset-parameter/910597.rdf
Name: Sampling_Date
Units: unitless
Description: <p>Date that sample was collected. Format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/910598.rdf
Name: Experimental_Sampling_Time
Units: hours
Description: <p>Number of hours since experiment start time</p>
http://lod.bco-dmo.org/id/dataset-parameter/910599.rdf
Name: Incubation_Treatment
Units: unitless
Description: <p>Two experimental treatments (Sponge Metabolome = Samples incubated in sponge exhalent water, Reef Metabolome = Samples incubated in ambient reef water)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910600.rdf
Name: Ultra_Violet_Humic_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak A - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910601.rdf
Name: Marine_Humic_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak M - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910602.rdf
Name: Visible_Humic_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak C - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910603.rdf
Name: Tryptophan_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak T - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910604.rdf
Name: Tyrosine_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak B - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910605.rdf
Name: Phenylalanine_like
Units: Ramen Units (R.U.)
Description: <p>Coble Peak F - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910606.rdf
Name: Fulvic_Acid_like
Units: Ramen Units (R.U.)
Description: <p>Peak D (Stedmon, 2003) - Flourescent Dissolved Organic Matter (fDOM)</p>
http://lod.bco-dmo.org/id/dataset-parameter/910607.rdf
Name: Phosphate
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved phosphate in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910608.rdf
Name: Total_Inorganic_Nitrogen
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved inorganic nitrogen (nitrate+nitrite) in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910609.rdf
Name: Silicate
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved silicate in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910610.rdf
Name: Nitrite
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved nitrite in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910611.rdf
Name: Nitrate
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved nitrate in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910612.rdf
Name: Ammonium
Units: micromoles per liter (umol/l)
Description: <p>Concentration of dissolved ammonium in micromoles per liter of sample water</p>
http://lod.bco-dmo.org/id/dataset-parameter/910613.rdf
Name: Picoplankton_Cell_Concentration
Units: cells per mL (cells/ml)
Description: <p>Abundance of all particles (bacteria including Synechococcus and Prochlorococcus) stained with SYBRGreen in number of cells mL-1, corrected for preservative, sample dilution, and stain volume; subgated in FSC-405 vs. 525-488 to minimize noise; Data results from flow cytometry analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/910614.rdf
Name: NPOC
Units: Micromolar (uM)
Description: <p>Micromolar concentration of non-purgeable dissolved organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/910615.rdf
Name: TN
Units: Micromolar (uM)
Description: <p>Micromolar concentration of total nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/910616.rdf
Name: Fucose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910617.rdf
Name: Rhamnose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910618.rdf
Name: Arabinose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910619.rdf
Name: Galactose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910620.rdf
Name: Glucose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910621.rdf
Name: Xylose_Mannose
Units: nanogram per millliter of sample (ng/ml)
Description: <p>Monosaccharides that cannot be distinguished from one another; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910622.rdf
Name: Fructose
Units: nanograms per liter (ng/l)
Description: <p>Monosaccharide; Concentration in nanogram per millliter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910623.rdf
Name: anthranilate
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910624.rdf
Name: phenylalanine
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910625.rdf
Name: inosine
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910626.rdf
Name: adenosine
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910627.rdf
Name: 4_methyl_2_oxopentanoic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910628.rdf
Name: 4_aminobenzoic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910629.rdf
Name: tyrosine
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910630.rdf
Name: S_5_adenosyl_L_homocysteine
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910631.rdf
Name: desthiobiotin
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910632.rdf
Name: pantothenic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910633.rdf
Name: glutathione_oxidized
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910634.rdf
Name: tryptophan
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910635.rdf
Name: n_acetyl_muramic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910636.rdf
Name: 4_hydroxybenzoic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910637.rdf
Name: riboflavin
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910638.rdf
Name: chorismate
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910639.rdf
Name: 3_3_dimethyl_2oxobutanoic_acid
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/910640.rdf
Name: 5_hydroxy_L_tryptophan
Units: nanograms per liter (ng/l)
Description: <p>Dissolved organic metabolite; Concentration in nanograms per liter of sample</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
5309
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/1907fca9-0507-4cd5-ae31-56dd519c0ca1/content
download
https://doi.org/10.26008/1912/bco-dmo.907866.1
download
onLine
dataset
<p><strong>Collection Media and inoculum:</strong></p>
<p>Sponge exhalent water and reef sea water, for use as media in the incubation experiment, were collected on 9-December-2020 from Looe Key Reef Sanctuary Preservation Area (24.54605, -81.40610) in the Florida Keys National Marine Sanctuary (FKNMS). Sponge exhalent water was collected from each of 4 individuals of two sponge species,&nbsp;<em>Niphates digitatalis</em>&nbsp;and&nbsp;<em>Xestospongia muta</em>. Exhalent water collection was completed by scuba divers using a three-way valve with one valve attached to a ~8cm piece of PharMed L/S 25 tubing (Masterflex® L/S® Precision Pump Tubing, Radnor, PA, USA) that was placed into the excurrent osculum of the sponge to collect exhalent water, a second valve attached to a syringe to create suction and pull in exhalent water, and the final valve attached to ~8cm piece of Teflon tubing that further attaches to the stainless-steel fitting on a 1 L FlexFoil PLUS bag (SKC, Eighty Four, PA, USA) for final exhalent water storage. Exhalent water was pulled into the syringe at a rate of ~2ml min<sup>-1</sup>, below the estimated pumping rate of both sponge species. Two bags (~1L) were filled per sponge and all sponges were located within 4 meters of one another at ~8m depth. Upon return to the boat all bags were sealed and placed in an ice-filled cooler until further processing in the lab (~2 hrs).&nbsp;</p>
<p>Reef surface water, for use as both reef metabolome media and picoplankton inoculum during the incubation experiment, was collected in 6 acid-washed 2 L Nalgene© HDPE bottles (Thermo Fisher Scientific, Waltham, MA, USA) from ~1 m below the surface just above the reef at Looe Key. Metabolome bottles were immediately placed in a cooler filled with ice until return to the lab (~1 hr). The reef picoplankton inoculum was kept in the dark at ambient seawater temperature.</p>
<p><strong>Picoplankton incubation experimental setup: </strong></p>
<p>The 48-hour experiment included two treatments, reef (i.e., control) and sponge metabolome, that were sampled at 0 hours, 24 hours, and 48 hours (T<sub>0</sub>, T<sub>24</sub>, T<sub>48</sub>, respectively). Surface seawater (6 L) for picoplankton inoculum was filtered through three 1.6 µm, 47 mm pre-combusted GF/A filter to remove larger eukaryotic plankton and particular matter. Filters were housed in a 47 mm acid-washed in-line PFA filter holder (Advantec, Cole-Parmer, Vernon Hills, IL, USA). Filtering was completed via peristalsis (MasterFlex L/S pump and pump heads, Cole-Parmer, Vernon Hills, IL, USA). Samples were filtered slowly (50 ml min<sup>-1</sup>) to avoid bursting of microbial cells on the filter membrane and filters were changed every 2 L. PharMed L/S 25 (Masterflex® L/S® Precision Pump Tubing, Radnor, PA, USA) acid-washed tubing was used for all filtration. The sponge and reef metabolome media (6 L each) were both passed through 0.22 µm, 47 mm polytetrafluoroethylene (PTFE) filters (Omnipore, EMD Millipore Corporation, Billerica, MA, USA) using the same process detailed above. Sponge metabolome media consisted of a 3:1 ratio of filtered sponge exhalent water (1:1 exhalent water from&nbsp;<em>X. muta</em>&nbsp;and&nbsp;<em>N. digitalis</em>) to 0.22 µm filtered sea water.</p>
<p>Following filtering, two 20 L food grade containers were used, one per treatment, to pool the filtered inoculum with the filtered media. Pooling was done to ensure consistent starting mixtures for each incubation bottle. Following initial (T<sub>0</sub>) sampling as detailed below, pooled treatments were evenly distributed into four 2 L Nalgene© bottles per treatment for an approximate ratio of 1:2 filtered picoplankton inoculum to filtered media. All incubation bottles were kept in a dark incubator at 26ºC for the duration of the 48-hr experiment and only removed for picoplankton community sampling at T<sub>24</sub>. Water chemistry and cell abundance was assessed for both the sponge and reef metabolome treatments at the start (T<sub>0</sub>) and end (T<sub>48</sub>) of the incubation experiment. Samples were also taken at T<sub>24</sub>, but they were only used to obtain cell abundance.</p>
Specified by the Principal Investigator(s)
<p><strong>Flow cytometry</strong></p>
<p>To quantify picoplankton abundances, 1 ml samples of water from each pooled treatment (T<sub>0</sub>; n=3 per treatment) and from each incubation bottle (n=4 per treatment) at both T<sub>24</sub>&nbsp;and T<sub>48</sub>&nbsp;was collected in a sterile cryovial and fixed with paraformaldehyde (1% final volume), incubated in the dark at 4ºC for 1-hr, and then frozen at -80ºC. The fixed samples were used for enumeration of total bacterial cells (<em>Prochlorococcus</em>,&nbsp;<em>Synechococcus</em>, picoeukaryotic cells, and unpigmented cells (heterotrophic bacteria and archaea)) via flow cytometry at Bigelow Laboratory for Ocean Sciences. Flow cytometry analysis was completed using a Bio-Rad ZE5 (Hercules, California, USA) with a 488 nm laser activated. Samples were thawed and pre-screened through 70 µm mesh and diluted 1:10 with Tris EDTA (TE) Buffer pH 8.0. Cells were then stained using 10x working stock DNA stain SYBRGreen I (Thermo Fisher Scientific, Waltham, MA, USA) following the protocol of Marie et al. (2005). A total of 180 µl of diluted sample was run at a flow rate of 0.5 µl sec -1. Particles were excited with the 488 nm blue later and data acquisition was triggered by green fluorescence. Data signals were recorded by detectors with three bandpass filters including forward scatter (FSC), right angle light scatter (SSC), and fluorescence emission in green (525/35nm). To minimize noise, samples were subgated in FSC-405. Data files logarithmic scatter plots of fluorescent and light scattering properties were analyzed and total bacterial counts were identified based on size and presence of the green fluorescence. All counts were converted to cell abundance based on sample volume (including adjustments for preservation, dilution, and staining).</p>
<p><strong>Biochemical Analyses</strong></p>
<p><em>Total Organic Carbon (TOC) and Total Nitrogen (TN)</em></p>
<p>For TOC and TN analyses, 20 ml of water was collected from the pooled treatments prior to their distribution into individual incubation bottles (T<sub>0</sub>: reef metabolome, n=3; sponge metabolome, n=3) and for each bottle at the end of the experiment (T<sub>48</sub>: n=4 per treatment) in acid-washed, combusted 40-ml amber EPA vials. Samples were immediately acidified to pH 3 using 12M trace-metal grade hydrochloroic acid (HCL, OptimaTM, Fisher Chemical, Fisher Scientific, Hampton, NH, USA) and stored in the dark at 4ºC. The acidified samples were processed at Woods Hole Oceanographic Institute using a Shimadzu TOC-L analyzer (Longnecker et al. 2015). Additionally,</p>
<p><em>Filtering for Biochemical Analyses</em></p>
<p>All other biochemical analyses were completed only on filtered water samples from the pooled treatments at T<sub>0</sub>&nbsp;(reef metabolome, n=1 and sponge metabolome, n=2) and T<sub>48</sub>&nbsp;incubation bottles (n=4 per treatment). Approximately 680 ml of water from each incubation bottle was individually passed through a 0.22 µm, 47 mm PTFE filter using peristalsis as previous detailed except for a slightly slower filtering rate (30 ml/min) to avoid bursting the microbial cells. Following filtration, the PTFE filters were placed in individual sterile cryovials and stored at -80ºC.&nbsp;</p>
<p><em>Inorganic macronutrients</em></p>
<p>For inorganic macronutrient analyses (PO<sub>4</sub><sup>3-</sup>, NO<sub>3</sub><sup>-</sup>, Silicate, NO<sub>2</sub>, NH<sub>4</sub><sup>+</sup>), ~25 ml of the 0.22 µm filtrate from each sample was collected in an acid-washed 30 ml break-proof Nalgene© HDPE bottle (Thermo Fisher Scientific, Waltham, MA, USA), frozen and stored at -20ºC before being shipped to College of Earth, Ocean, and Atmospheric Sciences at Oregon State University for inorganic macronutrient analyses. Phosphate (PO<sub>4</sub><sup>3-</sup>) and ammonium (NH<sub>4</sub><sup>+</sup>) were measured using a Technicon Auto Analyzer II (SEAL Analytical Inc., Mequon, Wisconsin, USA) and silicic acid (i.e., silicate), nitrate (NO<sub>3</sub><sup>-</sup>) and nitrate+nitrite (NO<sub>3</sub><sup>-</sup>&nbsp;+ NO<sub>2</sub><sup>-</sup>) were measured using an Alpkem RFA 300 colorimetric autoanalyzer (Alpkem, Kranj, Slovenia). Analytical methods and data processing were completed as described in Gordon et al. (1994), but a brief summary of each analysis is provided. The PO<sub>4</sub><sup>3-&nbsp;</sup>method was modified from the molybdenum blue procedure (Bernhardt and Wilhelms 1967), in which PO<sub>4</sub><sup>3-&nbsp;</sup>is determined as reduced phosphomolybdic acid employing hydrazine as the reductant. The indophenol blue method, modified from ALPKEM RFA methodology, was used for the measurement of NH<sub>4</sub><sup>+</sup>. Silicic acid was measured using the methodology of Atlas et al. (1971) in which the addition of an acidic molybdate reagent forms silicomolybdic acid that is then reduced by stannous chloride. Lastly, NO<sub>3</sub><sup>-</sup>&nbsp;and NO<sub>3</sub><sup>-</sup>+ NO<sub>2</sub><sup>-</sup>&nbsp;were measured based on the methods of Atlas et al. (1967) with modifications to improve precision. Sulfanilamide and N-(1-Napthyl)ethylenediamine dihydrochloride react with NO<sub>2</sub><sup>-</sup>&nbsp;to form a diazo compound. For the NO<sub>3</sub><sup>-</sup>&nbsp;+ NO<sub>2</sub><sup>-</sup>&nbsp;analysis, NO<sub>3</sub><sup>-</sup>&nbsp;is first reduced to NO<sub>2</sub><sup>-&nbsp;</sup>using an OTCR and imidazole buffer as described by Patton (1983). The NO<sub>2</sub><sup>-&nbsp;</sup>analysis is performed on a separate channel, omitting the cadmium reductor and the buffer.</p>
<p><em>Dissolved combined neutral sugars (DCNS)</em></p>
<p>Dissolved combined neutral sugars (DCNS) were measured from frozen 20 µl aliquots of 0.22 µm filtered seawater (collected in acid-washed, combusted 40-ml amber EPA vials and stored in the dark at 4ºC) at the Complex Carbohydrate Research Center, University of Georgia. Each sample was first desalted and hydrolyzed. For desalting, each sample was loaded onto a gravity column, containing forty milliliters of mixed ion exchange resins (AG 501-X8, 20-50 mesh, Bio-Rad), that was packed and prewashed with 200 ml (5x bed volume) of nano-pure water. Samples were then eluted with 120 ml (3x bed volume) of nano-pure water. The resulting flow-through and wash solution were lyophilized. Following lyopholization, the recovered materials were hydrolyzed wth 2 ml of 2 N TFA at 100ºC until high-performance anion exchange chromatography (HPAEC) analysis. By employing a specific HPAEC program, as detailed below, the neutral monosaccharides can be separated allowing the measurement of carbohydrates in each sample.</p>
<p>Monosaccharide standards, including fucose (Fuc), rhamnose (Rha), arabinose (Ara), glucose (Glc), galactose (Gal), xylose (Xyl), mannose (Man), and fructose (Frc), were hydrolyzed in the same manner and at the same time as the samples. Three concentrations of the standard mixture were prepared serially to establish a calibration equation. The quantity of each residue in the sample was calculated by linear interpolation of respective residue area units into the calibration equation.</p>
<p>Monosaccharides from each sample were analyzed by HPAEC with pulsed amperometric detection (HPAEC-PAD) using a DIONEX ICS3000 system (Thermo Fisher Scientific) equipped with a gradient pump and an electrochemical detector. The carbohydrates were separated by a Dionex CarboPac PA20 (3x150mm) analytical column with an amino trap column and eluted with degassed 12 mM NaOH. Injections were made every 40 min. Under the HPAEC conditons, Xyl and Man cannot be separated (Borch and Kirchman 1997) and are presented as combined results. Samples were analyzed in triplicate and mean values were reported as ng ml<sup>-1</sup>&nbsp;based on the volume analyzed.</p>
<p><em>Fluorescent dissolved organic matter (fDOM)</em></p>
<p>Flourescent dissolved organic matter (fDOM) was measured from cool (4ºC) aliquots of 0.22 µm filtered seawater (collected in acid-washed, combusted 40-ml amber EPA vials and stored in the dark at 4ºC) from each sample following the methods detailed in Nelson et al. (2015). Samples were analyzed using a Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp, Peltier-cooled CCD emission detector, and a simultaneous absorbance spectrometer (Horiba Scientific, Piscataway, New Jersey, USA). Samples were brought to room temperature and loaded into DIW-leached and rinsed quartz cuvettes (1 cm diameter). Excitation-emission matrices (EEMs), 3D contour plots of excitation and emission fluorescence, were measured for each sample. Analysis began and ended with 4 DIW-filled cuvettes as blanks. EEMs were processed with a MATLAB script (<a href="https://github.com/zquinlan/fDOMmatlab/script.md">https://github.com/zquinlan/fDOMmatlab/script.m</a>) that employs parallel factor analysis (PARAFAC) to identify peaks that correspond to previously characterized fDOM components (Coble 1996, Nelson et al. 2015).</p>
<p><em>Targeted metabolomics</em></p>
<p>For targeted metabolomics analysis, the remaining filtrate from each sample (~600 ml) was acidified to pH ~3 using 12M trace-metal grade hydrochloric acid (HCL) and the volume was recorded. Note that for targeted metabolomics analysis only one T<sub>0</sub>&nbsp;sample from each treatment was analyzed. Extracellular metabolites were concentrated and extracted from each acidified filtrate using solid phase extraction (SPE) with 1g/6cc BondElut PPL cartridges (Agilent, Santa Clara, CA, USA) using a vacuum manifold (Waters Corporation, Milford, MA, USA) following the protocols from Kido Soul et al. (2015) and Fiore et al. (2017). Briefly, the acidified filtrate from each sample is passed through acid-washed FEP tubing and a pre-conditioned (with 100% HPLC-grade methanol) 1g/6cc BondElut PPL cartridges (Agilent, Santa Clara, CA, USA). Following filtration, each cartridge is wrapped in combusted aluminum foil, placed in a labeled, sterile Whirl-Pak bag and frozen at -80ºC. Frozen cartridges were shipped to Appalachian State University where the extraction process was completed by rinsing each thawed cartridge with 4 volumes of 0.1 M HCL followed by a gentle 5 min drying cycle using vacuum pressure and finally eluted into acid-washed, combusted 8-ml glass vials with 6 ml of 100% methanol. Using combusted glass pipettes, the methanol extracts were transferred to acid-washed, combusted 8-ml amber EMP vials and dried down to a single droplet using vacuum centrifuged then stored at -20ºC.&nbsp;</p>
<p>Targeted metabolite analysis was performed at Woods Hole Oceanographic Institute using UPLC (Accela Open Autosampler and Accela 1250 Pump, Thermo Scientific) coupled with a heated electrospray ionization source (H-ESI) and a triple stage quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher Scientific) in selective reaction monitoring (SRM) mode per methods detailed in Kido Soule et al. (2015). The raw XCalibur files were converted to mzML files using msConvert (Chambers et al. 2012) and processed with MAVEN (Melamud et al. 2010) to obtain calibration curves based on the integrated peak area generated for each metabolite. To calculate environmental concentrations the concentration of the metabolite was divided by the volume of the original acidified filtrate passed through the PPL cartridge. Lastly, metabolites that met the threshold detection and quantification limits for the targeted analysis were corrected for extraction efficiency by dividing their environmental concentrations by their published extraction efficiency in sea water (Johnson et al. 2017).</p>
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* Adjusted parameter names to comply with database requirements.
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info@bco-dmo.org
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Alpkem RFA 300 colorimetric autoanalyzer, Alpkem, Kranj, Slovenia
Alpkem RFA 300 colorimetric autoanalyzer, Alpkem, Kranj, Slovenia
PI Supplied Instrument Name: Alpkem RFA 300 colorimetric autoanalyzer, Alpkem, Kranj, Slovenia 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/
Bio-Rad ZE5, Hercules, California, USA
Bio-Rad ZE5, Hercules, California, USA
PI Supplied Instrument Name: Bio-Rad ZE5, Hercules, California, USA 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/
Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp
Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp
PI Supplied Instrument Name: Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp PI Supplied Instrument Description:FDOM analysis: Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp, Peltier-cooled CCD emission detector, and a simultaneous absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA 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/
DIONEX ICS3000 system, Thermo Fisher Scientific
DIONEX ICS3000 system, Thermo Fisher Scientific
PI Supplied Instrument Name: DIONEX ICS3000 system, Thermo Fisher Scientific Instrument Name: Ion Chromatograph Instrument Short Name:Ion Chromatograph Instrument Description: Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
Shimadzu TOC-L analyzer
Shimadzu TOC-L analyzer
PI Supplied Instrument Name: Shimadzu TOC-L analyzer 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
Absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA
Absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA
PI Supplied Instrument Name: Absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA PI Supplied Instrument Description:FDOM analysis: Horiba Aqualog scanning fluorometer with 150 W Xe excitation lamp, Peltier-cooled CCD emission detector, and a simultaneous absorbance spectrometer, Horiba Scientific, Piscataway, New Jersey, USA Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Technicon Auto Analyzer II, SEAL Analytical Inc., Mequon, Wisconsin, USA
Technicon Auto Analyzer II, SEAL Analytical Inc., Mequon, Wisconsin, USA
PI Supplied Instrument Name: Technicon Auto Analyzer II, SEAL Analytical Inc., Mequon, Wisconsin, USA 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/