http://lod.bco-dmo.org/id/dataset/876461
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
2022-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Abundance of aggregates of the marine diatom Minutocellus polymorphus and particle-associated marine bacteria from culture and roller tank experiments in 2021-2022
2022-06-27
publication
2022-06-27
revision
BCO-DMO Linked Data URI
2022-06-27
creation
http://lod.bco-dmo.org/id/dataset/876461
Susanne Neuer
Arizona State University
principalInvestigator
Hinsby Cadillo-Quiroz
Arizona State University
principalInvestigator
Bianca N. Cruz
Arizona 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: Neuer, S., Cruz, B. N., Cadillo-Quiroz, H. (2022) Abundance of aggregates of the marine diatom Minutocellus polymorphus and particle-associated marine bacteria from culture and roller tank experiments in 2021-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-06-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/876461 [access date]
Methods and Sampling: <p>In this study, one diatom and three bacteria species were grown and measured.&nbsp;&nbsp;<em>Minutocellus polymorphus</em>&nbsp;were incubated with or without the addition of bacteria in flasks and sampled throughout their growth (representative of bloom conditions), to determine the production of transparent exopolymeric particles (TEP) and the formation of micro-aggregates, and in roller tanks to investigate the formation of sinking aggregates (representative of end of bloom conditions).&nbsp; Additional details are in Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
<p>Two growth experiments were carried out independently:<br />
1. Growth experiment 1 with the addition of&nbsp;<em>Marinobacter adhaerens</em><br />
2.&nbsp;Growth experiment 2 with the addition of&nbsp;<em>Pseudoalteromonas carrageenovora</em>&nbsp;and&nbsp;<em>Vibrio thalassae&nbsp;</em></p>
<p>Stock cultures of marine Minutocellus polymorphus (CCMP497, National Center for Marine Algae and Microbiota, NCMA) were maintained in L1 medium prepared in artificial seawater and incubated in an environmental growth chamber (Conviron) at 23 ± 1 °C.&nbsp; &nbsp;Stock cultures of&nbsp;<em>Vibrio thalassae&nbsp;</em>(DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH),&nbsp;<em>Pseudoalteromonas carrageenovora</em>&nbsp;(DSM6820, DSMZ), and&nbsp;<em>Marinobacter adhaerens</em>&nbsp;HP15 were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.&nbsp;</p>
<p>Triplicate cultures of&nbsp;<em>Minutocellus polymorphus&nbsp;</em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>M. adhaerens</em>,&nbsp;<em>P. carrageenovora,&nbsp;</em>and&nbsp;<em>V. thalassae</em>) were sampled every other day for 19-23 days for the quantification of:</p>
<ul>
<li>single cells [Cell Abundance dataset]</li>
<li>suspended microaggregates (aggregates ca. 5-60 μm) [this dataset]</li>
<li>TEP (Transparent Exopolymeric Particles) [TEP Concentration dataset]</li>
</ul>
<p>This dataset contains data on suspended microaggregates, while the other measurements can be found in the Related Datasets below.&nbsp;</p>
<p>Volume concentrations of micro-aggregates “suspended” in cultures (i.e., non-sinking particles with an equivalent spherical diameter [ESD] of 5–60 µm) were determined at every sampling period using a Multisizer 3 Particle Counter (Beckman Coulter, CA). Prior to fixation with glutaraldehyde, duplicate samples were diluted to a 1–10% final particle concentration with Isoton II diluent (Beckman Coulter, CA) and aggregates were measured and quantified with a 100 µm aperture tube. The volume concentration of aggregates was calculated in µm3 per mL.</p>
<p><strong>Aggregation in roller tanks</strong><br />
To investigate the formation of visible aggregates, cultures of the nanodiatom <em>Minutocellus polymorphus </em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>Marinobacter adhaerens </em>HP15, <em>Pseudoalteromonas carrageenovora</em>, and <em>Vibrio thalassae</em>) were incubated in&nbsp; cylindrical1.25 L Plexiglass roller tanks with artificial seawater (ASW) for 7 days in the dark at 3.5 revolutions per minute (RPM) after the methodology of Shanks and Edmondson (1989).&nbsp;</p>
<p>Two sets of experiments were performed:</p>
<ol>
<li>cultures were inoculated to cell concentrations simulating natural conditions in the Sargasso Sea (10<sup>^3&nbsp;</sup>cells per mL), and the experiment was performed with the addition of&nbsp;<em>M. adhaerens</em>&nbsp;alongside bacteria-only and diatom-only controls, as well as with the addition of microbeads</li>
<li>cultures were inoculated at higher cell concentrations (10<sup>^5</sup>&nbsp;cells per mL).</li>
</ol>
<p>All treatments were performed in triplicate (<em>n&nbsp;</em>= 3 tanks) in the 10<sup>^5</sup>&nbsp;cells mL<sup>-1</sup>&nbsp;experiments and in duplicate (<em>n</em>&nbsp;= 2 tanks) in the 10<sup>^3</sup>&nbsp;cells mL<sup>-1</sup>&nbsp;experiments. Aggregates formed were quantified, sized, and their sinking velocities were determined.&nbsp;&nbsp;Suspended microaggregates (i.e., non-sinking particles with an equivalent spherical diameter of&nbsp;5-60 microns) were quantified using a Multisizer 3 Particle Counter.&nbsp;&nbsp;TEP concentrations were determined as in Bittar et al. (2018). The stocks of Alcian-Blue dye used for TEP quantification had calibration factors (or f-factors) of 81.70 for experiments with&nbsp;<em>M. adhaerens</em>&nbsp;and 83.83 for experiments with&nbsp;<em>P. carrageenovora&nbsp;</em>and&nbsp;<em>V. thalassae</em>.</p>
<p>Only the axenic Minutocellus 10^5 experiment had hardy-enough aggregates for analysis.&nbsp; Please refer to the Supplemental document.&nbsp;&nbsp;</p>
<p>For additional Methods details, see Cruz &amp; Neuer, 2022.&nbsp;&nbsp;<br />
For size and velocity of sinking aggregates from roller tank experiments, see Supplemental Files section</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658527 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658527
onGoing
Susanne Neuer
Arizona State University
480-727-7254
College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall
Tempe
AZ
85287-4501
USA
susanne.neuer@asu.edu
pointOfContact
Hinsby Cadillo-Quiroz
Arizona State University
School of Life Sciences University of Arizona
Tempe
85287
AZ
hinsby@asu.edu
pointOfContact
Bianca N. Cruz
Arizona State University
bncruz1@mainex1.asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment_ID
Culture
Culture_type
Days
Susp_Microaggregate_Vol_Conc_rep1
Susp_Microaggregate_Vol_Conc_rep2
Susp_Microaggregate_Vol_Conc_rep3
Multisizer 3 Particle Counter
Epifluorescence microscope
Roller tank
theme
None, User defined
experiment id
experiment type
days
diatom abundance
featureType
BCO-DMO Standard Parameters
Coulter Counter
Fluorescence Microscope
Roller Tank
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.
Aggregation of Marine Picoplankton
https://osprey.bco-dmo.org/project/710239
Aggregation of Marine Picoplankton
<p>NSF abstract:</p>
<p>Marine phytoplankton are microscopic algae that live in the sunlit zone of the ocean. They play an important role in the uptake of carbon dioxide from the atmosphere through photosynthesis, similar to what plants do on land, and are the basis of the marine food web. However, instead of storing this organic carbon in leaf tissue and roots, marine phytoplankton are grazed by planktonic animals, or die and subsequently sink out of the sunlit zone in the form of aggregates, also called "Marine Snow". These particles not only export the organic carbon contained in their cells to the deep ocean, but also serve as food for animals and bacteria that live in the deep. A considerable portion of these phytoplankton are extremely small, among the tiniest of all organisms known. These extremely small cells have not been thought to play an important role in the formation and sinking of marine snow; however, recent findings challenge this view. This project will investigate how the smallest of these phytoplankton contribute to the rain of sinking particles from the sunlit surface to the deep ocean. This research is important because, in some of the largest expanses of the open oceans, these minute cells dominate the phytoplankton community, and larger plankton organisms are very sparse. The project, through a combination of work in the laboratory and at a field station, will shed light on how these tiny phytoplankton cells make aggregates, which ultimately enable them to sink as "Marine Snow". The project also provides unique opportunities for undergraduate students at Arizona State University, a land-locked public university, to gain experience in working with marine research. The project will serve to educate one PhD student, one MS student in an accelerated BS-MS program, and 8-10 undergraduate students/semester in a unique, inquiry based learning effort termed Microbial EducatioN Training and OutReach (MENTOR). The undergraduate students will also participate in Arizona State University (ASU)'s School of Life Sciences, Undergraduate Research Program (SOLUR), which seeks to increase the participation of minorities in science. They will also contribute towards developing web and classroom materials, based on this project, which will then be distributed through a partnership with the award-winning ASU-sponsored Ask A Biologist K-12 web site.</p>
<p>The oceanic "biological carbon pump", the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon and its subsequent export to deep water, functions as a significant driver of atmospheric carbon uptake by the oceans. The traditional view of the biological carbon pump in the ocean is that of sinking of large aggregates (marine snow) or fecal pellets, which are made up of large, mineral ballasted cells of phytoplankton. However, recent evidence, stemming from in situ investigations of particulate matter, trap studies and modelling studies, have shown that micron-sized phytoplankton such as picocyanobacteria as well as picoeukaryotes can contribute significantly to the sinking of particulate matter. The specific mechanisms behind the sinking of these micrometer sized cells remain elusive as the cells are too small to sink on their own, and mesozooplankton is likely unable to ingest single cells. Intriguingly, recent research by the investigators has shown that the ubiquitous picocyanobacteria Synechococcus are able to form aggregates and sink at velocities comparable to those of marine snow. They found that the matrix of the Synechococcus aggregates was made of Transparent Exopolymeric Particles (TEP), and that TEP production was enhanced under nutrient limited culture conditions. Interaction with clays and presence of heterotrophic bacteria also enhanced aggregation and sinking velocity. This study aims to further investigate aggregation of other common picoplankton in the laboratory and aggregation occurring in natural settings at an oligotrophic open ocean site, the Bermuda Atlantic Time-series Site (BATS). Ultimately, this project will increase and refine our understanding of the role of the smallest phytoplankton in aggregation and sinking - information vital to understanding carbon cycling processes in the oceans.</p>
Marine Plankton Aggregation
largerWorkCitation
project
eng; USA
biota
oceans
-111.92828937936
-111.92828937936
33.419410120974
33.419410120974
2021-12-01
2022-08-01
Bermuda Atlantic Time-Series station
0
BCO-DMO catalogue of parameters from Abundance of aggregates of the marine diatom Minutocellus polymorphus and particle-associated marine bacteria from culture and roller tank experiments in 2021-2022
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/883745.rdf
Name: Experiment_ID
Units: unitless
Description: <p>Experiment ID describing the experiment in which the organism grew</p>
http://lod.bco-dmo.org/id/dataset-parameter/883746.rdf
Name: Culture
Units: unitless
Description: <p>Experimental culture, listing the organisms grown</p>
http://lod.bco-dmo.org/id/dataset-parameter/883747.rdf
Name: Culture_type
Units: unitless
Description: <p>Culture type, either co-culture or axenic (diatom-only control)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883748.rdf
Name: Days
Units: days
Description: <p>Days since start of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/883749.rdf
Name: Susp_Microaggregate_Vol_Conc_rep1
Units: 10^6 cubic microns per milliliter (x10^6 um^3 per mL)
Description: <p>Replicate 1 volume concentration of aggregates with an equivalent spherical diameter of 5-60 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/883750.rdf
Name: Susp_Microaggregate_Vol_Conc_rep2
Units: cubic microns per milliliter (x10^6 um^3 per mL)
Description: <p>Replicate 2 volume concentration (times 10^6) of aggregates with an equivalent spherical diameter of 5-60 microns</p>
http://lod.bco-dmo.org/id/dataset-parameter/883751.rdf
Name: Susp_Microaggregate_Vol_Conc_rep3
Units: cubic microns per milliliter (x10^6 um^3 per mL)
Description: <p>Replicate 3 volume concentration (times 10^6) of aggregates with an equivalent spherical diameter of 5-60 microns</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
604170
https://datadocs.bco-dmo.org/docs/305/Marine_Plankton_Aggregation/data_docs/Cruz_Neuer_roller_tank_size_velocities.pdf
Cruz & Neuer 2022 Roller tank aggregate sizes and velocities
Sizes and velocities of aggregates from roller tank experiments as described in Cruz & Neuer, 2022.
download
https://osprey.bco-dmo.org/dataset/876461/data/download
download
onLine
dataset
<p>In this study, one diatom and three bacteria species were grown and measured.&nbsp;&nbsp;<em>Minutocellus polymorphus</em>&nbsp;were incubated with or without the addition of bacteria in flasks and sampled throughout their growth (representative of bloom conditions), to determine the production of transparent exopolymeric particles (TEP) and the formation of micro-aggregates, and in roller tanks to investigate the formation of sinking aggregates (representative of end of bloom conditions).&nbsp; Additional details are in Cruz &amp; Neuer, 2022.&nbsp;&nbsp;</p>
<p>Two growth experiments were carried out independently:<br />
1. Growth experiment 1 with the addition of&nbsp;<em>Marinobacter adhaerens</em><br />
2.&nbsp;Growth experiment 2 with the addition of&nbsp;<em>Pseudoalteromonas carrageenovora</em>&nbsp;and&nbsp;<em>Vibrio thalassae&nbsp;</em></p>
<p>Stock cultures of marine Minutocellus polymorphus (CCMP497, National Center for Marine Algae and Microbiota, NCMA) were maintained in L1 medium prepared in artificial seawater and incubated in an environmental growth chamber (Conviron) at 23 ± 1 °C.&nbsp; &nbsp;Stock cultures of&nbsp;<em>Vibrio thalassae&nbsp;</em>(DSM102810, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH),&nbsp;<em>Pseudoalteromonas carrageenovora</em>&nbsp;(DSM6820, DSMZ), and&nbsp;<em>Marinobacter adhaerens</em>&nbsp;HP15 were maintained on Marine Agar (BD Difco 2216, Becton Dickinson, NJ; ZoBell, 1941) plates at 23 ± 1 °C.&nbsp;</p>
<p>Triplicate cultures of&nbsp;<em>Minutocellus polymorphus&nbsp;</em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>M. adhaerens</em>,&nbsp;<em>P. carrageenovora,&nbsp;</em>and&nbsp;<em>V. thalassae</em>) were sampled every other day for 19-23 days for the quantification of:</p>
<ul>
<li>single cells [Cell Abundance dataset]</li>
<li>suspended microaggregates (aggregates ca. 5-60 μm) [this dataset]</li>
<li>TEP (Transparent Exopolymeric Particles) [TEP Concentration dataset]</li>
</ul>
<p>This dataset contains data on suspended microaggregates, while the other measurements can be found in the Related Datasets below.&nbsp;</p>
<p>Volume concentrations of micro-aggregates “suspended” in cultures (i.e., non-sinking particles with an equivalent spherical diameter [ESD] of 5–60 µm) were determined at every sampling period using a Multisizer 3 Particle Counter (Beckman Coulter, CA). Prior to fixation with glutaraldehyde, duplicate samples were diluted to a 1–10% final particle concentration with Isoton II diluent (Beckman Coulter, CA) and aggregates were measured and quantified with a 100 µm aperture tube. The volume concentration of aggregates was calculated in µm3 per mL.</p>
<p><strong>Aggregation in roller tanks</strong><br />
To investigate the formation of visible aggregates, cultures of the nanodiatom <em>Minutocellus polymorphus </em>(CCMP497) with and without the addition of known particle-associated marine bacteria (<em>Marinobacter adhaerens </em>HP15, <em>Pseudoalteromonas carrageenovora</em>, and <em>Vibrio thalassae</em>) were incubated in&nbsp; cylindrical1.25 L Plexiglass roller tanks with artificial seawater (ASW) for 7 days in the dark at 3.5 revolutions per minute (RPM) after the methodology of Shanks and Edmondson (1989).&nbsp;</p>
<p>Two sets of experiments were performed:</p>
<ol>
<li>cultures were inoculated to cell concentrations simulating natural conditions in the Sargasso Sea (10<sup>^3&nbsp;</sup>cells per mL), and the experiment was performed with the addition of&nbsp;<em>M. adhaerens</em>&nbsp;alongside bacteria-only and diatom-only controls, as well as with the addition of microbeads</li>
<li>cultures were inoculated at higher cell concentrations (10<sup>^5</sup>&nbsp;cells per mL).</li>
</ol>
<p>All treatments were performed in triplicate (<em>n&nbsp;</em>= 3 tanks) in the 10<sup>^5</sup>&nbsp;cells mL<sup>-1</sup>&nbsp;experiments and in duplicate (<em>n</em>&nbsp;= 2 tanks) in the 10<sup>^3</sup>&nbsp;cells mL<sup>-1</sup>&nbsp;experiments. Aggregates formed were quantified, sized, and their sinking velocities were determined.&nbsp;&nbsp;Suspended microaggregates (i.e., non-sinking particles with an equivalent spherical diameter of&nbsp;5-60 microns) were quantified using a Multisizer 3 Particle Counter.&nbsp;&nbsp;TEP concentrations were determined as in Bittar et al. (2018). The stocks of Alcian-Blue dye used for TEP quantification had calibration factors (or f-factors) of 81.70 for experiments with&nbsp;<em>M. adhaerens</em>&nbsp;and 83.83 for experiments with&nbsp;<em>P. carrageenovora&nbsp;</em>and&nbsp;<em>V. thalassae</em>.</p>
<p>Only the axenic Minutocellus 10^5 experiment had hardy-enough aggregates for analysis.&nbsp; Please refer to the Supplemental document.&nbsp;&nbsp;</p>
<p>For additional Methods details, see Cruz &amp; Neuer, 2022.&nbsp;&nbsp;<br />
For size and velocity of sinking aggregates from roller tank experiments, see Supplemental Files section</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
- Excel sheet "M.polymorphus_Microaggregates_and_TEP- Suspended Microaggregates.xlsx " was processed and saved as a CSV file
- added a conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Multisizer 3 Particle Counter
Multisizer 3 Particle Counter
PI Supplied Instrument Name: Multisizer 3 Particle Counter PI Supplied Instrument Description:Suspended microaggregates were quantified using a Multisizer 3 Particle Counter Instrument Name: Coulter Counter Instrument Short Name: Instrument Description: An apparatus for counting and sizing particles suspended in electrolytes. It is used for cells, bacteria, prokaryotic cells and virus particles. A typical Coulter counter has one or more microchannels that separate two chambers containing electrolyte solutions.
from https://en.wikipedia.org/wiki/Coulter_counter
Epifluorescence microscope
Epifluorescence microscope
PI Supplied Instrument Name: Epifluorescence microscope PI Supplied Instrument Description:Single cell abundance of diatoms and bacteria were determined using epifluorescence microscopy Instrument Name: Fluorescence Microscope Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/
Roller tank
Roller tank
PI Supplied Instrument Name: Roller tank PI Supplied Instrument Description:Cultures were incubated in 1.25 L roller tanks for 7 days in the dark at 3.5 revolutions per minute (RPM) Instrument Name: Roller Tank Instrument Short Name:Roller Tank Instrument Description: Rolling tanks, which keep particles in suspension, thus simulating aggregate formation in situ.
Marine snow experiments are conducted in roller tanks, which turn continuously, keeping marine snow in suspension. It is important for marine snow not to touch surfaces. The rolling tanks, which keep particles in suspension, thus simulate aggregate formation in situ. Marine snow formation due to different types of oil was tested. Some treatments are easily identifiable as containing oil by their color (middle). UCSB, CA 2012.