http://lod.bco-dmo.org/id/dataset/949181
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
2025-01-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Counts of faunal colonists found on experimental settlement surfaces deployed at Tica Vent in East Pacific Rise on R/V Atlantis cruise AT42-21 and R/V Roger Revelle cruise RR2102 from Dec 2019 to Apr 2021
2025-01-23
publication
2025-01-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-11
publication
https://doi.org/10.26008/1912/bco-dmo.949181.1
Shawn M. Arellano
Western Washington University
principalInvestigator
Lauren S. Mullineaux
Woods Hole Oceanographic Institution
principalInvestigator
Costantino Vetriani
Rutgers University
principalInvestigator
Tanika Ladd
Western Washington University
principalInvestigator
Susan Mills
Woods Hole Oceanographic Institution
principalInvestigator
Matteo Selci
Rutgers 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: Ladd, T., Arellano, S. M., Mullineaux, L., Vetriani, C., Selci, M., Davis, D., Mills, S., Plowman, C. Q., Cannon, O., Schlegel, I., Inaba, A. (2025) Counts of faunal colonists found on experimental settlement surfaces deployed at Tica Vent in East Pacific Rise on R/V Atlantis cruise AT42-21 and R/V Roger Revelle cruise RR2102 from Dec 2019 to Apr 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-01-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949181.1 [access date]
Colonization experiment Tica Vent AT42-21 and RR2102 Dataset Description: Methods and Sampling: <p><strong>Study site and experiment details</strong></p>
<p>A short-term in-situ colonization experiment was conducted at Tica Vent (9°50.3987 N, 104°17.4970 W) in the 9°50’ N region of the EPR. Colonization surfaces, comprised of 6 stacked polycarbonate plates separated by spacers and termed “sandwiches” (described by Mullineaux et al., 2010 and Dykman et al., 2021), were deployed by the deep submergence vehicles HOV Alvin and ROV Jason over two cruises; one aboard the R/V Atlantis in December 2019 and the other on the R/V Roger Revelle in March-April 2021.</p>
<p>During the first deployment in December 2019, 12 sandwiches were covered in 200 µm nylon mesh bags termed “purses” to prevent animal colonization while allowing for microbial biofilm development. The purses were custom designed with handles and completely enclosed around the sandwich with hook and loop fasteners so that they could be removed in-situ by vehicle manipulators (L. Lavigne, Anacortes, WA). Four replicate “pursed sandwiches” were placed within each of three biogenic zones (<em>Alvinella</em>-dominated, <em>Riftia</em>-dominated, and mussel-dominated) that span a gradient of temperature and chemical conditions. The colonization experiment was initiated when the ROV Jason revisited the pursed sandwiches approximately 15 months later. Several pursed sandwiches (3 from the Alvinellid zone and 2 from the <em>Riftia</em> zone) were lost due to overgrowth by animal communities, resulting in the discovery of 7 of the initial 12 pursed sandwiches. For the 7 pursed sandwiches that were discovered, purses were removed, and the established biofilm sandwiches were placed back in the location they had been found. Fresh sandwiches (no previously developed biofilm) were deployed next to each of the 7 established biofilm sandwiches to act as paired controls. The sandwiches were left on the seafloor for approximately 15 days to allow for animal colonization. After which, they were recovered into separate sealed collection compartments on the ROV Jason.</p>
<p>Although most sandwiches were brought to the surface before preservation, one established biofilm sandwich from each zone (including the only established biofilm sandwich in the Alvinellid zone) was recovered into individual cylinders specifically designed for immediate preservation of samples in-situ (Analytical Instrument Systems, Ringoes, NJ) that were filled with an RNA stabilization solution (25 mM sodium citrate, 10 mM EDTA, 70 g ammonium sulfate per 100 mL solution, adjusted to pH 7.0 with sulfuric acid); preservation in the RNA stabilization buffer makes these samples available for other work not reported here. A temperature probe held at the base of each sandwich for approximately 1-2 minutes was used to record the temperature maximum at deployments and recoveries of all sandwiches.</p>
<p><strong>Shipboard preservation and processing of sandwiches</strong></p>
<p>Upon vehicle recovery, containers holding sandwiches were transported to a cold room (4 °C). Attached weights and polypropylene handles were removed and the zipties holding each sandwich together were cut to remove the top sandwich plate. Any animals visible on the top plate were gently removed and placed into a separate container filled with RNA preservative. The top plate was then placed into a plastic bag with enough RNA preservative to cover the entire plate and frozen at -80 °C until further processing for 16S rRNA gene sequencing (not included in the dataset here). The remaining parts of the sandwich were placed into separate plastic bags, submerged in RNA preservative, and stored at 4 °C until further processing for animal colonization. To collect any fauna that had fallen off the sandwiches, seawater or RNA preservative in the sandwich collection compartments was poured and rinsed over a 63 µm mesh sieve, then stored in RNA preservative at 4 °C until further processing.</p>
<p><strong>Characterizing animal colonist communities</strong></p>
<p>At Western Washington University’s Shannon Point Marine Center (SPMC) faunal colonists from each sandwich were observed and counted under a stereo microscope (Olympus) at 4x magnification. Both sides of each sandwich plate were carefully inspected under a microscope and attached organisms were removed and counted. Additionally, any organisms in the RNA stabilization solution in the containers holding the sandwich plates and sieved sandwich compartment contents were sorted and counted. Individual colonists were grouped into morphotypes based on visual features while any damaged organisms that could not be assigned to a morphotype group were grouped into a broad unknown taxonomic group (e.g., unknown polychaete, unknown gastropod, etc.). Representative organisms from morphotype groups were imaged on either a stereo microscope (Leica; magnification range 0.8-10x) or a compound microscope (Leica; 20x magnification) for possible further taxonomic identification and to create a morphotype guide (See supplemental files: RR2102_morphotype_guide.pdf).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948580 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948580
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1947735 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1947735
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1948623 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1948623
completed
Shawn M. Arellano
Western Washington University
360-650-3634
Western Washington University 1900 Shannon Point Road
Anacortes
WA
98221
USA
arellas@wwu.edu
pointOfContact
Lauren S. Mullineaux
Woods Hole Oceanographic Institution
508-289-2898
Redfield 1-20 MS #34
Woods Hole
MA
02543
USA
lmullineaux@whoi.edu
pointOfContact
Costantino Vetriani
Rutgers University
732-932-6555 x373
Rutgers University 71 Dudley Road
New Brunswick
NJ
08901
USA
vetriani@marine.rutgers.edu
pointOfContact
Tanika Ladd
Western Washington University
laddt@wwu.edu
pointOfContact
Susan Mills
Woods Hole Oceanographic Institution
266 Woods Hole Road MS 34
Woods Hole
MA
0254
USA
smills@whoi.edu
pointOfContact
Matteo Selci
Rutgers University
selcimatteo@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
ID
Sample_type
Lat
Lon
Site_name
Zone
Cruise_deployed
Dive_deployed
ISO_DateTime_UTC_deployed
Exp_start_temp
Pursed
Cruise_purse_removal
Dive_purse_removal
ISO_DateTime_UTC_purse_removal
Cruise_recovered
Dive_recovered
ISO_DateTime_UTC_recovered
Recovery_temp
Nearby
Biofilm_dev_time
Larval_set_time
ID_pairs
AMP1
ISO1
BIV1
COP1
COP2
COP3
COP4
FOR1
GAS1
GAS2
GAS3
GAS4
GAS5
GASU
GAV1
GAV2
GAV3
GAVU
GAS6
GAS7
GAS8
GAS9
GAS10
MIT1
MUS1
CNP1
NEC1
POL17
NEC2
NEC3
POL18
NEC4
POL19
NEC5
NEC6
NEC7
NEC8
POL21
POL22
POL27
NEM1
NECU
OPH1
OST1
POL1
POL2
POL3
POL4
POL5
POL6
POL7
POL8
POL9
POL11
POL12
POL15
POL16
POLU
HOV Alvin, Heat Flow Probes (temperature sensors)
Heat Flow Probes
In-situ RNA preservation samplers
Olympus SZ stereo microscope
Leica M125 stereo microscope
Leica DM5500 B compound microscope
ROV Jason, Heat Flow Probes (temperature sensors)
theme
None, User defined
experiment id
experiment type
latitude
longitude
site
site description
Cruise identfier
dive_id
ISO_DateTime_UTC
temperature of sample or a generic measurement (not in-situ water temp)
time_elapsed
count
featureType
BCO-DMO Standard Parameters
HOV Alvin
HOV Alvin Heatflow Probe 0.66m
In-situ RNA preservation sampler (Analytical Instrument Systems)
Microscope - Optical
Microscope - Optical
Microscope - Optical
ROV Jason
instrument
BCO-DMO Standard Instruments
AT42-21
RR2102
service
Deployment Activity
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.
RUI: Collaborative: The Predictive Nature of Microbial Biofilms for Cuing Larval Settlement at Deep-Sea Hydrothermal Vents
https://osprey.bco-dmo.org/project/851182
RUI: Collaborative: The Predictive Nature of Microbial Biofilms for Cuing Larval Settlement at Deep-Sea Hydrothermal Vents
<p><em>NSF Award Abstract:</em><br />
Over four decades of research have shown that tiny free-swimming offspring of the unique inhabitants of hydrothermal vents can disperse effectively between their specialized habitats. Yet, we know almost nothing about how these larval animals complete the journey by locating and settling down in suitable locations. This question remains one of the key unresolved puzzles in the ecology of the deep sea and is becoming increasingly important to solve as hydrothermal vents are becoming threatened by human impacts. The investigators suggest that the films of bacteria that first form at vents are good signposts for settlement of larvae because they indicate that the hydrothermal vents are suitable for life. This project uses a combined program of field experiments, cutting-edge molecular biology techniques, and shipboard experiments with hydrothermal-vent larvae and cultured bacterial films. The project also connects undergraduate research interns at a primarily undergraduate institution (Western Washington University) with undergraduate research interns at two research institutions (Rutgers and Woods Hole Oceanographic Institution) while working on the project at sea together. Finally, the team is producing a science-in-action documentary filled with ocean science and exploration intended for television distribution and museum screenings. The investigators are using footage of the deep-sea vents, shipboard and diving operations, and laboratory work to create a documentary that highlights the foundation of scientific research—hypothesis-driven research, the application of the scientific method, and the importance of critical thinking—all in the framework of the study of an exciting, but threatened, ecosystem.</p>
<p>Hydrothermal vents are particularly tractable systems in which to study questions about the roles of biofilms in larval settlement because biofilms at vents are relatively low-complexity; vent animals are strictly dependent on vent microbes, often through symbiotic partnerships acquired after settlement; and environmental variations are present within the range of a common larval pool. Moreover, decades of research on settlement in model organisms give us good insight into biofilm cues; there is solid foundational understanding about colonization patterns at vents; we now have excellent tools to collect, identify, and culture vent larvae and microbes; and modern environmental "-omics" techniques are a good tool to characterize biological cues produced by biofilms. The project provides an unprecedented, quantitative look into the role of microbial biofilms in structuring larval settlement at hydrothermal vents, achieved only through the close collaboration of microbial and larval ecologists. The combined field program of short-term settlement experiments, microbial "-omics" work, and subsequent shipboard settlement experiments allows the investigative team to use field experiments to statistically model the factors that best predict larval settlement in the field, then test those predictions with shipboard experiments that decouple covarying conditions. This extensive characterization of putative larval settlement cues and their relationship to colonization success in heterogeneous vent habitat niches will contribute to a broader understanding of colonization success across diverse marine ecosystems. Understanding the role that the initial settlement of larvae plays in the recovery and resilience of hydrothermal-vent ecosystems is critical to developing informed management plans for deep-sea mining.</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>
Vent Settlement Cues
largerWorkCitation
project
eng; USA
biota
oceans
-104.29168
-104.29162
9.84004
9.84008
2019-12-29
2021-04-01
East Pacific Rise, 9 North hydrothermal vents
0
BCO-DMO catalogue of parameters from Counts of faunal colonists found on experimental settlement surfaces deployed at Tica Vent in East Pacific Rise on R/V Atlantis cruise AT42-21 and R/V Roger Revelle cruise RR2102 from Dec 2019 to Apr 2021
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/949238.rdf
Name: ID
Units: unitless
Description: <p>Unique ID code for each sandwich</p>
http://lod.bco-dmo.org/id/dataset-parameter/949239.rdf
Name: Sample_type
Units: unitless
Description: <p>Experiment condition of "pursed sandwich" or "sandwich"; if the sandwich was ever covered with mesh = "pursed"</p>
http://lod.bco-dmo.org/id/dataset-parameter/949240.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of sandwich deployment, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/949241.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of sandwich deployment, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/949242.rdf
Name: Site_name
Units: unitless
Description: <p>Name of experimental site</p>
http://lod.bco-dmo.org/id/dataset-parameter/949243.rdf
Name: Zone
Units: unitless
Description: <p>Biogenic zone in which a sandwich was deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/949244.rdf
Name: Cruise_deployed
Units: unitless
Description: <p>Cruise ID when sandwich was initially deployed</p>
http://lod.bco-dmo.org/id/dataset-parameter/949245.rdf
Name: Dive_deployed
Units: unitless
Description: <p>Alvin or Jason dive number for sandwich deployment</p>
http://lod.bco-dmo.org/id/dataset-parameter/949246.rdf
Name: ISO_DateTime_UTC_deployed
Units: unitless
Description: <p>Datetime (UTC) sandwich was initially deployed in ISO format</p>
http://lod.bco-dmo.org/id/dataset-parameter/949247.rdf
Name: Exp_start_temp
Units: degrees Celsius
Description: <p>Temperature (degrees Celsius) under the sandwich at experiment start</p>
http://lod.bco-dmo.org/id/dataset-parameter/949248.rdf
Name: Pursed
Units: unitless
Description: <p>"Y" or "N", if the sandwich was ever covered with mesh = "Y"</p>
http://lod.bco-dmo.org/id/dataset-parameter/949249.rdf
Name: Cruise_purse_removal
Units: unitless
Description: <p>Cruise ID when sandwich mesh (purse) was removed</p>
http://lod.bco-dmo.org/id/dataset-parameter/949250.rdf
Name: Dive_purse_removal
Units: unitless
Description: <p>Alvin or Jason dive number for sandwich mesh (purse) removal</p>
http://lod.bco-dmo.org/id/dataset-parameter/949251.rdf
Name: ISO_DateTime_UTC_purse_removal
Units: unitless
Description: <p>Datetime (UTC) sandwich mesh (purse) was removed in ISO format</p>
http://lod.bco-dmo.org/id/dataset-parameter/949252.rdf
Name: Cruise_recovered
Units: unitless
Description: <p>Cruise ID when sandwich was recovered</p>
http://lod.bco-dmo.org/id/dataset-parameter/949253.rdf
Name: Dive_recovered
Units: unitless
Description: <p>Alvin or Jason dive number for sandwich recovery</p>
http://lod.bco-dmo.org/id/dataset-parameter/949254.rdf
Name: ISO_DateTime_UTC_recovered
Units: unitless
Description: <p>Datetime (UTC) sandwich was recovered in ISO format</p>
http://lod.bco-dmo.org/id/dataset-parameter/949255.rdf
Name: Recovery_temp
Units: degrees Celsius
Description: <p>Temperature (degrees Celsius) under the sandwich at experiment end (recovery)</p>
http://lod.bco-dmo.org/id/dataset-parameter/949256.rdf
Name: Nearby
Units: unitless
Description: <p>Unique ID code for pursed sandwiches that were the target pairs for fresh sandwiches</p>
http://lod.bco-dmo.org/id/dataset-parameter/949257.rdf
Name: Biofilm_dev_time
Units: days
Description: <p>Length of time in days that pursed sandwiches were pursed</p>
http://lod.bco-dmo.org/id/dataset-parameter/949258.rdf
Name: Larval_set_time
Units: days
Description: <p>Length of time in days that fauna could colonize the sandwich</p>
http://lod.bco-dmo.org/id/dataset-parameter/949259.rdf
Name: ID_pairs
Units: unitless
Description: <p>unique ID for each sandwich pair</p>
http://lod.bco-dmo.org/id/dataset-parameter/949260.rdf
Name: AMP1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Amphipod Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949261.rdf
Name: ISO1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Isopod Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949262.rdf
Name: BIV1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Bivalve Veliger Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949263.rdf
Name: COP1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Copepod Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949264.rdf
Name: COP2
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Copepod Type 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/949265.rdf
Name: COP3
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Copepod Type 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/949266.rdf
Name: COP4
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Copepod Type 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/949267.rdf
Name: FOR1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Foraminifera</p>
http://lod.bco-dmo.org/id/dataset-parameter/949268.rdf
Name: GAS1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - conical spiral</p>
http://lod.bco-dmo.org/id/dataset-parameter/949269.rdf
Name: GAS2
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - semicircle</p>
http://lod.bco-dmo.org/id/dataset-parameter/949270.rdf
Name: GAS3
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - angular spiral</p>
http://lod.bco-dmo.org/id/dataset-parameter/949271.rdf
Name: GAS4
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - macaroni</p>
http://lod.bco-dmo.org/id/dataset-parameter/949272.rdf
Name: GAS5
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - white spiral</p>
http://lod.bco-dmo.org/id/dataset-parameter/949273.rdf
Name: GASU
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod - unknown</p>
http://lod.bco-dmo.org/id/dataset-parameter/949274.rdf
Name: GAV1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod Veliger Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949275.rdf
Name: GAV2
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod Veliger Type 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/949276.rdf
Name: GAV3
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod Veliger Type 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/949277.rdf
Name: GAVU
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Gastropod Veliger - unknown</p>
http://lod.bco-dmo.org/id/dataset-parameter/949278.rdf
Name: GAS6
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Limpet type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949279.rdf
Name: GAS7
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Limpet type 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/949280.rdf
Name: GAS8
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Limpet type 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/949281.rdf
Name: GAS9
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Limpet type 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/949282.rdf
Name: GAS10
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Limpet type 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/949283.rdf
Name: MIT1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Marine mite</p>
http://lod.bco-dmo.org/id/dataset-parameter/949284.rdf
Name: MUS1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Juvenile Mussel</p>
http://lod.bco-dmo.org/id/dataset-parameter/949285.rdf
Name: CNP1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nauplius - Copepod various</p>
http://lod.bco-dmo.org/id/dataset-parameter/949286.rdf
Name: NEC1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949287.rdf
Name: POL17
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 17</p>
http://lod.bco-dmo.org/id/dataset-parameter/949288.rdf
Name: NEC2
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/949289.rdf
Name: NEC3
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/949290.rdf
Name: POL18
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 18</p>
http://lod.bco-dmo.org/id/dataset-parameter/949291.rdf
Name: NEC4
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/949292.rdf
Name: POL19
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 19</p>
http://lod.bco-dmo.org/id/dataset-parameter/949293.rdf
Name: NEC5
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/949294.rdf
Name: NEC6
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 6</p>
http://lod.bco-dmo.org/id/dataset-parameter/949295.rdf
Name: NEC7
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/949296.rdf
Name: NEC8
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete Type 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/949297.rdf
Name: POL21
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 21</p>
http://lod.bco-dmo.org/id/dataset-parameter/949298.rdf
Name: POL22
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 22</p>
http://lod.bco-dmo.org/id/dataset-parameter/949299.rdf
Name: POL27
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 27</p>
http://lod.bco-dmo.org/id/dataset-parameter/949300.rdf
Name: NEM1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nematode</p>
http://lod.bco-dmo.org/id/dataset-parameter/949301.rdf
Name: NECU
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Nectochaete - unknown</p>
http://lod.bco-dmo.org/id/dataset-parameter/949302.rdf
Name: OPH1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Ophiuroid</p>
http://lod.bco-dmo.org/id/dataset-parameter/949303.rdf
Name: OST1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Ostracod</p>
http://lod.bco-dmo.org/id/dataset-parameter/949304.rdf
Name: POL1
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/949305.rdf
Name: POL2
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/949306.rdf
Name: POL3
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/949307.rdf
Name: POL4
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 4</p>
http://lod.bco-dmo.org/id/dataset-parameter/949308.rdf
Name: POL5
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 5</p>
http://lod.bco-dmo.org/id/dataset-parameter/949309.rdf
Name: POL6
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 6</p>
http://lod.bco-dmo.org/id/dataset-parameter/949310.rdf
Name: POL7
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 7</p>
http://lod.bco-dmo.org/id/dataset-parameter/949311.rdf
Name: POL8
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 8</p>
http://lod.bco-dmo.org/id/dataset-parameter/949312.rdf
Name: POL9
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 9</p>
http://lod.bco-dmo.org/id/dataset-parameter/949313.rdf
Name: POL11
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 11</p>
http://lod.bco-dmo.org/id/dataset-parameter/949314.rdf
Name: POL12
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 12</p>
http://lod.bco-dmo.org/id/dataset-parameter/949315.rdf
Name: POL15
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 15</p>
http://lod.bco-dmo.org/id/dataset-parameter/949316.rdf
Name: POL16
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete Type 16</p>
http://lod.bco-dmo.org/id/dataset-parameter/949317.rdf
Name: POLU
Units: unitless
Description: <p>Counts for each colonist morphotype from each sandwich: Polychaete - unknown</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
4599
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/add97705-56d3-48a8-9baa-683aa8ff9229/content
download
https://doi.org/10.26008/1912/bco-dmo.949181.1
download
onLine
dataset
<p><strong>Study site and experiment details</strong></p>
<p>A short-term in-situ colonization experiment was conducted at Tica Vent (9°50.3987 N, 104°17.4970 W) in the 9°50’ N region of the EPR. Colonization surfaces, comprised of 6 stacked polycarbonate plates separated by spacers and termed “sandwiches” (described by Mullineaux et al., 2010 and Dykman et al., 2021), were deployed by the deep submergence vehicles HOV Alvin and ROV Jason over two cruises; one aboard the R/V Atlantis in December 2019 and the other on the R/V Roger Revelle in March-April 2021.</p>
<p>During the first deployment in December 2019, 12 sandwiches were covered in 200 µm nylon mesh bags termed “purses” to prevent animal colonization while allowing for microbial biofilm development. The purses were custom designed with handles and completely enclosed around the sandwich with hook and loop fasteners so that they could be removed in-situ by vehicle manipulators (L. Lavigne, Anacortes, WA). Four replicate “pursed sandwiches” were placed within each of three biogenic zones (<em>Alvinella</em>-dominated, <em>Riftia</em>-dominated, and mussel-dominated) that span a gradient of temperature and chemical conditions. The colonization experiment was initiated when the ROV Jason revisited the pursed sandwiches approximately 15 months later. Several pursed sandwiches (3 from the Alvinellid zone and 2 from the <em>Riftia</em> zone) were lost due to overgrowth by animal communities, resulting in the discovery of 7 of the initial 12 pursed sandwiches. For the 7 pursed sandwiches that were discovered, purses were removed, and the established biofilm sandwiches were placed back in the location they had been found. Fresh sandwiches (no previously developed biofilm) were deployed next to each of the 7 established biofilm sandwiches to act as paired controls. The sandwiches were left on the seafloor for approximately 15 days to allow for animal colonization. After which, they were recovered into separate sealed collection compartments on the ROV Jason.</p>
<p>Although most sandwiches were brought to the surface before preservation, one established biofilm sandwich from each zone (including the only established biofilm sandwich in the Alvinellid zone) was recovered into individual cylinders specifically designed for immediate preservation of samples in-situ (Analytical Instrument Systems, Ringoes, NJ) that were filled with an RNA stabilization solution (25 mM sodium citrate, 10 mM EDTA, 70 g ammonium sulfate per 100 mL solution, adjusted to pH 7.0 with sulfuric acid); preservation in the RNA stabilization buffer makes these samples available for other work not reported here. A temperature probe held at the base of each sandwich for approximately 1-2 minutes was used to record the temperature maximum at deployments and recoveries of all sandwiches.</p>
<p><strong>Shipboard preservation and processing of sandwiches</strong></p>
<p>Upon vehicle recovery, containers holding sandwiches were transported to a cold room (4 °C). Attached weights and polypropylene handles were removed and the zipties holding each sandwich together were cut to remove the top sandwich plate. Any animals visible on the top plate were gently removed and placed into a separate container filled with RNA preservative. The top plate was then placed into a plastic bag with enough RNA preservative to cover the entire plate and frozen at -80 °C until further processing for 16S rRNA gene sequencing (not included in the dataset here). The remaining parts of the sandwich were placed into separate plastic bags, submerged in RNA preservative, and stored at 4 °C until further processing for animal colonization. To collect any fauna that had fallen off the sandwiches, seawater or RNA preservative in the sandwich collection compartments was poured and rinsed over a 63 µm mesh sieve, then stored in RNA preservative at 4 °C until further processing.</p>
<p><strong>Characterizing animal colonist communities</strong></p>
<p>At Western Washington University’s Shannon Point Marine Center (SPMC) faunal colonists from each sandwich were observed and counted under a stereo microscope (Olympus) at 4x magnification. Both sides of each sandwich plate were carefully inspected under a microscope and attached organisms were removed and counted. Additionally, any organisms in the RNA stabilization solution in the containers holding the sandwich plates and sieved sandwich compartment contents were sorted and counted. Individual colonists were grouped into morphotypes based on visual features while any damaged organisms that could not be assigned to a morphotype group were grouped into a broad unknown taxonomic group (e.g., unknown polychaete, unknown gastropod, etc.). Representative organisms from morphotype groups were imaged on either a stereo microscope (Leica; magnification range 0.8-10x) or a compound microscope (Leica; 20x magnification) for possible further taxonomic identification and to create a morphotype guide (See supplemental files: RR2102_morphotype_guide.pdf).</p>
Specified by the Principal Investigator(s)
- Imported "RR2102_colonist_counts.csv" into BCO-DMO system
- Converted deployment, purse recovery, and recovery dates into ISO 8601 format: YYYY-MM-DD HH:MM
- Renamed fields to conform with BCO-DMO naming conventions
- Saved the file as "949181_v1_colonization_exp_tica_vent.csv"
Scientific names in the supplemental files were checked using World Register of Marine Species (WoRMS) Taxon Match. All scientific names in the data are valid and accepted names as of 2025-02-07.
Both "RR2102_morphotype_guide.pdf" and "Morphcode_info.csv" have been attached as supplemental files. The file "RR2102_morphotype_guide.pdf" provides a visual guide of the morphotypes and the "Morphcode_info.csv" file provides the textual information in a structured table.
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
HOV Alvin, Heat Flow Probes (temperature sensors)
HOV Alvin, Heat Flow Probes (temperature sensors)
PI Supplied Instrument Name: HOV Alvin, Heat Flow Probes (temperature sensors) PI Supplied Instrument Description:Deployment and recovery of sandwiches utilized deep submergence vehicles HOV Alvin and ROV Jason.
Heat Flow Probes (temperature sensors): used to measure maximum temperatures below sandwiches on both HOV Alvin and ROV Jason during the colonization experiment, measurable temperature range is 0 to 40 °C, with 0.2 degree accuracy and .001 degree resolution. Additionally, a temperature pulse can be generated and monitored to observe temperature decay in sediments. Data from the heat flow probe is normally displayed on the observer’s internal video overlays and is additionally recorded in the submersible’s computer data files. Instrument Name: HOV Alvin Instrument Short Name: Instrument Description: Human Occupied Vehicle (HOV) Alvin is part of the National Deep Submergence Facility (NDSF). Alvin enables in-situ data collection and observation by two scientists to depths reaching 6,500 meters, during dives lasting up to ten hours.
Commissioned in 1964 as one of the world’s first deep-ocean submersibles, Alvin has remained state-of-the-art as a result of numerous overhauls and upgrades made over its lifetime. The most recent upgrades, begun in 2011 and completed in 2021, saw the installation of a new, larger personnel sphere with a more ergonomic interior; improved visibility and overlapping fields of view; longer bottoms times; new lighting and high-definition imaging systems; improved sensors, data acquisition and download speed. It also doubled the science basket payload, and improved the command-and-control system allowing greater speed, range and maneuverability.
With seven reversible thrusters, it can hover in the water, maneuver over rugged topography, or rest on the sea floor. It can collect data throughout the water column, produce a variety of maps and perform photographic surveys. Alvin also has two robotic arms that can manipulate instruments, obtain samples, and its basket can be reconfigured daily based on the needs of the upcoming dive.
Alvin's depth rating of 6,500m gives researchers in-person access to 99% of the ocean floor. Alvin is a proven and reliable platform capable of diving for up to 30 days in a row before requiring a single scheduled maintenance day. Recent collaborations with autonomous vehicles such as Sentry have proven extremely beneficial, allowing PIs to visit promising sites to collect samples and data in person within hours of their being discovered, and UNOLs driven technological advances have improved the ability for scientific outreach and collaboration via telepresence
Alvin is named for Allyn Vine, a WHOI engineer and geophysicist who helped pioneer deep submergence research and technology.
(from https://www.whoi.edu/what-we-do/explore/underwater-vehicles/hov-alvin/, accessed 2022-09-09)
Heat Flow Probes
Heat Flow Probes
PI Supplied Instrument Name: Heat Flow Probes PI Supplied Instrument Description:Heat Flow Probes (temperature sensors): used to measure maximum temperatures below sandwiches on both HOV Alvin and ROV Jason during the colonization experiment, measurable temperature range is 0 to 40 °C, with 0.2 Instrument Name: HOV Alvin Heatflow Probe 0.66m Instrument Short Name:Alvin Heatflow Probe 0.66m Instrument Description: The Heatflow probe is a temperature measuring device on the submersible Alvin. It is a 0.6 m titanium tube containing a linear heater and 5 thermistors. The Heatflow probe is designed to measure temperature gradients when inserted into soft sediments.
Heat Flow Probe (from https://ndsf.whoi.edu/alvin/systems/)
Alvin has a 0.6-meter long, five-element temperature sensor. This is used to measure temperature gradients when inserted into soft sediments. Measurable temperature range is 0 to 40 °C, with 0.2 degree accuracy and .001 degree resolution. Additionally, a temperature pulse can be generated and monitored to observe temperature decay in sediments. Data from the heat flow probe is normally displayed on the observer's internal video overlays and is additionally recorded in the submersible's computer data files. Water weight is 4 lbs, and basket space is required to carry the unit and quiver. Community Standard Description: http://vocab.nerc.ac.uk/collection/P10/current/GI000949/
In-situ RNA preservation samplers
In-situ RNA preservation samplers
PI Supplied Instrument Name: In-situ RNA preservation samplers PI Supplied Instrument Description:In-situ RNA preservation samplers: cylinders filled with RNA preservative specifically designed for use with vehicle manipulators (Analytical Instrument Systems, Ringoes, NJ) Instrument Name: In-situ RNA preservation sampler (Analytical Instrument Systems) Instrument Short Name: Instrument Description: The in-situ RNA preservation sampler is a cylindrical instrument, developed by Analytical Instrument Systems (Ringoes, NJ), that is filled with RNA stabilization solution and specifically designed for use with vehicle manipulators to preserve biofilm samples in situ. The sampler was first described in Ladd et al., 2024 (doi: 10.1016/j.dsr.2024.104314).
Olympus SZ stereo microscope
Olympus SZ stereo microscope
PI Supplied Instrument Name: Olympus SZ stereo microscope PI Supplied Instrument Description:Olympus SZ stereo microscope: used to count and identify fauna associated with sandwiches Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Leica M125 stereo microscope
Leica M125 stereo microscope
PI Supplied Instrument Name: Leica M125 stereo microscope PI Supplied Instrument Description:Leica M125 stereo microscope: used to image fauna (magnification range 0.8-10x) Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Leica DM5500 B compound microscope
Leica DM5500 B compound microscope
PI Supplied Instrument Name: Leica DM5500 B compound microscope PI Supplied Instrument Description:Leica DM5500 B compound microscope: used to image fauna (magnification range 5-40x) Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
ROV Jason, Heat Flow Probes (temperature sensors)
ROV Jason, Heat Flow Probes (temperature sensors)
PI Supplied Instrument Name: ROV Jason, Heat Flow Probes (temperature sensors) PI Supplied Instrument Description:Deployment and recovery of sandwiches utilized deep submergence vehicles HOV Alvin and ROV Jason.
Heat Flow Probes (temperature sensors): used to measure maximum temperatures below sandwiches on both HOV Alvin and ROV Jason during the colonization experiment, measurable temperature range is 0 to 40 °C, with 0.2 degree accuracy and .001 degree resolution. Additionally, a temperature pulse can be generated and monitored to observe temperature decay in sediments. Data from the heat flow probe is normally displayed on the observer’s internal video overlays and is additionally recorded in the submersible’s computer data files. Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument Description: The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL. https://ndsf.whoi.edu/jason/
Cruise: AT42-21
AT42-21
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT42-21
Jason B. Sylvan
Texas A&M University
Cruise: RR2102
RR2102
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR2102
Daniel Fornari
Woods Hole Oceanographic Institution
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel