http://lod.bco-dmo.org/id/dataset/820556
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
2020-08-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Bacterial production of bulk water and large volume samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic.
2020-08-12
publication
2020-08-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-09-24
publication
https://doi.org/10.26008/1912/bco-dmo.820556.1
Carol Arnosti
University of North Carolina at Chapel Hill
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: Arnosti, C. (2020) Bacterial production of bulk water and large volume samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-08-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.820556.1 [access date]
Dataset Description: <p>Bacterial production was estimated from 3H-leucine incorporation by heterotrophic bacteria using a cold trichloroacetic acid (TCA) and microcentrifuge extraction method (Kirchman, 2001).&nbsp; All work and incubations were performed in a UNOLS isotope lab.</p> Methods and Sampling: <p>Samples were collected in one of two ways:</p>
<ul>
<li>Bulk water from each station was collected by combining equal portions from three niskin bottles triggered at each depth into an acid washed glass media bottle.&nbsp;</li>
<li>After shaking, large volume (mesocosm) incubations were sampled by pouring into 500 mL acid washed glass media bottles.</li>
</ul>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1736772 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1736772
completed
Carol Arnosti
University of North Carolina at Chapel Hill
919-962-5754
Dept. of Marine Sciences 3117A Venable/Murray Hall
Chapel Hill
NC
27599-3300
USA
arnosti@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
deployment
station
latitude
longitude
date
time
cast_number
depth_sequence
depth_actual
sample_type
unammended_ammended
substrate
timepoint
time_elapsed
incorporation_rate
incorporation_rate_std_dev
ISO_DateTime_UTC
PerkinElmer Tri-Carb 2910TR LSA, PerkinElmer Tri-Carb 3110TR LSA
theme
None, User defined
Cruise identfier
station
latitude
longitude
date
time of day
cast
depth
sample description
sample time
incubation time or duration
leucine incorporation rate
standard deviation of leucine incorporation rate
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Liquid Scintillation Counter
instrument
BCO-DMO Standard Instruments
EN638
service
Deployment Activity
Northern Atlantic
place
Locations
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.
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
https://osprey.bco-dmo.org/project/809975
A mechanistic microbial underpinning for the size-reactivity continuum of dissolved organic carbon degradation
<p><em>NSF Award Abstract:</em><br />
Marine dissolved organic matter (DOM) is one of the largest actively-cycling reservoirs of organic carbon on the planet, and thus a major component of the global carbon cycle. The high molecular weight (HMW) fraction of DOM is younger in age and more readily consumed by microbes than lower molecular weight (LMW) fractions of DOM, but the reasons for this difference in reactivity between HMW DOM and LMW DOM are unknown. Two factors may account for the greater reactivity of HMW DOM: (i) targeted uptake of HMW DOM by specific bacteria, a process the PI and her collaborators at the Max Planck Institute for Marine Microbiology (MPI) recently identified in surface ocean waters; and (ii) a greater tendency of HMW DOM to aggregate and form gels and particles, which can be colonized by bacteria that are well-equipped to breakdown organic matter. Scientists and students from the University of North Carolina (UNC) - Chapel Hill will collaborate with researchers at the MPI for Marine Microbiology (Bremen, Germany) to investigate this breakdown of HMW DOM by marine microbial communities. These investigations will include a field expedition in the North Atlantic, during which HMW DOM degradation rates and patterns will be compared in different water masses and under differing conditions of organic matter availability. DOM aggregation potential, and degradation rates of these aggregates, will also be assessed. Specialized microscopy will be used in order to pinpoint HMW DOM uptake mechanisms and rates. The work will be complemented by ongoing studies of specific bacteria that breakdown HMW DOM, their genes, and their proteins. Graduate as well as undergraduate students will participate as integral members of the research team in all aspects of the laboratory and field work; aspects of the project will also be integrated into classes the scientist teaches at UNC.</p>
<p>The existence of a size-reactivity continuum of DOM - observations and measurements showing that HMW DOM tends to be younger and more reactive than lower MW DOM - has been demonstrated in laboratory and field investigations in different parts of the ocean. A mechanistic explanation for the greater reactivity of HMW DOM has been lacking, however. This project will investigate the mechanisms and measure rates of HMW DOM degradation, focusing on identifying the actors and determining the factors that contribute to rapid cycling of HMW DOM. Collaborative work at UNC and MPI-Bremen recently identified a new mechanism of HMW substrate uptake common among pelagic marine bacteria: these bacteria rapidly bind, partially hydrolyze, and transport directly across the outer membrane large fragments of HMW substrates that can then be degraded within the periplasmic space, avoiding production of LMW DOM in the external environment. This mode of substrate processing has been termed selfish, since targeted HMW substrate uptake sequesters resources away from other members of microbial communities. Measurements and models thus must account for three modes of substrate utilization in the ocean: selfish, sharing (external hydrolysis, leading to low molecular weight products), and scavenging (uptake of low molecular weight hydrolysis products without production of extracellular enzymes). Using field studies as well as mesocosm experiments, the research team will investigate the circumstances and locations at which different modes of substrate uptake predominate. A second focal point of the project is to determine the aggregation potential and microbial degradation of aggregated HMW DOM. Preliminary studies have demonstrated that particle-associated microbial communities utilize a broader range of enzymatic capabilities than their free-living counterparts. These capabilities equip particle-associated communities to effectively target a broad range of complex substrates. The project will thus focus on two key aspects of HMW DOM - the abilities of specialized bacteria to selectively sequester HMW substrates, as well as the greater potential of HMW substrates to aggregate ? and will quantify these factors at different locations and depths in the ocean. The project will thereby provide a mechanistic underpinning for observations of the DOC size-reactivity continuum, an essential part of developing an overall mechanistic understanding of organic matter degradation in the ocean.</p>
Microbial DOC Degradation
largerWorkCitation
project
eng; USA
oceans
Northern Atlantic
-75.67819
-53.3949
34.50102
42.83954
2019-05-14
2019-06-10
Northern Atlantic, Southern Indian Ocean, Svalbard
0
BCO-DMO catalogue of parameters from Bacterial production of bulk water and large volume samples taken aboard the R/V Endeavor EN638, May 2019 in the Northern Atlantic.
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/822265.rdf
Name: deployment
Units: unitless
Description: <p>Cruise ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/822266.rdf
Name: station
Units: unitless
Description: <p>Station number for cruise</p>
http://lod.bco-dmo.org/id/dataset-parameter/822267.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/822268.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/822269.rdf
Name: date
Units: unitless
Description: <p>Date of sample collection in ISO format (yyyy-mm-dd), US Eastern Time (UTC-05:00)</p>
http://lod.bco-dmo.org/id/dataset-parameter/822270.rdf
Name: time
Units: unitless
Description: <p>Time of sample collection in ISO format (hh:mm:ss), US Eastern Time (UTC-05:00)</p>
http://lod.bco-dmo.org/id/dataset-parameter/822271.rdf
Name: cast_number
Units: unitless
Description: <p>Cast number (refers to cast of CTD/Niskin bottles on cruise)</p>
http://lod.bco-dmo.org/id/dataset-parameter/822272.rdf
Name: depth_sequence
Units: unitless
Description: <p>Sequence of depths sampled (1 is surface; higher numbers at greater depths)</p>
http://lod.bco-dmo.org/id/dataset-parameter/822273.rdf
Name: depth_actual
Units: meters (m)
Description: <p>Actual depth at which water was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/822274.rdf
Name: sample_type
Units: unitless
Description: <p>Sample from bulk water or Large Volume incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/822275.rdf
Name: unammended_ammended
Units: unitless
Description: <p>Whether high molecular weight thalassiosira weissflogii extract was added or not; A, B, C refers to incubation depth, and the following number corresponds to incubation replicate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/822276.rdf
Name: substrate
Units: unitless
Description: <p>[3H] Leucine substrate added for measurement of bacterial productivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/822277.rdf
Name: timepoint
Units: unitless
Description: <p>sampling point (0, 1, 2, …) post-incubation</p>
http://lod.bco-dmo.org/id/dataset-parameter/822278.rdf
Name: time_elapsed
Units: hours (hrs)
Description: <p>Incubation time</p>
http://lod.bco-dmo.org/id/dataset-parameter/822279.rdf
Name: incorporation_rate
Units: pmol L-1 h-1
Description: <p>Average 3H-Leu (pM) incorporation/hr</p>
http://lod.bco-dmo.org/id/dataset-parameter/822280.rdf
Name: incorporation_rate_std_dev
Units: pmol L-1 h-1
Description: <p>Deviation of incorporation rates</p>
http://lod.bco-dmo.org/id/dataset-parameter/822281.rdf
Name: ISO_DateTime_UTC
Units: yyyy-MM-dd'T'HH:mm:ss'Z'
Description: <p>Datetime of sample collection in ISO format in UTC timezone (yyyy-mm-dd:hh:mm:ssZ)</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
23187
https://darchive.mblwhoilibrary.org/bitstream/1912/26219/1/dataset-820556_en638-bacterial-productivity__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.820556.1
download
onLine
dataset
<p>Samples were collected in one of two ways:</p>
<ul>
<li>Bulk water from each station was collected by combining equal portions from three niskin bottles triggered at each depth into an acid washed glass media bottle.&nbsp;</li>
<li>After shaking, large volume (mesocosm) incubations were sampled by pouring into 500 mL acid washed glass media bottles.</li>
</ul>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>To 1.5ml triplicate subsamples and one 100% (w/v) TCA -killed control 23 uL of L-[3,4,5-3H(N)]-Leucine (PerkinElmer, NET460250UC) was added and incubated between 10 and 40 hours at near in situ temperature.&nbsp; Live samples were then killed with 89 uL of 100% (w/v) TCA and centrifuged (10,000 rpm at 4°C for 10 min) to pelletize cell material.&nbsp; The supernatant liquid was removed and 1 mL of 5% (w/v) TCA solution was added followed by vortex mixing and centrifugation.&nbsp; Supernatant removal, mixing, and centrifugation were repeated using 1 mL of 80% ethanol solution.&nbsp; Again, the supernatant liquid was removed and each sample was left to dry in a hood overnight.&nbsp; After drying, 1 mL of scintillation cocktail (ScintiSafe 30% Cocktail, Fisher SX23-5) was added and incorporated radioactivity was measured using a PerkinElmer Tri-Carb 2910TR LSA scintillation counter for bulk, and PerkinElmer Tri-Carb 3110TR LSA for large volume (mesocosm) samples.&nbsp; Radioactivity was compared to 1 mL of scintillation cocktail spiked with 23 uL of L-[3,4,5-3H(N)]-Leucine radioactivity and divided by incubation time to calculate.</p>
<p>Data processing was done using excel.</p>
<p>BCO-DMO processing notes:</p>
<ul>
<li>Adjusted column names to comply with database requirements</li>
<li>Added ISO_DateTine_UTC column</li>
<li>Converted data to ISO format (yyyy-mm-dd)</li>
</ul>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
PerkinElmer Tri-Carb 2910TR LSA, PerkinElmer Tri-Carb 3110TR LSA
PerkinElmer Tri-Carb 2910TR LSA, PerkinElmer Tri-Carb 3110TR LSA
PI Supplied Instrument Name: PerkinElmer Tri-Carb 2910TR LSA, PerkinElmer Tri-Carb 3110TR LSA Instrument Name: Liquid Scintillation Counter Instrument Short Name:LSC Instrument Description: Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used to quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.
Liquid scintillation counters are instruments assaying alpha and beta radiation by quantitative detection of visible light produced by the passage of rays or particles through a suitable scintillant incorporated into the sample. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/
Cruise: EN638
EN638
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN638
Carol Arnosti
University of North Carolina at Chapel Hill
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel