http://lod.bco-dmo.org/id/dataset/989909
eng; USA
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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.
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2025-12-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Rates of methanogenesis in subsurface sediments from R/V JOIDES Resolution IODP-385 drilling expedition in the Guaymas Basin between September and November, 2019
2025-12-03
publication
2025-12-03
revision
BCO-DMO Linked Data URI
2025-12-03
creation
http://lod.bco-dmo.org/id/dataset/989909
Samantha B. Joye
University of Georgia
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: Joye, S. B. (2025) Rates of methanogenesis in subsurface sediments from R/V JOIDES Resolution IODP-385 drilling expedition in the Guaymas Basin between September and November, 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-12-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/989909 [access date]
Guaymas Basin Leg 385 Methanogenesis Rates Dataset Description: <p><strong>Study Results</strong></p>
<p>Thermodynamic calculations and C1/C2+ ratios indicated that methane in the relatively cooler, shallower layers, was predominantly of biogenic origin. Radiotracer experiments provided direct evidence for the coexistence of multiple methanogenic pathways, hydrogenotrophic, acetoclastic, and methylotrophic, across the sediment column. Methanogenic activity from multiple methanogenic pathways occurred over a wide temperature range (3°C to 80°C), highlighting the unexpectedly high metabolic versatility of methanogens in deep, thermally heated sediments. High methanogenesis rates were detected in near-surface sediments driven predominantly by methylotrophic methanogenesis, followed by hydrogenotrophic pathways. However, these rates declined sharply with depth, particularly within the 40–60°C interval, indicating a transition from mesophilic to thermophilic microbial communities, due to rising temperatures, reductions in gene expression, and decreasing microbial cell densities. Methylotrophic methanogenesis remained detectable down to 320 meters below the seafloor and was the dominant methane-producing pathway at temperatures up to 60°C. In sediments increasingly influenced by sill intrusions, hydrogenotrophic and acetoclastic methanogenesis became the predominant modes of methane production.</p>
<p>Methanogenic activity rates from multiple substrates at 80°C were comparable to rates in near-surface sediments. This deep, hot activity is attributed to the presence of active microbial biomass and the enhanced reactivity and bioavailability of organic matter in deep, hydrothermally-heated sediments, which provided abundant substrates for methanogenesis.&nbsp;These findings expand the current understanding of methanogenesis in the deep biosphere and reveal the discovery of the contemporaneous activity of multiple methanogenic pathways in deep, hydrothermally-influenced sediments.&nbsp;</p>
<p>See related datasets for all data referenced in these findings.</p> Methods and Sampling: <p>Subsurface sediment samples were collected from four drilling sites in the Guaymas Basin, Gulf of California, during IODP Expedition 385 “Guaymas Basin Tectonics and Biosphere” using the research vessel R/V JOIDES Resolution. Rates of methanogenesis were determined at four sites. Sites 1545 (27º38.230’N, 111º53.329’W) and 1546 (27º37.884’N, 111º52.781’W) were located roughly 52 km and 51 km, respectively, northwest of the axial graben of the northern spreading segment. Both sites are highly sedimented and a 75-meter thick inactive (~thermally equilibrated) basaltic/doleritic/gabbroic sill was present at site 1546 between ~355 to 431 meters below the seafloor (mbsf). Site U1545 is considered a reference site since it was free of sill intrusions and unaffected by active hydrothermal circulation. Samples to determine methanogenesis rates were collected from the "B" hole at every site (during IODP expeditions, several, closely-spaced holes are drilled at each site so that sufficient sediment is available for all of the proposed work.</p>
<p>The geothermal gradient at hole U1545B was 227ºC/km. The geothermal gradient at site U1546B was similar to that measured in hole U1545B, 221ºC/km, since the sill at 1546B was thermally equilibrated. Sites U1547 (27º30.413’N, 111º40.734’W) was located inside the periphery of an active, sill-associated hydrothermal mound located about 27 km northwest of the axial graben of the northern spreading segment. Temperatures in hole U1547B exceeded 50°C in the upper 50 mbsf. The geothermal gradient at this site was between 511ºC to 960ºC/km. Site U1549 was located near a cold seep sustained by a deeply buried, thermally equilibrated sill intrusion at several hundred meters depth. The geothermal gradient at hole U1549B was 194ºC/km.</p>
<p>Sediment samples were collected using an advanced piston coring system (APC) and a half-length APC (Teske et al. 2021). After retrieval on deck, sediment cores were sectioned in a designated core cutting area. Approximately 0.5 cm of the outer sediment layer was carefully removed to minimize potential contamination. For analysis of hydrocarbon gases, ~ 5 mL sediment was transferred into 21.5 mL clean, pre-combusted glass vials using a cut-off syringe. The vials were sealed immediately with polytetrafluoroethylene septa and aluminum caps and were incubated for 30 min at 70°C to allow dissolved hydrocarbon gases to equilibrate with the headspace before analysis, as described in Teske et al. (2021). For molecular hydrogen analysis, duplicate 3 mL sediment samples were collected immediately after core recovery using a cut-off syringe. The subsample was transferred into 21.5 mL glass vials and incubated and processed according to the procedures of Lin et al. (2012).</p>
<p>Whole round core (WRC) segments for methanogenic activity measurements were cut from cores retrieved from hole B at each site and stored temporarily in a nitrogen-filled glove bags until processing in the radioisotope tracer isolation space on the R/V JOIDES Resolution. Manipulation of samples for rate measurements were carried out in an anaerobic chamber (95:5 [V/V] N2:H2) to prevent oxygen contamination. Methanogenesis rate assays were carried using modifications of our previous methods (Bowles et al. 2011, Zhuang et al. 2018, Zhuang et al. 2019); the modifications increased the sensitivity of the rate measurements. Replicates for each sample were prepared in quadruplicate (three live and one killed control) for each substrate by transferring 5 cm<sup>3</sup> of sediment from the inner-most part of a whole round core into a modified cut-end Hungate tube (Bellco Glass, 2407-00125) using a sterile cut-end syringe inside an anaerobic chamber (95%:5%, N<sub>2</sub>:H<sub>2</sub>). The headspace was removed by inserting a modified butyl rubber stopper (Bellco Glass, 2048-11800A) into the cut-end of the tube, and then a septum (Bellco Glass, 2047-11600) and screw cap (Bellco Glass, 2047-16000) were placed on top of the tube to seal the sample. All vials, stoppers, and septa were autoclaved and stored anoxically prior to use as described by Zhuang et al. (2019).</p>
<p>Replicate and control samples were injected with 100 μL of <sup>14</sup>C -labeled substrate (American Radiolabeled Chemicals, Inc.). Radiotracer stocks were diluted into pH-adjusted (pH-7) milliQ water to achieve the target activity in a 100 µL injection, which was 390 to 427 kBq for <sup>2-14</sup>C-acetate, 637 to 1286 for <sup>14</sup>C-bicarbonate, 427 to 451 kBq for <sup>14</sup>C-formate, 417 to 3294 kBq for <sup>14</sup>C-methanol, or 155 to 375 kBq for <sup>14</sup>C-methylamine. Prior to the addition of radiotracer, the killed control samples were amended with 4 mL of helium-purged 2M NaOH and homogenized using a vortex. Live and killed samples were incubated for 2-4 weeks at 1 atmosphere and temperatures near <em>in situ </em>values (within 10°C of <em>in situ</em> temperature). The live incubations were terminated by adding 4 mL of helium-purged 2M NaOH and homogenizing samples using a vortex. All samples were stored at room temperature for shore-based processing and analysis in the University of Georgia laboratory.</p>
<p>Methanogenic activity was determined by converting the <sup>14</sup>C-CH<sub>4</sub> produced within each sample to <sup>14</sup>C-CO<sub>2</sub> via combustion at 850°C using a copper oxide catalyst and trapping the evolved <sup>14</sup>C-CO<sub>2</sub>. For each sample, both atmospheric air and 100 μL of ultra-high purity <sup>12</sup>C-CH<sub>4</sub> were added to generate a headspace and serve as a carrier, respectively. The produced <sup>14</sup>C-CH<sub>4</sub> was driven into the headspace by vortexing the samples and <sup>14</sup>C-CH<sub>4</sub>was removed from the sample by flushing the headspace with 5% O<sub>2</sub> in a balance of N<sub>2</sub> for 1 hour. Carry-over of <sup>14</sup>C-labeled organic substrates or<sup> </sup>carbon dioxide during <sup>14</sup>C-CH<sub>4 </sub>recovery would inflate the calculated rates, the carrier gas stream from the sample was purified through a series of substrate-dependent traps between exiting the sample vial and entering the combustion oven. The two parent tracer traps for bicarbonate, acetate, and formate consisted of 2M NaOH in saturated NaCl (trap 1) and NaOH pellets (trap 2). The three parent tracer traps for methylamine consisted of 1M H<sub>2</sub>SO<sub>4</sub> (trap 1), 2M NaOH in saturated NaCl (trap 2), and NaOH pellets (trap 3). The four parent tracer traps for methanol were immersed in an ice bath and consisted of 1M NaOH (trap 1), 2M NaOH in saturated NaCl (trap 2), NaOH pellets (trap 3), and silica gel (trap 4). Extra traps were required for methanol due to its inherent volatility.</p>
<p>Downstream of the combustion oven, the evolved <sup>14</sup>C-CO<sub>2</sub> was collected in a trap of 1.5 mL of 3-methoxypropylamine (Thermo Scientific, 99% purity, catalog number #AAB24095AU) and 4 mL of scintillation cocktail (Research Products International, Bio-SafeII, catalog number 111195) after passing through an empty trap that was in place to eliminate sample backflow into the combustion column. After one hour, the content of the final trap was transferred to a 7 mL scintillation vial and the <sup>14</sup>C-activity was quantified using a liquid scintillation counter. Recovery tests with <sup>14</sup>C-CH<sub>4</sub> showed that we recovered <u>&gt;</u> 90% of the known activity of added. Blanks (empty tubes) were included in each sample set served to identify any carryover or contamination between runs.</p>
<p>The rate of <sup>14</sup>C-substrate turnover to <sup>14</sup>C-methane, the turnover constant, <em>k</em>, was calculated using the activity of the produced methane (<sup>14</sup>C-CH<sub>4</sub>; disintegrations per minute (dpm)), the activity of the substrate added to the sample (<sup>14</sup>C-substrate; dpm), and the incubation period (t; days) (Equation 1). Potential rates of methanogenesis (pmol cm<sup>-3</sup> day<sup>-1</sup>) were calculated using the equation below, where the turnover constant <em>k</em> (day<sup>-1</sup>) was multiplied by the porosity-corrected substrate concentration in nmol cm<sup>-3</sup> wet sediment which was derived from multiplying the substrate concentration, nmol mL<sup>-1</sup>, by the water content, mL water cm<sup>-3</sup> wet sediment, assuming that the mass of water in grams is equivalent to its volume in mL or cm<sup>-3</sup>, and the isotopic fractionation factor, α. The following fractionation factors were used: 1.02 for acetate; 1.04 for bicarbonate; 1.07 for methanol; 1.06 for methylamine; 1.02 for formate) were used (Krzycki et al. 1987, Summons et al. 1998, Whiticar 1999). A factor of 1000 was applied to convert the rate from nmol cm<sup>-3</sup> day<sup>-1</sup> to pmol cm<sup>-3</sup> day<sup>-1</sup>.&nbsp;Equation 1:</p>
<blockquote>
<p>Methanogenesis rate (pmol cm<sup>-3</sup> d<sup>-1</sup>) =<br />
turnover constant (d<sup>-1</sup>) x [substrate] (nmol cm<sup>-3</sup>) x α x 1000 (pmol nmol<sup>-1</sup>)</p>
</blockquote>
<p>Sample counts were corrected for the killed control by subtracting the minimum detectable dpm (average dpm of killed controls plus three times the standard deviation of the killed controls, dpm) from the measured <sup>14</sup>C-CH<sub>4</sub> activity (dpm) of each live sample. Samples with <sup>14</sup>C-CH<sub>4</sub> activity (dpm) less than the minimum detectable dpm were considered to be below the detection limit.&nbsp;</p>
<p>The <strong>detection limits for the different methanogenesis rates</strong> were: 1.26 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for H<sub>2</sub>/CO<sub>2</sub>, 0.05 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for acetate, 0.01pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for formate, 0.03 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup>for methanol, and 0.01 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for methylamine.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023575 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023575
onGoing
Samantha B. Joye
University of Georgia
706-542-5893
Dept. of Marine Sciences 325 Sanford Drive
Athens
GA
30602
USA
mjoye@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Site
Hole
Latitude
Longitude
Water_Depth
Sediment_Depth
H2_CO2_1
H2_CO2_1_flag
H2_CO2_2
H2_CO2_2_flag
H2_CO2_3
H2_CO2_3_flag
Acetate_1
Acetate_1_flag
Acetate_2
Acetate_2_flag
Acetate_3
Acetate_3_flag
Formate_1
Formate_1_flag
Formate_2
Formate_2_flag
Formate_3
Formate_3_flag
Methanol_1
Methanol_1_flag
Methanol_2
Methanol_2_flag
Methanol_3
Methanol_3_flag
Methylamine_1
Methylamine_1_flag
Methylamine_2
Methylamine_2_flag
Methylamine_3
Methylamine_3_flag
Advanced piston coring system (APC)
incubator
Liquid scintillation counter
vortex
theme
None, User defined
site
latitude
longitude
depth
depth below seafloor
No BCO-DMO term
quality flag
featureType
BCO-DMO Standard Parameters
Advanced Piston Corer
Incubator
Liquid Scintillation Counter
vortex mixer
instrument
BCO-DMO Standard Instruments
IODP-385
service
Deployment Activity
Guaymas Basin 27 N 111 W
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.
Pathways and regulation of transformation of low molecular weight carbon compounds in subseafloor sediments from the Guaymas Basin (Gulf of California)
https://osprey.bco-dmo.org/project/853204
Pathways and regulation of transformation of low molecular weight carbon compounds in subseafloor sediments from the Guaymas Basin (Gulf of California)
<p><em>NSF Award Abstract:</em><br />
This research will explore carbon cycling in one of the largest carbon reservoirs on Earth, marine sediments, located at bottom of the ocean. This carbon is recycled gradually over time through interacting geological, chemical, and biological processes. This project will document how each of these processes transforms carbon in marine sediments from the Guaymas Basin (Gulf of California). This setting offers the chance to study carbon cycling across a broad range of chemical and temperature gradients, providing an opportunity to tease apart the factors regulating carbon cycling in marine sediments. This project will investigate the role of ocean sediments in the global carbon cycle. These research objectives represent key science priorities in a time of global environmental change. For outreach activities, the scientist, in collaboration with Jim Toomey Education, would continue the "Adventures of Zack and Molly" educational video series. In this instance, the video would document results from this study and its broader significance. The scientist also would create a learning guide for teachers. Both the video and the learning guide would be disseminated to educators. One graduate and one undergraduate student would be supported and trained as part of this project.</p>
<p>Subsurface sediments in the Guaymas Basin (Gulf of California) offer an accessible window for investigating carbon cycling in a dynamic, yet tractable, marine environment. This work will study how heating of subsurface sediments affects the production, consumption, and fate of low molecular weight dissolved organic carbon. The research will track the fate of key carbon species – including formate, acetate, and methanol – as they are processed through a gauntlet of microbial-mediated processes. Samples were collected during Expedition 385 of the International Ocean Discovery Program in September-October 2019. Some experiments were conducted on the research vessel and additional experiments will be conducted in the laboratory. The study will constrain the magnitudes of transformation and the fate of low molecular weight carbon substrates using a combination of direct rate, pool size, and stable isotopic measurements coupled to thermodynamic modeling and probative laboratory experiments. Key topics for investigation include: (1) What is the dominant production mode for organic compounds in subsurface sediments? (2) What are the dominant pathways of methanogenesis along geochemical and temperature gradients? (3) What are the temperature limits of microbially-driven carbon cycling processes? (4) How does the fate of organic compounds change along geochemical and/or temperature gradients?</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>
Guaymas Basin Sediments
largerWorkCitation
project
eng; USA
oceans
Guaymas Basin 27 N 111 W
-111.889
-111.48
27.472
27.637
2019-09-15
2019-11-15
Guaymas Basin (Gulf of California)
0
BCO-DMO catalogue of parameters from Rates of methanogenesis in subsurface sediments from R/V JOIDES Resolution IODP-385 drilling expedition in the Guaymas Basin between September and November, 2019
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/996150.rdf
Name: Site
Units: unitless
Description: <p>Site name</p>
http://lod.bco-dmo.org/id/dataset-parameter/996151.rdf
Name: Hole
Units: unitless
Description: <p>Hole Designation (A, B, C)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996152.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling latitude, North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/996154.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling longitude, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/996156.rdf
Name: Water_Depth
Units: m
Description: <p>Water column depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/996158.rdf
Name: Sediment_Depth
Units: mbsf
Description: <p>Depth below the seafloor in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/996159.rdf
Name: H2_CO2_1
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from H2/CO2 - replicate 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996160.rdf
Name: H2_CO2_1_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996161.rdf
Name: H2_CO2_2
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from H2/CO2 - replicate 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996162.rdf
Name: H2_CO2_2_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996163.rdf
Name: H2_CO2_3
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from H2/CO2 - replicate 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996164.rdf
Name: H2_CO2_3_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996165.rdf
Name: Acetate_1
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from acetate - replicate 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996166.rdf
Name: Acetate_1_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996167.rdf
Name: Acetate_2
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from acetate - replicate 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996168.rdf
Name: Acetate_2_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996169.rdf
Name: Acetate_3
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from acetate - replicate 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996170.rdf
Name: Acetate_3_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996171.rdf
Name: Formate_1
Units: pmol cm⁻³ d⁻¹
Description: <p>methanogenesis rate from formate - replicate 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996172.rdf
Name: Formate_1_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996173.rdf
Name: Formate_2
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from formate - replicate 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996174.rdf
Name: Formate_2_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996175.rdf
Name: Formate_3
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from formate - replicate 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996176.rdf
Name: Formate_3_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996177.rdf
Name: Methanol_1
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methanol - replicate 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996178.rdf
Name: Methanol_1_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996179.rdf
Name: Methanol_2
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methanol - replicate 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996180.rdf
Name: Methanol_2_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996181.rdf
Name: Methanol_3
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methanol - replicate 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996182.rdf
Name: Methanol_3_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996183.rdf
Name: Methylamine_1
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methylamine - replicate 1</p>
http://lod.bco-dmo.org/id/dataset-parameter/996184.rdf
Name: Methylamine_1_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996185.rdf
Name: Methylamine_2
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methylamine - replicate 2</p>
http://lod.bco-dmo.org/id/dataset-parameter/996186.rdf
Name: Methylamine_2_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</p>
http://lod.bco-dmo.org/id/dataset-parameter/996187.rdf
Name: Methylamine_3
Units: pmol cm⁻³ d⁻¹
Description: <p>Methanogenesis rate from methylamine - replicate 3</p>
http://lod.bco-dmo.org/id/dataset-parameter/996188.rdf
Name: Methylamine_3_flag
Units: unitless
Description: <p>Flag to indicate sample status; n.s. = no sample available for this substrate; L = sample lost during processing; BDL = below the detection limit</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
https://osprey.bco-dmo.org/dataset/989909/data/download
download
onLine
dataset
<p>Subsurface sediment samples were collected from four drilling sites in the Guaymas Basin, Gulf of California, during IODP Expedition 385 “Guaymas Basin Tectonics and Biosphere” using the research vessel R/V JOIDES Resolution. Rates of methanogenesis were determined at four sites. Sites 1545 (27º38.230’N, 111º53.329’W) and 1546 (27º37.884’N, 111º52.781’W) were located roughly 52 km and 51 km, respectively, northwest of the axial graben of the northern spreading segment. Both sites are highly sedimented and a 75-meter thick inactive (~thermally equilibrated) basaltic/doleritic/gabbroic sill was present at site 1546 between ~355 to 431 meters below the seafloor (mbsf). Site U1545 is considered a reference site since it was free of sill intrusions and unaffected by active hydrothermal circulation. Samples to determine methanogenesis rates were collected from the "B" hole at every site (during IODP expeditions, several, closely-spaced holes are drilled at each site so that sufficient sediment is available for all of the proposed work.</p>
<p>The geothermal gradient at hole U1545B was 227ºC/km. The geothermal gradient at site U1546B was similar to that measured in hole U1545B, 221ºC/km, since the sill at 1546B was thermally equilibrated. Sites U1547 (27º30.413’N, 111º40.734’W) was located inside the periphery of an active, sill-associated hydrothermal mound located about 27 km northwest of the axial graben of the northern spreading segment. Temperatures in hole U1547B exceeded 50°C in the upper 50 mbsf. The geothermal gradient at this site was between 511ºC to 960ºC/km. Site U1549 was located near a cold seep sustained by a deeply buried, thermally equilibrated sill intrusion at several hundred meters depth. The geothermal gradient at hole U1549B was 194ºC/km.</p>
<p>Sediment samples were collected using an advanced piston coring system (APC) and a half-length APC (Teske et al. 2021). After retrieval on deck, sediment cores were sectioned in a designated core cutting area. Approximately 0.5 cm of the outer sediment layer was carefully removed to minimize potential contamination. For analysis of hydrocarbon gases, ~ 5 mL sediment was transferred into 21.5 mL clean, pre-combusted glass vials using a cut-off syringe. The vials were sealed immediately with polytetrafluoroethylene septa and aluminum caps and were incubated for 30 min at 70°C to allow dissolved hydrocarbon gases to equilibrate with the headspace before analysis, as described in Teske et al. (2021). For molecular hydrogen analysis, duplicate 3 mL sediment samples were collected immediately after core recovery using a cut-off syringe. The subsample was transferred into 21.5 mL glass vials and incubated and processed according to the procedures of Lin et al. (2012).</p>
<p>Whole round core (WRC) segments for methanogenic activity measurements were cut from cores retrieved from hole B at each site and stored temporarily in a nitrogen-filled glove bags until processing in the radioisotope tracer isolation space on the R/V JOIDES Resolution. Manipulation of samples for rate measurements were carried out in an anaerobic chamber (95:5 [V/V] N2:H2) to prevent oxygen contamination. Methanogenesis rate assays were carried using modifications of our previous methods (Bowles et al. 2011, Zhuang et al. 2018, Zhuang et al. 2019); the modifications increased the sensitivity of the rate measurements. Replicates for each sample were prepared in quadruplicate (three live and one killed control) for each substrate by transferring 5 cm<sup>3</sup> of sediment from the inner-most part of a whole round core into a modified cut-end Hungate tube (Bellco Glass, 2407-00125) using a sterile cut-end syringe inside an anaerobic chamber (95%:5%, N<sub>2</sub>:H<sub>2</sub>). The headspace was removed by inserting a modified butyl rubber stopper (Bellco Glass, 2048-11800A) into the cut-end of the tube, and then a septum (Bellco Glass, 2047-11600) and screw cap (Bellco Glass, 2047-16000) were placed on top of the tube to seal the sample. All vials, stoppers, and septa were autoclaved and stored anoxically prior to use as described by Zhuang et al. (2019).</p>
<p>Replicate and control samples were injected with 100 μL of <sup>14</sup>C -labeled substrate (American Radiolabeled Chemicals, Inc.). Radiotracer stocks were diluted into pH-adjusted (pH-7) milliQ water to achieve the target activity in a 100 µL injection, which was 390 to 427 kBq for <sup>2-14</sup>C-acetate, 637 to 1286 for <sup>14</sup>C-bicarbonate, 427 to 451 kBq for <sup>14</sup>C-formate, 417 to 3294 kBq for <sup>14</sup>C-methanol, or 155 to 375 kBq for <sup>14</sup>C-methylamine. Prior to the addition of radiotracer, the killed control samples were amended with 4 mL of helium-purged 2M NaOH and homogenized using a vortex. Live and killed samples were incubated for 2-4 weeks at 1 atmosphere and temperatures near <em>in situ </em>values (within 10°C of <em>in situ</em> temperature). The live incubations were terminated by adding 4 mL of helium-purged 2M NaOH and homogenizing samples using a vortex. All samples were stored at room temperature for shore-based processing and analysis in the University of Georgia laboratory.</p>
<p>Methanogenic activity was determined by converting the <sup>14</sup>C-CH<sub>4</sub> produced within each sample to <sup>14</sup>C-CO<sub>2</sub> via combustion at 850°C using a copper oxide catalyst and trapping the evolved <sup>14</sup>C-CO<sub>2</sub>. For each sample, both atmospheric air and 100 μL of ultra-high purity <sup>12</sup>C-CH<sub>4</sub> were added to generate a headspace and serve as a carrier, respectively. The produced <sup>14</sup>C-CH<sub>4</sub> was driven into the headspace by vortexing the samples and <sup>14</sup>C-CH<sub>4</sub>was removed from the sample by flushing the headspace with 5% O<sub>2</sub> in a balance of N<sub>2</sub> for 1 hour. Carry-over of <sup>14</sup>C-labeled organic substrates or<sup> </sup>carbon dioxide during <sup>14</sup>C-CH<sub>4 </sub>recovery would inflate the calculated rates, the carrier gas stream from the sample was purified through a series of substrate-dependent traps between exiting the sample vial and entering the combustion oven. The two parent tracer traps for bicarbonate, acetate, and formate consisted of 2M NaOH in saturated NaCl (trap 1) and NaOH pellets (trap 2). The three parent tracer traps for methylamine consisted of 1M H<sub>2</sub>SO<sub>4</sub> (trap 1), 2M NaOH in saturated NaCl (trap 2), and NaOH pellets (trap 3). The four parent tracer traps for methanol were immersed in an ice bath and consisted of 1M NaOH (trap 1), 2M NaOH in saturated NaCl (trap 2), NaOH pellets (trap 3), and silica gel (trap 4). Extra traps were required for methanol due to its inherent volatility.</p>
<p>Downstream of the combustion oven, the evolved <sup>14</sup>C-CO<sub>2</sub> was collected in a trap of 1.5 mL of 3-methoxypropylamine (Thermo Scientific, 99% purity, catalog number #AAB24095AU) and 4 mL of scintillation cocktail (Research Products International, Bio-SafeII, catalog number 111195) after passing through an empty trap that was in place to eliminate sample backflow into the combustion column. After one hour, the content of the final trap was transferred to a 7 mL scintillation vial and the <sup>14</sup>C-activity was quantified using a liquid scintillation counter. Recovery tests with <sup>14</sup>C-CH<sub>4</sub> showed that we recovered <u>&gt;</u> 90% of the known activity of added. Blanks (empty tubes) were included in each sample set served to identify any carryover or contamination between runs.</p>
<p>The rate of <sup>14</sup>C-substrate turnover to <sup>14</sup>C-methane, the turnover constant, <em>k</em>, was calculated using the activity of the produced methane (<sup>14</sup>C-CH<sub>4</sub>; disintegrations per minute (dpm)), the activity of the substrate added to the sample (<sup>14</sup>C-substrate; dpm), and the incubation period (t; days) (Equation 1). Potential rates of methanogenesis (pmol cm<sup>-3</sup> day<sup>-1</sup>) were calculated using the equation below, where the turnover constant <em>k</em> (day<sup>-1</sup>) was multiplied by the porosity-corrected substrate concentration in nmol cm<sup>-3</sup> wet sediment which was derived from multiplying the substrate concentration, nmol mL<sup>-1</sup>, by the water content, mL water cm<sup>-3</sup> wet sediment, assuming that the mass of water in grams is equivalent to its volume in mL or cm<sup>-3</sup>, and the isotopic fractionation factor, α. The following fractionation factors were used: 1.02 for acetate; 1.04 for bicarbonate; 1.07 for methanol; 1.06 for methylamine; 1.02 for formate) were used (Krzycki et al. 1987, Summons et al. 1998, Whiticar 1999). A factor of 1000 was applied to convert the rate from nmol cm<sup>-3</sup> day<sup>-1</sup> to pmol cm<sup>-3</sup> day<sup>-1</sup>.&nbsp;Equation 1:</p>
<blockquote>
<p>Methanogenesis rate (pmol cm<sup>-3</sup> d<sup>-1</sup>) =<br />
turnover constant (d<sup>-1</sup>) x [substrate] (nmol cm<sup>-3</sup>) x α x 1000 (pmol nmol<sup>-1</sup>)</p>
</blockquote>
<p>Sample counts were corrected for the killed control by subtracting the minimum detectable dpm (average dpm of killed controls plus three times the standard deviation of the killed controls, dpm) from the measured <sup>14</sup>C-CH<sub>4</sub> activity (dpm) of each live sample. Samples with <sup>14</sup>C-CH<sub>4</sub> activity (dpm) less than the minimum detectable dpm were considered to be below the detection limit.&nbsp;</p>
<p>The <strong>detection limits for the different methanogenesis rates</strong> were: 1.26 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for H<sub>2</sub>/CO<sub>2</sub>, 0.05 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for acetate, 0.01pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for formate, 0.03 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup>for methanol, and 0.01 pmol cc⁻<sup>1</sup> day⁻<sup>1</sup> for methylamine.</p>
Specified by the Principal Investigator(s)
<p>Rate calculations are described in the methods.</p>
Specified by the Principal Investigator(s)
- Imported "OCE-2023575_Methanogenesis.csv" into the BCO-DMO system
- Replaced spaces and special characters in parameter names with an underscore
- Flag columns were generated to indicate samples marked ‘n.s.’ (no sample) or ‘L’ (sample lost); removed text from numeric fields
- Exported file as "989909_v1_iodp385_methanogenesis.csv"
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
Advanced piston coring system (APC)
Advanced piston coring system (APC)
PI Supplied Instrument Name: Advanced piston coring system (APC) PI Supplied Instrument Description:Sediment samples were collected using an advanced piston coring system (APC) and a half-length APC (Teske et al. 2021). Instrument Name: Advanced Piston Corer Instrument Short Name:APC Instrument Description: The JOIDES Resolution's Advanced Piston Corer (APC) is used in soft ooze and sediments. The APC is a hydraulically actuated piston corer designed to recover relatively undisturbed samples from very soft to firm sediments.
More information is available from IODP (PDF).
incubator
incubator
PI Supplied Instrument Name: incubator PI Supplied Instrument Description:Live and killed samples were incubated for 2-4 weeks at 1 atmosphere and temperatures near in situ values (within 10°C of in situ temperature). Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled.
Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).
Liquid scintillation counter
Liquid scintillation counter
PI Supplied Instrument Name: Liquid scintillation counter PI Supplied Instrument Description:After one hour, the content of the final trap was transferred to a 7 mL scintillation vial and the 14C-activity was quantified using a liquid scintillation counter. 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/
vortex
vortex
PI Supplied Instrument Name: vortex PI Supplied Instrument Description:Prior to the addition of radiotracer, the killed control samples were amended with 4 mL of helium-purged 2M NaOH and homogenized using a vortex. Instrument Name: vortex mixer Instrument Short Name: Instrument Description: A vortex mixer is an electrical rotator that blends or mixes substances or ingredients, in whirling or rotary motion, for homogenizing samples.
Cruise: IODP-385
IODP-385
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel
IODP-385
Andreas Teske
R/V JOIDES Resolution
Community Standard Description
International Council for the Exploration of the Sea
R/V JOIDES Resolution
vessel