| URL | https://www.bco-dmo.org/dataset/782742 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/782742/data/download |
| Media Type | text/tab-separated-values |
| Created | November 22, 2019 |
| Modified | July 14, 2020 |
| State | Final no updates expected |
Sediment samples were stored at 4°C prior to analysis. Proteinaceous material was extracted and quantified with Qubit fluorescent reagent (Life Technologies), following Estes et al. (2016) as modified from Ehrenreich and Widdel (1994).
Assay was quantified using bovine serum albumin standard (Bio-Rad).
See Estes el al. 2019, for complete methods.
BCO-DMO Data Manager Processing Notes:
* exported data in xlsx file “Estes protein data.xlsx” to csv file
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as “nd” for “no data.” nd is the default missing data identifier in the BCO-DMO system.
* latitude and longitude in degrees decimal minutes converted to decimal degrees then rounded to 5 decimal places.
* protein and prot_stdev rounded to two decimal places
* date format converted to ISO 8601 format yyyy-mm-dd
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).
Latitude
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Longitude
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Observation/sample depth below the sea surface. Units often reported as: meters, feet.
When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
Standard deviation of the content of proteinaceous material (triplicate analyses).
Protein concentration
date sample collection in ISO 8601 format yyyy-mm-dd
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
| Name | Affiliation | Contact |
|---|---|---|
| Emily R. Estes | Texas A&M University (TAMU) | ✓ |
| Colleen M. Hansel | Texas A&M University (TAMU) | ✓ |
| Amber York | Woods Hole Oceanographic Institution (WHOI) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere |
|---|---|
| Acronym | Org C Sed I |
| URL | https://www.bco-dmo.org/project/779223 |
| Created | October 16, 2019 |
| Modified | October 16, 2019 |
Abstract from the C-DEBI project page:
Minerals have recently been identified as a primary host for organic carbon (OC) within marine sediments. This strong physical and chemical carbon-mineral association is believed to reduce, and in some cases completely eliminate, the bioavailablilty of this carbon for microbial life. The paucity of information regarding the nature of this carbon-mineral association and the composition of the hosted carbon, however, precludes our ability to predict the ultimate fate of this OC and its involvement in deep subsurface life. Here, we addressed this knowledge gap by using a suite of bulk and spatially-resolved geochemical and mineralogical techniques to characterize OC-mineral associations within the deep subsurface. We characterized sediment samples collected on the 2014 North Atlantic long coring expedition (KN223) in the western subtropical North Atlantic that included three geochemically distinct long cores to a depth of 24-30 m and spanned OC-limited oxic to anoxic sediments. We find measurable and relevant OC concentrations throughout the sediment cores, that decreases linearly over ~25 meters burial depth, from ~0.15 to 0.075 mol OC/kg solid. OC within the sediments is compositionally complex on both a macro- and micro-scale, spanning a gradient of lability even at depth. Proteins are observed throughout the sediment depth profiles, where they appear to constitute a substantial fraction of the TOC. Correspondingly, a low C:N ratio is observed, consistent with proteinaceous carbon within the sediments. In sum, these findings point to a substantial mineral-hosted OC reservoir within the deep subsurface that may fuel the deep biosphere and select for protein-based heterotrophy.
| Name | Affiliation | Role |
|---|---|---|
| Colleen M. Hansel | Woods Hole Oceanographic Institution (WHOI) | Principal Investigator |
| Gariela Farfan | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Emily R. Estes | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Project Title | Geochemical controls on organic carbon quantity and quality in the deep subsurface |
|---|---|
| Acronym | Org C Sed II |
| URL | https://www.bco-dmo.org/project/779216 |
| Created | October 15, 2019 |
| Modified | October 16, 2019 |
Abstract from the C-DEBI project page:
Sediment underlying ocean gyres receives minimal input of fresh organic matter yet sustains a small but active heterotrophic microbial community. The concentration and composition of the organic carbon (OC) available to this deep biosphere however is unknown. We analyzed the content and composition of OC in pelagic sediment in order to identify mechanism(s) that dictate the balance between OC preservation and utilization by microorganisms. Sediment cores from the North Atlantic gyre (KN223), South Pacific Gyre (Knox02-RR), and Peru Basin (IODP site 1231) allowed for a global comparison and a test of how sediment lithology and redox state affect OC preservation. OC was present in low concentrations in all samples (0.01—0.61%), at depths up to 112 meters below seafloor and estimated sediment ages of up to 50 million years. Synchrotron-based near edge X-ray absorption fine structure (NEXAFS) spectroscopy was conducted on over 100 samples, one of the first applications of NEXAFS to sedimentary environments. NEXAFS revealed an OC reservoir dominated by amide and carboxylic functionalities in a scaffolding of O-alkyl and aliphatic carbons. Detection of extractable, extracellular proteins supports this composition and suggests that sedimentary OC is protein-derived. This composition was common across all sites and depths, implicating physical rather than chemical mechanisms in OC preservation on long timescales. This study thereby points to physical access rather than energy or metabolic potential as a key constraint on subsurface heterotrophic life.
| Name | Affiliation | Role |
|---|---|---|
| Emily R. Estes | Woods Hole Oceanographic Institution (WHOI) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/782736 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/782736/data/download |
| Media Type | text/tab-separated-values |
| Created | November 22, 2019 |
| Modified | July 14, 2020 |
| State | Final no updates expected |
Sediment samples were stored at 4°C prior to analysis. Organic carbon, total nitrogen, and d13C were analyzed via element-analyzer isotope ratio mass spectrometry. Prior to analysis, samples were freeze-dried and acidified to remove carbonate.
Instrument: Carlo Erba Elemental Analyzer Model 1108 and Finnegan-MAT DeltaPlus isotope ratio monitoring mass spectrometer. The instrument was calibrated and data drift-corrected with USGS-40 (L-glutamic acid) reference material and an in-house glycine standard.
See Estes el al. 2019, for complete methods.
Data was drift corrected and normalized to sample mass in Excel.
BCO-DMO Data Manager Processing Notes:
* exported data in xlsx file “Estes CN data.xlsx” to csv file
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as “nd” for “no data.” nd is the default missing data identifier in the BCO-DMO system.
* latitude and longitude in degrees decimal minutes converted to decimal degrees
* date format converted to ISO 8601 format yyyy-mm-dd
Carlo Erba Elemental Analyzer Model 1108 and Finnegan-MAT DeltaPlus isotope ratio monitoring mass spectrometer. The instrument was calibrated and data drift-corrected with USGS-40 (L-glutamic acid) reference material and an in-house glycine standard.
Carlo Erba Elemental Analyzer Model 1108 and Finnegan-MAT DeltaPlus isotope ratio monitoring mass spectrometer. The instrument was calibrated and data drift-corrected with USGS-40 (L-glutamic acid) reference material and an in-house glycine standard.
Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
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).
Latitude
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Longitude
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Observation/sample depth below the sea surface. Units often reported as: meters, feet.
When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
date sample collection in ISO 8601 format yyyy-mm-dd
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
| Name | Affiliation | Contact |
|---|---|---|
| Emily R. Estes | Texas A&M University (TAMU) | ✓ |
| Colleen M. Hansel | Texas A&M University (TAMU) | ✓ |
| Amber York | Woods Hole Oceanographic Institution (WHOI) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Elucidating the extent and composition of mineral-hosted carbon in the deep biosphere |
|---|---|
| Acronym | Org C Sed I |
| URL | https://www.bco-dmo.org/project/779223 |
| Created | October 16, 2019 |
| Modified | October 16, 2019 |
Abstract from the C-DEBI project page:
Minerals have recently been identified as a primary host for organic carbon (OC) within marine sediments. This strong physical and chemical carbon-mineral association is believed to reduce, and in some cases completely eliminate, the bioavailablilty of this carbon for microbial life. The paucity of information regarding the nature of this carbon-mineral association and the composition of the hosted carbon, however, precludes our ability to predict the ultimate fate of this OC and its involvement in deep subsurface life. Here, we addressed this knowledge gap by using a suite of bulk and spatially-resolved geochemical and mineralogical techniques to characterize OC-mineral associations within the deep subsurface. We characterized sediment samples collected on the 2014 North Atlantic long coring expedition (KN223) in the western subtropical North Atlantic that included three geochemically distinct long cores to a depth of 24-30 m and spanned OC-limited oxic to anoxic sediments. We find measurable and relevant OC concentrations throughout the sediment cores, that decreases linearly over ~25 meters burial depth, from ~0.15 to 0.075 mol OC/kg solid. OC within the sediments is compositionally complex on both a macro- and micro-scale, spanning a gradient of lability even at depth. Proteins are observed throughout the sediment depth profiles, where they appear to constitute a substantial fraction of the TOC. Correspondingly, a low C:N ratio is observed, consistent with proteinaceous carbon within the sediments. In sum, these findings point to a substantial mineral-hosted OC reservoir within the deep subsurface that may fuel the deep biosphere and select for protein-based heterotrophy.
| Name | Affiliation | Role |
|---|---|---|
| Colleen M. Hansel | Woods Hole Oceanographic Institution (WHOI) | Principal Investigator |
| Gariela Farfan | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Emily R. Estes | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Project Title | Geochemical controls on organic carbon quantity and quality in the deep subsurface |
|---|---|
| Acronym | Org C Sed II |
| URL | https://www.bco-dmo.org/project/779216 |
| Created | October 15, 2019 |
| Modified | October 16, 2019 |
Abstract from the C-DEBI project page:
Sediment underlying ocean gyres receives minimal input of fresh organic matter yet sustains a small but active heterotrophic microbial community. The concentration and composition of the organic carbon (OC) available to this deep biosphere however is unknown. We analyzed the content and composition of OC in pelagic sediment in order to identify mechanism(s) that dictate the balance between OC preservation and utilization by microorganisms. Sediment cores from the North Atlantic gyre (KN223), South Pacific Gyre (Knox02-RR), and Peru Basin (IODP site 1231) allowed for a global comparison and a test of how sediment lithology and redox state affect OC preservation. OC was present in low concentrations in all samples (0.01—0.61%), at depths up to 112 meters below seafloor and estimated sediment ages of up to 50 million years. Synchrotron-based near edge X-ray absorption fine structure (NEXAFS) spectroscopy was conducted on over 100 samples, one of the first applications of NEXAFS to sedimentary environments. NEXAFS revealed an OC reservoir dominated by amide and carboxylic functionalities in a scaffolding of O-alkyl and aliphatic carbons. Detection of extractable, extracellular proteins supports this composition and suggests that sedimentary OC is protein-derived. This composition was common across all sites and depths, implicating physical rather than chemical mechanisms in OC preservation on long timescales. This study thereby points to physical access rather than energy or metabolic potential as a key constraint on subsurface heterotrophic life.
| Name | Affiliation | Role |
|---|---|---|
| Emily R. Estes | Woods Hole Oceanographic Institution (WHOI) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/686389 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/686389/data/download |
| Media Type | text/tab-separated-values |
| Created | March 28, 2017 |
| Modified | November 12, 2017 |
| State | Final no updates expected |
| Brief Description | North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 |
All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (this dataset). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (see microbial production dataset).
Twenty ml of anaerobic saline media was added to the 30 ml sediment within each serum vial and mixed to create a sediment slurry. MPN assays were initiated on-board and were designed to quantify the abundance of viable microbial cells with specified metabolisms. Hungate tubes with synthetic marine base salts media were amended with various combinations of electron donors (acetate, peptone) and acceptors (oxygen, nitrate, and manganese(IV) oxide):
Saline basal medium was composed of (g/L): 0.2 NH4Cl, 30 NaCl, 2.8 MgCl2, 0.33 KCl, 0.3 CaCl2, 0.3 KH2PO4, 0.01 NaBr, 0.015 H3BO3, 0.02 SrCl2, 0.02 KI, 0.02 FeCl3, 0.0075 MnSO4, 0.0045 Na2WO4.2H2O, 0.003 NiCl2, 0.02 CoSO4, 0.0015 ZnSO4, 0.002 CuSO4, and 0.0015 Na2MoO4. pH was adjusted to 6.2.
In the case of anaerobic MPN assays, Hungate tubes and their contents were boiled and purged with high purity N2 for 30 min. Aerobic assay tubes were prepared in air and were not purged. MPN assays were inoculated with 1 ml of sediment slurry and were diluted using 10-fold dilutions. MPN assays were incubated for 6-12 months at room temperature and were then assayed for activity/growth. Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector. Additionally, colorimetric approaches specific to each anaerobic metabolism were used: the azo dye method (Strickland and Parsons 1968, Bull Fish Res Board Can 167:71) to detect the reduction of nitrate to nitrite and the T(4-CP)P method (Madison et al. 2011, Talanta, 84:374) to quantify production of Mn(II) from Mn(IV). Blank tubes were similarly prepared but not inoculated; these were analyzed to establish background levels of metabolites.
MPN assays were successful for all incubations using oxygen, Mn(IV) or nitrate as electron acceptors. However, the Mn(II) assay suffered from unidentified interferences in many cases. Growth as identified by CO2 accumulation was used where results of the Mn(II) assay were ambiguous. MPN results were converted to estimates of viable cell concentrations as follows. The highest dilution exhibiting evidence of growth was multiplied by the initial 1.6667-fold dilution used to make the sediment slurry. This count was considered the minimum MPN; the next higher dilution was considered the maximum MPN. For example, an assay exhibiting growth at 10^3 dilution but not at 10^4 dilution was considered to have a viable cell concentration of between 1,667-16,667 cells per cm^3 of sediment. For any subsequent calculations, such as cell turnover, the geometric mean of these values was used; e.g., 52,705 cells per cm^3 in this example case. In cases where no growth occurred at the lowest dilution or positive growth occurred at the highest dilution, MPN can only be constrained to be lower or higher than these estimates, respectively, and the MPN column is left blank.
For each electron acceptor/donor combination from each core section, the highest dilution MPN tube exhibiting growth was targeted for further culture transfers and eventual microbial identification/isolation. We have noted where PCR products were successfully obtained from these tubes, providing additional validation of the corresponding MPN result.
BCO-DMO Processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– re-formatted date to yyyy-mm-dd;
– replaced missing data with “nd”;
– replaced “R/V Knorr” with “RV_Knorr” in data.
The sediment subsamples were collected from long piston cores or shorter gravity cores.
The sediment subsamples were collected from long piston cores or shorter gravity cores.
Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector.
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Sediment thickness
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
name of the ship or vessel (See also platform.)
Core identification number or label; often used with ice, rock, sediment, or coral cores.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.
Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.
| Name | Affiliation | Contact |
|---|---|---|
| Eric Boyd | Montana State University | |
| Maximiliano J. Amenabar | Montana State University | |
| John E. Dore | Montana State University | |
| Shannon Rauch | Montana State University | |
| Shannon Rauch | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities |
|---|---|
| Acronym | Subseafloor metabolisms |
| URL | https://www.bco-dmo.org/project/676615 |
| Created | January 27, 2017 |
| Modified | February 13, 2017 |
Abstract from C-DEBI:
Deep marine sediments harbor an abundance of microbial cells that, if active, are likely to exert a strong influence on element biogeochemical cycling. Despite decades of study, our understanding of the fraction of cells that are active in situ and the metabolic processes that sustain them remain under-explored. We propose an integrated set of analyses aimed at unraveling the links between geochemical heterogeneity, cellular viability and synthesis, and metabolism along a vertical depth profile in four sediment cores collected during the North Atlantic long coring expedition. These sediment columns exhibit varying levels of organic carbon and differences in the degree of oxygen penetration along the depth profile which we hypothesize exert strong influence on the extent and nature of microbial life. Most probable number assays containing nine different selective enrichment conditions were initiated using subsamples from these cores in Nov. 2014. Separate subsamples were preserved for use in measuring rates of secondary production. Multivariate modeling tools will be applied to integrate these measurements with co-registered geochemical measurements, cell counts, and molecular data provided by collaborators. This work will provide new insight into the dynamic interplay between O2 and organic carbon and microbial activity, viability, and productivity in deep marine sediments.
NOTE: This project follows the C-DEBI program Data Management Plan (PDF).
| Name | Affiliation | Role |
|---|---|---|
| Maximiliano J. Amenabar | Montana State University | http://ocean-data.org/schema/Co-ChiefScientistRole |
| Eric Boyd | Montana State University | Lead Principal Investigator |
| John E. Dore | Montana State University | Contact |
| URL | https://www.bco-dmo.org/dataset/685944 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/685944/data/download |
| Media Type | text/tab-separated-values |
| Created | March 27, 2017 |
| Modified | October 2, 2017 |
| State | Final no updates expected |
| Brief Description | 3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 |
All samples used in this work were collected as part of the North Atlantic long-coring expedition in Oct.-Dec. 2014 (R/V Knorr, Cruise KN223); this project focuses on sediments from 4 sites (2, 3, 11, 12) exhibiting variations in the depth to which oxygen penetrates. The sediment subsamples were collected from long piston cores or shorter gravity cores. While oxygen penetrates through the full long core depth at sites 11 and 12, oxygen was consumed in the sediment column at site 3 and especially at site 2. All samples were collected anaerobically in order to perform on-board culture enrichments via the most probable number (MPN) method. Sediments were placed in sterile serum vials, capped with butyl rubber stoppers and flushed with N2 for 2 min and maintained at 4 degrees C for immediate shipboard MPN inoculation work (see MPN dataset). Parallel samples were similarly collected from these and additional core sections and maintained at 4 degrees C for later determination of microbial production rates (this dataset).
We assessed microbial production on selected core sections at sites 11 and 12 using proxies for DNA synthesis (incorporation of methyl-3H thymidine) and protein synthesis (incorporation of 4,5-3H leucine). Core material was retained at 4 degrees C under an N2 atmosphere prior to slurry preparation. Aerobic slurry was prepared 1:1 by volume with 0.2 um-filtered deep seawater and incubations began immediately thereafter. Incubations (n=4 live treatments, n=4 TCA-killed controls) of 0.5 ml slurry each were conducted in sterile microfuge tubes for each label addition. Seawater-only blanks incubated and processed along with samples exhibited near background levels of activity. 50 ul of working 3H-Thy or 3H-Leu stock was added at time zero. This equates to 3.75 uCi Leu or 4.4375 uCi Thy per sample at concentrations of appx. 114 nmol label compound per liter slurry final. Incubations were carried out at 4 degrees C in the dark.
Incubations were terminated at 18-24 hr; a time-course experiment confirmed linearity of incorporation out to at least 24 hr. Live incubations were terminated with TCA and an extraction protocol modified from Dixon & Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation; the DNA fraction alone was isolated and similarly analyzed for 3H-Thy incorporation. Rates are reported as pmol leucine or thymidine incorporated per ml of sediment per day (based on mean treatment minus mean control). Errors were calculated by propagating the standard deviations of treatments and controls.
These data represent short-term rates of label incorporation at the stated levels of addition. No corrections for potential isotope dilution were attempted, given the overall low metabolic rates of the system. Rates are reported as determined; therefore, where mean controls exceeded mean treatments, negative rates are reported.
BCO-DMO Processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– re-formatted date to yyyy-mm-dd;
– replaced “R/V Knorr” with “RV_Knorr” in data.
The sediment subsamples were collected from long piston cores or shorter gravity cores.
The sediment subsamples were collected from long piston cores or shorter gravity cores.
Live incubations were terminated with TCA and an extraction protocol modified from Dixon & Turley (2001, Microb. Ecol. 42:549) was used to isolate the protein + DNA fraction, which was analyzed by liquid scintillation counting for 3H-Leu incorporation.
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Sediment thickness
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
name of the ship or vessel (See also platform.)
Core identification number or label; often used with ice, rock, sediment, or coral cores.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Sample depth
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
heterotrophic bacteria; leucine incorporation rate
standard deviation of leucine incorporation rates
thymidine incorporation rate; file dependent
| Name | Affiliation | Contact |
|---|---|---|
| Eric Boyd | Montana State University | |
| Maximiliano J. Amenabar | Montana State University | |
| John E. Dore | Montana State University | |
| Shannon Rauch | Montana State University | |
| Shannon Rauch | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities |
|---|---|
| Acronym | Subseafloor metabolisms |
| URL | https://www.bco-dmo.org/project/676615 |
| Created | January 27, 2017 |
| Modified | February 13, 2017 |
Abstract from C-DEBI:
Deep marine sediments harbor an abundance of microbial cells that, if active, are likely to exert a strong influence on element biogeochemical cycling. Despite decades of study, our understanding of the fraction of cells that are active in situ and the metabolic processes that sustain them remain under-explored. We propose an integrated set of analyses aimed at unraveling the links between geochemical heterogeneity, cellular viability and synthesis, and metabolism along a vertical depth profile in four sediment cores collected during the North Atlantic long coring expedition. These sediment columns exhibit varying levels of organic carbon and differences in the degree of oxygen penetration along the depth profile which we hypothesize exert strong influence on the extent and nature of microbial life. Most probable number assays containing nine different selective enrichment conditions were initiated using subsamples from these cores in Nov. 2014. Separate subsamples were preserved for use in measuring rates of secondary production. Multivariate modeling tools will be applied to integrate these measurements with co-registered geochemical measurements, cell counts, and molecular data provided by collaborators. This work will provide new insight into the dynamic interplay between O2 and organic carbon and microbial activity, viability, and productivity in deep marine sediments.
NOTE: This project follows the C-DEBI program Data Management Plan (PDF).
| Name | Affiliation | Role |
|---|---|---|
| Maximiliano J. Amenabar | Montana State University | http://ocean-data.org/schema/Co-ChiefScientistRole |
| Eric Boyd | Montana State University | Lead Principal Investigator |
| John E. Dore | Montana State University | Contact |
| URL | https://www.bco-dmo.org/dataset/668648 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/668648/data/download |
| Media Type | text/tab-separated-values |
| Created | December 6, 2016 |
| Modified | January 21, 2020 |
| State | Final no updates expected |
| Brief Description | Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments |
In the Marmara Sea, surficial sediments were collected by multicorer, and deeper sediments from 570-585 cm and 520-530 cm were collected by gravity corer. Eastern Mediterranean sediments were collected by gravity corer. Guaymas Basin sediments were collected by push core.
Sediment incubations with fluorescently labeled organic substrates were set up with three live incubations, a kill control, and one live blank. Incubations were subsampled over time, and each subsample was centrifuged and syringe filtered through a 0.2 um GF filter. Porewater containing partially hydrolyzed fluorescent substrate products were processed using gel permeation chromatography with fluorescence detection. Standards of fluorescent substrates of known molecular weight were also run for the purpose of rate calculations.
GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.
Eastern Mediterranean sediments were collected by gravity corer. In the Marmara Sea, deeper sediments (from 570-585 cm and 520-530 cm) were collected by gravity corer.
In the Marmara Sea, surficial sediments were collected by multicorer.
Guaymas Basin sediments were collected by push core.
Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
GPC chromatographic analysis was conducted on a Shimadzu liquid chromatography system and a Hitachi fluorescence detector.
Instruments that separate components in aqueous or organic solution based on molecular size generally for molecular weight determination. Gel permeation chromatography (GPC) is a type of size exclusion chromatography (SEC), that separates analytes on the basis of size.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Experimental conditions applied to experimental units. In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.
| Name | Affiliation | Contact |
|---|---|---|
| Adrienne Hoarfrost | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | ✓ |
| Carol Arnosti | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | ✓ |
| Shannon Rauch | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | |
| Shannon Rauch | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | |
| Shannon Rauch | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Investigating microbial activities driving organic matter transformations in the deep subsurface |
|---|---|
| Acronym | SedS |
| URL | https://www.bco-dmo.org/project/662055 |
| Created | October 20, 2016 |
| Modified | October 20, 2016 |
Project description from C-DEBI:
Heterotrophic organisms are central to subsurface microbial communities and play an important role in carbon cycling. Most approaches to measuring enzymatic activities rely on the addition of a fluorescently labeled substrate to a sediment incubation. However, quantifying rates of extracellular enzymatic hydrolysis of organic matter is often problematic due to the tendency for a fluorescently labeled organic substrate to sorb to the sediment matrix. This results in lower fluorescence intensities and distorted, inaccurate hydrolysis rate calculations. In this project, a desorption treatment was developed to counteract the adverse effects of sorption on enzymatic activity measurements. Upon subsampling a sediment incubation amended with a fluorescently labeled substrate, the subsample is treated with a concentrated solution of unlabeled substrate, along with 0.2% sodium dodecyl sulfate (SDS), in order to competitively desorb the adsorbed, fluorescent substrate target. This treatment improves measured fluorescence intensities by a median of 62.5%, and is particularly effective at desorbing high molecular weight substrate products, resulting in debiased hydrolysis rates that are 14.75 nM/hr lower on average. Competitive desorption treatment was demonstrated to be effective for multiple substrates and in a broad range of sediments from diverse geological and geochemical contexts. Future applications of this method will result in more quantitative and comparable hydrolysis rates in subsurface sediments, will enable enzymatic activity measurements in problematic sediments that were previously infeasible, and will facilitate physiological characterization of microbial communities and model organisms in order to better understand heterotrophic carbon cycling in the subsurface environment.
This project was funded by a C-DEBI Graduate Fellowship.
| Name | Affiliation | Role |
|---|---|---|
| Adrienne Hoarfrost | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | Principal Investigator |
| Carol Arnosti | University of North Carolina at Chapel Hill (UNC-Chapel Hill) | Co-Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/671260 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/671260/data/download |
| Media Type | text/tab-separated-values |
| Created | December 27, 2016 |
| Modified | July 3, 2017 |
| State | Final no updates expected |
| Brief Description | Pore fluid chemistry from gravity cores |
Gravity core sampling took place at Dorado Outcrop off the west coast of Costa Rica in the Pacific Ocean during the R/V Atlantis cruise AT26-24. For more information about operations of this cruise see the cruise page which contains a link to the cruise report (AT26-24).
Phosphate, N+N, silicate, and NH4, were all run at Oregon State University using standard colorimetric techniques. Dissolved inorganic carbon (DIC) was run at Oregon State University using coulometry. Remaining elements were analyzed using Inductively Coupled Plasma Optical Emission Spectrophotometer (ICPOES). Comparison of Si measured via the two techniques shows an offset with the colorimetric results being ~7 uM higher than the ICP-OES results.
The data have not been processed further.
BCO-DMO Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* BD indicates Below Detection
* blank values replaced with no data value ‘nd’
* added ,dive_date, dive_lat, dive_lon from information in the cruise report (Table 4)
Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
Depth below sea floor of sample
depth below seafloor. Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).
Gravity core identifier
Core identification number or label; often used with ice, rock, sediment, or coral cores.
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
Alvin submersible dive latitude; north is positive
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Alvin submersible dive longitude; east is positive
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Orthophosphate (phosphate, reactive phosphorus), Various units.
Nitrate and Nitrite, µM (micromolar) or µg-at NO3-N and NO2-N/l
Silicate (Orthosilicic Acid), Si(OH)4, uM (micromolar) or ug-at Si(OH)4-Si/l (colloquially known as 'silicate') [Note: this parameter name was redefined to remove the parentheses.)
Ammonium and ammonia concentration parameters in any body of fresh or salt water.
Stable carbon isotope ratio of dissolved inorganic carbon (13C/12C ratio in DIC).
Stable carbon isotope ratio of dissolved inorganic carbon (13C/12C ratio in DIC).
Delta 13C (d13C) is the ratio of stable isotopes 13C:12C, reported in parts per thousand (per mil, 0/00).
Ba (Barium). May be reported in parts per million, nanomoles per Liter, or other units. Refer to dataset metadata for units.
B (Boron) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Manganese (Mn). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Iron (Fe). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Silicon (Si). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Sr (Strontium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Concentration of a trace element in seawater. Does not include trace metals and metaloids. Refer to dataset for element name and units.
Sodium (Na). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Calcium (Ca). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Mg (magnesium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
K (potassium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF) | ✓ |
| James McManus | University of Alaska Fairbanks (UAF) | ✓ |
| Beth N. Orcutt | University of Akron (UAkron) | |
| Andrew T. Fisher | University of Akron (UAkron) | |
| Samuel M. Hulme | Bigelow Laboratory for Ocean Sciences | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Discovery, sampling, and quantification of flows from cool yet massive ridge-flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean |
|---|---|
| Acronym | Dorado Outcrop |
| URL | https://www.bco-dmo.org/project/627844 |
| Created | November 30, 2015 |
| Modified | December 1, 2015 |
Description from NSF award abstract:
Pristine fluids from a typical ridge-flank hydrothermal system have never been sampled, mainly because it has not been possible to locate a site of focused discharge where representative samples could be collected. The PIs have located a small basement feature, Dorado outcrop, on 23 m.y.-old seafloor on the eastern flank of the East Pacific Rise that they plan to sample to determine the fluid composition, and to assess the rate of discharge from the outcrop, so that they can quantify the chemical impact of this hydrothermal system. They plan an 18-day expedition that combines the surveying capabilities of the AUV Sentry (bathymetric, sub-bottom sonar, photo mosaics, water column anomalies) and an ocean-class vessel capable of collecting high-quality multi-beam data and CTD samples, and supporting the survey and sampling capabilities of the ROV Jason II for collection of spring and plume fluids, heat flow data, sediment push cores, and still and video photography. These data and samples will be combined hopefully to generate the first well-constrained estimates of hydrothermal flows from Dorado outcrop. This expedition will result in the collection of samples and data from a “fire hose” of ridge-flank, hydrothermal system, challenging the commonly held view that discharge from ridge flank hydrothermal systems occurs primarily from diffuse seeps.
| Name | Affiliation | Role |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF-IMS) | Principal Investigator |
| Andrew T. Fisher | University of California-Santa Cruz (UC Santa Cruz) | Principal Investigator |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/671199 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/671199/data/download |
| Media Type | text/tab-separated-values |
| Created | December 27, 2016 |
| Modified | July 3, 2017 |
| State | Final no updates expected |
| Brief Description | Solid phase chemistry from gravity cores |
Gravity core sampling took place at Dorado Outcrop off the west coast of Costa Rica in the Pacific Ocean during the R/V Atlantis cruise AT26-24. For more information about operations of this cruise see the cruise page which contains a link to the cruise report (AT26-24).
Total inorganic carbon (TIC) was measured using coulometry and CaCO3 is calculated from this value. Organic carbon (OC) and nitrogen (N) were measured on a Perkin Elmer Series II 2400 CHNS/O analyzer. The Fe, Cr, Cu, Mn, and Zn represent results from dithionite extractions (see Roy et al., 2012, Continental Shelf Research, 54, 67-79). Metals were analyzed by Inductively Coupled Plasma Optical Emission Spectrophotometer (ICPOES) at the University of Akron. d13C was measured on a Carlo Erba NA-1500 elemental analyzer connected to a DeltaPlus XL mass spectrometer at Oregon State University.
The data have not been processed further.
BCO-DMO Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* BD indicates Below Detection
* blank values replaced with no data value ‘nd’
* added dive_id,dive_date,dive_lat, and dive_lon from information in the cruise report (Table 4)
Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
Carlo Erba NA-1500 elemental analyzer connected to a DeltaPlus XL mass spectrometer.
Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
Gravity core identifier
Core identification number or label; often used with ice, rock, sediment, or coral cores.
date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)
Alvin submersible dive latitude; north is positive
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Alvin submersible dive longitude; east is positive
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Calcium Carbonate, in sediments as percent; or CaCO3 from water samples reported in various units; CAUTION measured in sediment and water column samples
Calcium Carbonate, in sediments as percent; or CaCO3 from water samples reported in various units; CAUTION measured in sediment and water column samples
Dissolved Inorganic Carbon
Dissolved Inorganic Carbon
Concentration of a trace element in seawater. Does not include trace metals and metaloids. Refer to dataset for element name and units.
Concentration of a trace element in seawater. Does not include trace metals and metaloids. Refer to dataset for element name and units.
Delta 13C (d13C) is the ratio of stable isotopes 13C:12C, reported in parts per thousand (per mil, 0/00).
Delta 13C (d13C) is the ratio of stable isotopes 13C:12C, reported in parts per thousand (per mil, 0/00).
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF) | ✓ |
| James McManus | University of Alaska Fairbanks (UAF) | ✓ |
| Beth N. Orcutt | University of Akron (UAkron) | |
| Andrew T. Fisher | University of Akron (UAkron) | |
| Samuel M. Hulme | Bigelow Laboratory for Ocean Sciences | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Discovery, sampling, and quantification of flows from cool yet massive ridge-flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean |
|---|---|
| Acronym | Dorado Outcrop |
| URL | https://www.bco-dmo.org/project/627844 |
| Created | November 30, 2015 |
| Modified | December 1, 2015 |
Description from NSF award abstract:
Pristine fluids from a typical ridge-flank hydrothermal system have never been sampled, mainly because it has not been possible to locate a site of focused discharge where representative samples could be collected. The PIs have located a small basement feature, Dorado outcrop, on 23 m.y.-old seafloor on the eastern flank of the East Pacific Rise that they plan to sample to determine the fluid composition, and to assess the rate of discharge from the outcrop, so that they can quantify the chemical impact of this hydrothermal system. They plan an 18-day expedition that combines the surveying capabilities of the AUV Sentry (bathymetric, sub-bottom sonar, photo mosaics, water column anomalies) and an ocean-class vessel capable of collecting high-quality multi-beam data and CTD samples, and supporting the survey and sampling capabilities of the ROV Jason II for collection of spring and plume fluids, heat flow data, sediment push cores, and still and video photography. These data and samples will be combined hopefully to generate the first well-constrained estimates of hydrothermal flows from Dorado outcrop. This expedition will result in the collection of samples and data from a “fire hose” of ridge-flank, hydrothermal system, challenging the commonly held view that discharge from ridge flank hydrothermal systems occurs primarily from diffuse seeps.
| Name | Affiliation | Role |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF-IMS) | Principal Investigator |
| Andrew T. Fisher | University of California-Santa Cruz (UC Santa Cruz) | Principal Investigator |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/664422 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/664422/data/download |
| Media Type | text/tab-separated-values |
| Created | November 10, 2016 |
| Modified | July 3, 2017 |
| State | Final no updates expected |
| Brief Description | DO of pore water from sediment gravity and push cores |
Sampling took place at Dorado Outcrop off the west coast of Costa Rica in the Pacific Ocean during the R/V Atlantis cruises AT26-09 and AT26-24. For more information about operations of this cruise see the cruise pages which contain links to cruise reports ( AT26-09, AT26-24).
Dissolved oxygen (DO) was measured at-sea in pore waters from sediment gravity cores and cores collected by the submersible ALVIN with a needle-type oxygen optode inserted radially into sediment cores, following published protocols (e.g., Orcutt et al., 2013).
Reference:
Orcutt, B. N., Wheat, C. G., Rouxel, O., Hulme, S., Edwards, K. J., Bach, W., 2013. Oxygen Consumption rates in subseafloor basaltic crust derived from a reaction transport model, Nature Comm., published 27 Sep 2013, pg. 1-8, doi:10.1038/ncomms3539.
The data have not been processed further.
BCO-DMO Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values replaced with no data value ‘nd’
* added approximate lat/lon values for Dorado Outcrop sample site
Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
Approximate latitude of Dorado Outcrop
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Approximate longitude of Dorado Outcrop
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Core identifier
Core identification number or label; often used with ice, rock, sediment, or coral cores.
Depth in core sample
Dissolved oxygen
Oxygen; dissolved; reported in units of micromoles/liter
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF) | ✓ |
| James McManus | University of Alaska Fairbanks (UAF) | ✓ |
| Beth N. Orcutt | University of Akron (UAkron) | |
| Andrew T. Fisher | University of Akron (UAkron) | |
| Samuel M. Hulme | Bigelow Laboratory for Ocean Sciences | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Discovery, sampling, and quantification of flows from cool yet massive ridge-flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean |
|---|---|
| Acronym | Dorado Outcrop |
| URL | https://www.bco-dmo.org/project/627844 |
| Created | November 30, 2015 |
| Modified | December 1, 2015 |
Description from NSF award abstract:
Pristine fluids from a typical ridge-flank hydrothermal system have never been sampled, mainly because it has not been possible to locate a site of focused discharge where representative samples could be collected. The PIs have located a small basement feature, Dorado outcrop, on 23 m.y.-old seafloor on the eastern flank of the East Pacific Rise that they plan to sample to determine the fluid composition, and to assess the rate of discharge from the outcrop, so that they can quantify the chemical impact of this hydrothermal system. They plan an 18-day expedition that combines the surveying capabilities of the AUV Sentry (bathymetric, sub-bottom sonar, photo mosaics, water column anomalies) and an ocean-class vessel capable of collecting high-quality multi-beam data and CTD samples, and supporting the survey and sampling capabilities of the ROV Jason II for collection of spring and plume fluids, heat flow data, sediment push cores, and still and video photography. These data and samples will be combined hopefully to generate the first well-constrained estimates of hydrothermal flows from Dorado outcrop. This expedition will result in the collection of samples and data from a “fire hose” of ridge-flank, hydrothermal system, challenging the commonly held view that discharge from ridge flank hydrothermal systems occurs primarily from diffuse seeps.
| Name | Affiliation | Role |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF-IMS) | Principal Investigator |
| Andrew T. Fisher | University of California-Santa Cruz (UC Santa Cruz) | Principal Investigator |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/567215 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/567215/data/download |
| Media Type | text/tab-separated-values |
| Created | September 16, 2015 |
| Modified | August 19, 2016 |
| State | Final no updates expected |
| Brief Description | Microbial cell counts in sediment cores collected during KN195-03. |
Coring systems used:
EQP-01: Multi Corer, Piston Corer (long core)
EQP-02: Multi Corer, Gravity Corer
EQP-03: Gravity Corer
EQP-03a: Multi Corer, Gravity Corer (used long core system as a gravity corer)
EQP-04: Multi Corer, Gravity Corer (used long core system as a gravity corer), Piston Corer (long core)
EQP-05: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-06: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-06a: Gravity Corer
EQP-07: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-08: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-09: Gravity Corer
EQP-10: Multi Corer, Gravity Corer, Piston Corer (long core)
EQP-11: Multi Corer, Gravity Corer, Piston Corer (long core)
Excerpt from Kallmeyer et al. (2012) Supplemental Information:
For each cell enumeration, we took 2-cm3 samples from the center of a freshly cut core end using a sterile cutoff 3-cm3 syringe. We carried out cell counts according to the method of Kallmeyer et al. (2008). We extruded the 2-cm3 sediment plug into a sterile 15-mL centrifuge tube containing 8 mL of 2.5% (wt/vol) NaCl solution with 2% (vol/vol) formalin as a fixative and then thoroughly shook the tube to form a homogenous suspension. In cases where cell densities were high enough (> 105 cells/cm−3), we made direct cell counts by staining this slurry with SYBR Green I, placing a small aliquot of the slurry directly on a 0.2-μm pore size filter and enumerating manually under a fluorescence microscope (Noble and Fuhrman, 1998). Counts obtained with SYBR Green I have been found to be indistinguishable from acridine orange direct counts (AODCs) (Morono et al., 2009).
References:
Kallmeyer, J., Smith, D.C., D’Hondt, S.L., & Spivack, A.J. 2008. New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6:236–245. doi:10.4319/lom.2008.6.236
Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D’Hondt, S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences, 109(40), 16213-16216. doi:10.1073/pnas.1203849109
Noble, R.T., Fuhrman, J.A. 1998. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol 14(2):113–118. doi:10.3354/ame014113
Morono, Y., Terada, T., Masui, N., & Inagak,i F. 2009. Discriminative detection and enumeration of microbial life in marine subsurface sediments. ISME J 3:503–511. doi:10.1038/ismej.2009.1
Excerpt from Kallmeyer et al. (2012) Supplemental Information:
Independent of the stain used, direct counting has a minimum detection limit (MDL) around 105 cells/cm−3 (Kallmeyer, 2011). For samples with lower cell abundances, we found it necessary to detach and separate the cells from the mineral matrix using a cell extraction protocol (Kallmeyer et al. 2008). Most counts at North Pacific Gyre sites were of extracted cells because gyre cell abundances drop below the direct count MDL within decimeters to meters below the seafloor; for the same reason, a few counts of the deepest equatorial Pacific sediment were also of cell extracts.
References:
Kallmeyer J. 2011. Detection and quantification of microbial cells in subsurface sediments. Advances in Applied Microbiology, eds Laskin AI, Sariaslani S, Gadd GM (Elsevier, San Diego), Vol 76. doi:10.1016/B978-0-12-387048-3.00003-9
Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C., & D’Hondt, S. 2012. Global distribution of microbial abundance and biomass in subseafloor sediment. Proceedings of the National Academy of Sciences, 109(40), 16213-16216. doi:10.1073/pnas.1203849109
Kallmeyer, J., Smith, D.C., D’Hondt, S.L., & Spivack, A.J. 2008. New cell extraction procedure applied to deep subsurface sediments. Limnol Oceanogr Methods 6:236–245. doi:10.4319/lom.2008.6.236
BCO-DMO Processing:
– Modified parameter names to conform with BCO-DMO naming conventions;
– Converted lat and lon from degrees and decimal minutes to decimal degrees.
Direct cell counts were obtained by placing a small aliquot of the slurry directly on a 0.2-um pore size filter and enumerating manually under a fluorescence microscope.
Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.
Cruise identification number.
Station identification number.
Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Meters Below Seafloor (MBSF).
Standard deviation of cell density.
| Name | Affiliation | Contact |
|---|---|---|
| Steven L. D'Hondt | University of Rhode Island (URI-GSO) | |
| David C. Smith | University of Rhode Island (URI-GSO) | |
| Robert Pockalny | University of Rhode Island (URI-GSO) | |
| Arthur J. Spivack | University of Rhode Island (URI-GSO) | |
| Jens Kallmeyer | University of Rhode Island (URI-GSO) | |
| Shannon Rauch | University of Rhode Island (URI-GSO) | |
| Arthur J. Spivack | University of Rhode Island (URI-GSO) | |
| Arthur J. Spivack | University of Rhode Island (URI-GSO) | |
| Shannon Rauch | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Oceanographic control and global distributions of subseafloor microbial life and activity |
|---|---|
| Acronym | Subseafloor Microbial Life |
| URL | https://www.bco-dmo.org/project/2182 |
| Created | November 8, 2011 |
| Modified | January 18, 2012 |
Recent studies of subseafloor life, that is microbes living deep below the ocean&aposs seafloor, have produced astonishing results that challenge fundamental ideas about the limits and distributions of life. These include: (1) that the microbial biomass of subseafloor sediments is spatially much more variable and possibly much smaller than previously believed; (2) that rates of subseafloor sedimentary microbial activity are far below the rate required for cell maintenance, implying that either most subseafloor cells are inactive or that the energy required for their cellular maintenance is lower than anticipated; and (3) the global distributions of subseafloor sedimentary microbes and their activities are significantly affected by the oceanographic properties of the overlying water column. This proposal will conduct fieldwork to test these ideas at a range of sites in the equatorial Pacific. To do this the principal investigators will conduct a transect study where the following samples and measurements will be taken: (1) coring the sediment to ~18 meter or more below seafloor (mbsf) at 12 sites in the Pacific Ocean; (2) conducting extensive microbiological and biogeochemical analyses of these cores; (3) surveying the oceanographic and geologic characteristics of each site; and (4) using the results to test and refine models for the global distribution of subseafloor microbial abundances and their metabolic activities. Using these data the investigators will then address four important questions: (1) What are the principal controls on the magnitude and geographic distribution of subseafloor sedimentary cell abundance and steady-state rates of microbial activities? (2) Can we accurately estimate the magnitude and global distribution of subseafloor sedimentary cell abundance? (3) Can we accurately estimate the global distribution of organic carbon-fueled microbial activity in subseafloor sediment? and (4) Do different subseafloor sediments with very different cell abundances and rates of metabolic activity characterized by different groups of organisms? This study will significantly advance our understanding of life in the subseafloor ocean and will provide samples for diverse independent studies, including the International Census of Marine Microbes. This project will also have a strong research and training impact at both the graduate and undergraduate levels as the inherently multidisciplinary nature of subsurface life provides an ideal entry into collaborative modern science.
| Name | Affiliation | Role |
|---|---|---|
| Steven L. D'Hondt | University of Rhode Island (URI-GSO) | Principal Investigator |
| David C. Smith | University of Rhode Island (URI-GSO) | Co-Principal Investigator |
| Robert Pockalny | University of Rhode Island (URI-GSO) | Co-Principal Investigator |
| Arthur J. Spivack | University of Rhode Island (URI-GSO) | Co-Principal Investigator |
