URLhttps://www.bco-dmo.org/dataset/637804
Download URLhttps://www.bco-dmo.org/dataset/637804/data/download
Media Typetext/tab-separated-values
CreatedFebruary 3, 2016
ModifiedAugust 19, 2016
Brief DescriptionThe acetate and inorganic carbon uptake rates as determined via stable isotopic tracers; data generated using the formation fluids recovered from the CORKs installed at the North Pond in 2012.

Acquisition Description

To determine potential rates of autotrophic and heterotrophic metabolism within crustal aquifer fluids and deep Atlantic bottom water, fluids were incubated with either 13C-labeled bicarbonate (autotrophy) or 13C-labeled acetate (heterotrophy). For this, 20 mL of freshly sampled fluids were injected into sterile, butyl stoppered Balch tubes using a 60 mL syringe and hypodermic needle using sterile technique. Overpressure was released by insertion of a second hypodermic needle. The tubes were pre-amended with a mix of either unlabeled bicarbonate and 10% 13C-labeled bicarbonate (to a final concentration of 1.8 mM NaHCO3 and 0.2 mM NaH13CO3) or unlabeled acetate and 10% 13C-labeled acetate (to a final concentration of 13.5 uM C2H3NaO2 and 1.5 uM 13C2H3NaO2). All tubes were additionally amended with resarzurin (20 uM final concentration) in order to follow the change in redox potential as a result of oxygen consumption throughout the incubation period. Sterile controls were set up as described above but with an additional filter (0.2 um pore size) inserted between the syringe outlet and the hypodermic needle. Tubes were incubated in the dark at either 5 or 25 degrees C. Incubations were stopped at distinct time intervals by addition of either 0.5 mL of a 1 M NaOH solution (for incubations with bicarbonate) or 5 mL of a 20% zinc acetate solution (for incubations with acetate). Tubes were stored at –20 degrees C until further processing.

For analysis of 13C-labeled biomass, tubes were thawed and the residual pool of bicarbonate or acetate was removed by acidification to a pH of 2 by adding 25% HCl (molecular grade) while stirring and sparging with N2 for at least 30 minutes. The entire volume was then filtered through a pre-combusted glass fiber filter (25mm diameter, 0.7 um particle retention, Whatman, UK). The filters were dried in a desiccator overnight and stored at 5 degrees C until further processing. Filters were weighed into tin capsules and analyzed for 13C/12C ratios with an automated Isotope Cube elemental analyzer (Elementar, Germany) interfaced to a Delta Advantage isotope ratio mass spectrometer (Thermo, Germany). Rates of potential autotrophic metabolism (carbon fixation from 13C-labeled bicarbonate) and heterotrophic metabolism (degradation of 13C-labeled acetate) were calculated from δ13C of the carbon pool on the filters at the start and the end of the incubations (time intervals of not more than 13 days). For this, the transfer of 13C between pools was calculated, according to the following equation:

δBiomass-Final · CBiomass-Final ·VFinal = (CBiomass-Initial · V · δBiomass-Initial) + (CTransferred· V · δLabel)

where δ is the isotopic ratio ((Rsample/ Rstandard –1) · 1000), V is the volume of the incubation (20mL) and C is the concentration of carbon pool. For incubations with 13C-labeled bicarbonate we assumed a concentration of 2.3 mM endogenous dissolved inorganic carbon (DIC) in addition to the added mix of 13C-labeled bicarbonate, thus decreasing the amount of label in the substrate pool. For incubations with 13C-labeled acetate we assumed a concentration of 150 uM endogenous dissolved organic carbon (DOC) in addition to the added 13C-labeled acetate.

Processing Description

Comments from Middlestead lab in re: C-contet:
1) Due to the nature of the samples (on ggf), and the small quantities being analysed, the standard deviation is higher than normal.
2) Nitrogen data is included where the peak size is at about the minimum. This data should not actually be used.
3) The quantities of N and C are not as accurate as on an EA-only run.
4) Even the standards start to have homogeneity issues at this level.

Blind std C-55: C13: -28.3; n = 2; std dev = 0.90. Expected value to date = -28.50

BCO-DMO Processing:
- Modified parameter names to conform with BCO-DMO naming conventions;
- Replaced spaces with underscores;
- Moved incubation_duration from comment to a column;
- Created notes column for additional comments;
- Replaced blanks with 'nd' (ie. in the 'Background control' row).

Instruments

Isotope Cube elemental analyzer [Elemental Analyzer]
Details
Instance Description (Isotope Cube elemental analyzer)

Filters were weighed into tin capsules and analyzed for 13C/ 12C ratios with an automated Isotope Cube elemental analyzer (Elementar, Germany) interfaced to a Delta Advantage isotope ratio mass spectrometer (Thermo, Germany).

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.

Delta Advantage isotope ratio mass spectrometer [Isotope-ratio Mass Spectrometer]
Details
Instance Description (Delta Advantage isotope ratio mass spectrometer)

Filters were weighed into tin capsules and analyzed for 13C/ 12C ratios with an automated Isotope Cube elemental analyzer (Elementar, Germany) interfaced to a Delta Advantage isotope ratio mass spectrometer (Thermo, Germany).

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Parameters

study [unknown]
Details
study
Excel sheet.
association with a community-wide standard parameter is not yet defined
incubation [unknown]
Details
incubation
Fluids were incubated with either 13C-labeled bicarbonate (autotrophy) or 13C-labeled acetate (heterotrophy).
association with a community-wide standard parameter is not yet defined
sample [sample]
Details
sample
Sample identifer/location.

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

Details
temp
Temperature. RT = ?
water temperature at measurement depth
time_point [time_point]
Details
time_point
Time point.

Arbitrary time point of sampling in a sampling sequence (T0, T1,....Tn)

delta_13Cvpdb_DOC [unknown]
Details
delta_13Cvpdb_DOC
delta 13Cvpdb DOC
association with a community-wide standard parameter is not yet defined
incubation_duration [unknown]
Details
incubation_duration
How long the incubation lasted.
association with a community-wide standard parameter is not yet defined
DOC [DOC]
Details
DOC
Dissolved organic carbon (DOC). C-content only.
dissolved organic Carbon
filter_one_punch [unknown]
Details
filter_one_punch
Filter (- one punch)
association with a community-wide standard parameter is not yet defined
notes [unknown]
Details
notes
Notes/comments.
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Peter R. GirguisHarvard University
Julie A. HuberMarine Biological Laboratory (MBL)
Brian T. GlazerUniversity of Hawaii at Manoa (SOEST)
Beate KraftHarvard University
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleCollaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling
AcronymNorth Pond Microbes
URLhttps://www.bco-dmo.org/project/554914
CreatedApril 3, 2015
ModifiedAugust 29, 2019
Project Description

Description from NSF award abstract:
Current estimates suggest that the volume of ocean crust capable of sustaining life is comparable in magnitude to that of the oceans. To date, there is little understanding of the composition or functional capacity of microbial communities in the sub-seafloor, or their influence on the chemistry of the oceans and subsequent consequences for global biogeochemical cycles. This project focuses on understanding the relationship between microbial communities and fluid chemistry in young crustal fluids that are responsible for the transport of energy, nutrients, and organisms in the crust. Specifically, the PIs will couple microbial activity measurements, including autotrophic carbon, nitrogen and sulfur metabolisms as well as mineral oxide reduction, with quantitative assessments of functional gene expression and geochemical transformations in basement fluids. Through a comprehensive suite of in situ and shipboard analyses, this research will yield cross-disciplinary advances in our understanding of the microbial ecology and geochemistry of the sub-seafloor biosphere. The focus of the effort is at North Pond, an isolated sediment pond located on ridge flank oceanic crust 7-8 million years old on the western side of the Mid-Atlantic Ridge. North Pond is currently the target for drilling on IODP expedition 336, during which it will be instrumented with three sub-seafloor basement observatories.

The project will leverage this opportunity for targeted and distinct sampling at North Pond on two German-US research cruises to accomplish three main objectives:

1. to determine if different basement fluid horizons across North Pond host distinct microbial communities and chemical milieus and the degree to which they change over a two-year post-drilling period.

2. to quantify the extent of autotrophic metabolism via microbially-mediated transformations in carbon, nitrogen, and sulfur species in basement fluids at North Pond.

3. to determine the extent of suspended particulate mineral oxides in basement fluids at North Pond and to characterize their role as oxidants for fluid-hosted microbial communities.

Specific outcomes include quantitative assessments of microbial activity and gene expression as well as geochemical transformations. The program builds on the integrative research goals for North Pond and will provide important data for guiding the development of that and future deep biosphere research programs. Results will increase understanding of microbial life and chemistry in young oceanic crust as well as provide new insights into controls on the distribution and activity of marine microbial communities throughout the worlds oceans.

There are no data about microbial communities in ubiquitous cold, oceanic crust, the emphasis of the proposed work. This is an interdisciplinary project at the interface of microbial ecology, chemistry, and deep-sea oceanography with direct links to international and national research and educational organizations.

Project Maintainers
NameAffiliationRoleContact
Julie A. HuberMarine Biological Laboratory (MBL)Lead Principal Investigator
Peter R. GirguisHarvard UniversityPrincipal Investigator
Brian T. GlazerUniversity of Hawaii at Manoa (SOEST)Principal Investigator
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