URLhttps://www.bco-dmo.org/dataset/686389
Download URLhttps://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

Acquisition Description

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):

table of electron donors and acceptors used in this studySaline 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.

Processing Description

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.

Instruments

long piston core [Piston Corer]
Details
Instance Description (long piston core)

The sediment subsamples were collected from long piston cores or shorter gravity cores.

The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.
gravity core [Gravity Corer]
Details
Instance Description (gravity core)

The sediment subsamples were collected from long piston cores or shorter gravity cores.

The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079).
infrared gas detector [Gas Analyzer]
Details
Instance Description (infrared gas detector)

Activity in MPN assays was evaluated by determining the headspace concentration of CO2 using an infrared gas detector.

Gas Analyzers - Instruments for determining the qualitative and quantitative composition of gas mixtures.

Parameters

site [site]
Details
site
Site name
Sampling site identification.
lat [latitude]
Details
lat
Site latitude

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

lon [longitude]
Details
lon
Site longitude

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

depth_w [depth_w]
Details
depth_w
Water depth

water depth, in meters

sed_thickness [sed_thickness]
Details
sed_thickness
Sediment thickness

Sediment thickness

basement_age [unknown]
Details
basement_age
Basement age
association with a community-wide standard parameter is not yet defined
date_coring [date]
Details
date_coring
Date of coring in yyyy-mm-dd format

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)

cruise_id [cruise_id]
Details
cruise_id
Cruise identifier
cruise designation; name
platform [ship]
Details
platform
Platform (e.g. vessel) name

name of the ship or vessel (See also platform.)

core [core_id]
Details
core
Core identifier. LC = long core; GC = gravity core.

core number/identification, to be used with ice, rock and sediment cores

core_section [sample]
Details
core_section
Core section

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

depth_mbsf [meters below seafloor]
Details
depth_mbsf
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.

electron_donor [unknown]
Details
electron_donor
Organic compound added as an electron donor (acetate or peptone)
association with a community-wide standard parameter is not yet defined
electron_acceptor [unknown]
Details
electron_acceptor
Inorganic addition serving as an electron acceptor (nitrate, oxygen, or manganese(IV) oxide)
association with a community-wide standard parameter is not yet defined
MPN_min [cell_concentration]
Details
MPN_min
Minimum MPN; true viable (under these culture conditions) cell concentration is likely to be greater than or equal to this figure.

Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.

MPN_max [cell_concentration]
Details
MPN_max
Maxiumum MPN; True viable (under these culture conditions) cell concentration is likely to be less than or equal to this figure.

Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.

notes [unknown]
Details
notes
Indicates samples for which no growth was noted at the lowest dilution tested as well as samples for which positive growth was detected at the highest dilution tested.
association with a community-wide standard parameter is not yet defined
PCR_products [unknown]
Details
PCR_products
PCR products obtained? Yes = highest dilution exhibiting growth yielded PCR products; No = highest dilution exhibiting growth did not yield PCR products; N/A = not applicable because no growth was noted at any dilution and therefore no attempt was made to extract DNA for PCR amplification.
association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Eric BoydMontana State University
Maximiliano J. AmenabarMontana State University
John E. DoreMontana State University
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Defining the interplay between oxygen, organic carbon, and metabolism in subseafloor sediment communities
Acronym Subseafloor metabolisms
URLhttps://www.bco-dmo.org/project/676615
Created January 27, 2017
Modified February 13, 2017
Project Description

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).

Data Project Maintainers
NameAffiliationRole
Maximiliano J. AmenabarMontana State Universityhttp://ocean-data.org/schema/Co-ChiefScientistRole
Eric BoydMontana State UniversityLead Principal Investigator
John E. DoreMontana State UniversityContact
Menu