Download URLhttps://www.bco-dmo.org/dataset/630288/data/download
Media Type text/tab-separated-values
Created December 29, 2015
Modified August 19, 2016
Brief Description

Microbial cell counts derived from the formation fluids recovered from the CORKs installed at the North Pond in 2012 and 2014.

Acquisition Description

Whole formation fluids and bottom seawater were fixed with 3.7% formaldehyde for cell counts. Up to 19.8 ml of fixed fluids were filtered onto a 0.2 um GTBP polycarbonate filter (Millipore), stained with DAPI (4′,6′-diamidino-2-phenylindole; Sigma), and counted via epiflourescent microscopy. For fluorescence in situ hybridization (FISH), cells were filtered onto 0.2 um GTTP polycarbonate filters (Millipore) and fixed with 2% paraformaldehyde, rinsed with milliQ H2O, air dried and stored at –20 degrees C until further use. Cells on filters were hybridized with HRP-labeled 16S rRNA targeted oligonucleotide probes EUB338, ARCH915 and NON338(Biomers GmbH, Ulm, Germany), and the signal was amplified as described elsewhere using Alexa 488® tyramides (Invitrogen). The permeabilization step of the protocol before probe hybridization was modified, such that the cells on the filters were first permeabilized with Proteinase K (0.005 U ul –1 in 0.05 M EDTA, 0.1 M Tris-HCl, at pH 8) for 30 minutes at 37 degrees C. Filters were then washed in 50 ml 1X PBS at room temperature, followed by a second permeabilization treatment with Lysozyme (10^6 U ml–1, in 0.05 M EDTA, 0.1 M Tris-HCl, at pH 8) for 30 minutes at 37 degrees C. After signal amplification, all cells were counterstained with DAPI and counted via epiflourescent microscopy.

Processing Description

BCO-DMO Processing:
– Modified parameter names to conform with BCO-DMO naming conventions;
– Replaced blanks (missing data) with ‘nd’ to indicate ‘no data’;
– Added cruise id numbers.


epiflourescent microscopy [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_id [cruise_id]
Cruise identifier.
cruise designation; name
year [year]
4-digit year of cruise.

year, reported as YYYY, e.g. 1995

date [date]


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)

sample [sample]

Sample identifier. The nomenclature refers to the IODP hole and formation horizon. For example, U1383C-shallow means the fluids came from IODP CORK drillhole 1383C in the shallowest accessible porewater horizon.

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

lat [latitude]
Latitude of sample. Positive = North.

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

lon [longitude]
Longitude of sample. Negative = South.

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

dive_num [unknown]
Dive number.
association with a community-wide standard parameter is not yet defined
cells_per_mL [count]

Cell count.

Number of individuals counted in sample or sample fraction
mean [mean]
Mean cell count for the sample.

A central value of a discrete set of numbers: specifically, the sum of the values divided by the number of values

Dataset Maintainers

Peter R. GirguisHarvard University
Julie A. HuberHarvard University
Brian T. GlazerMarine Biological Laboratory (MBL)
Beate KraftMarine Biological Laboratory (MBL)
Shannon RauchUniversity of Hawaii at Manoa (SOEST)
Shannon RauchUniversity of Hawaii at Manoa (SOEST)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling
Acronym North Pond Microbes
Created April 3, 2015
Modified August 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.

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