Download URLhttps://www.bco-dmo.org/dataset/573508/data/download
Media Type text/tab-separated-values
Created September 28, 2015
Modified August 19, 2016
State Final no updates expected
Brief Description

v6 16S rRNA from IODP boreholes, seawater, and drilling mud at North Pond.

Acquisition Description

Crustal fluids were collected from the single horizon at U1382A and from the shallow, middle, and deep horizons at U1383C using an ROV-based pumping and filtration system tailored for microbial sampling. The mobile pumping system (or MPS) is described in:
Cowen, J. P. et al. 2012.Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere. Deep-Sea Research Part I: Oceanographic Research Papers 61, 43-56, doi:10.1016/j.dsr.2011.11.004

Individual CORK fluid delivery lines were flushed using the MPS at a rate of ~4 liters per minute for at least 3 times volume of the fluid delivery line (~20-30 minutes) prior to diverting fluid flow to six 15 L foil-lined sample bags (Jensen Inert Products) that were acid cleaned and sterilized using gamma irradiation prior to deployment. Fluids were not sampled until at least 15-30 minutes of stable, reproducible measurements were observed, indicating a fully flushed fluid delivery system and access to crustal fluids. In addition, ~5 L of fluid from each of the three horizons in U1383C was filtered in situ onto 47 mm SUPOR filters in pancake-style filter holders (McLane Inc). These filtered samples were preserved in situ using a reservoir of RNA Later (Qiagen) that is part of the MPS pumping system. Once recovered, ten liters of each sample was filtered onto a 0.22 um Sterivex-GP filter at 5 degrees C for microbial analysis. Similarly, bottom seawater was collected by CTD at 100 m above the sea floor and filtered in the same manner. In situ and ship-based filters were fixed at 4 degrees C for 18 hours with RNA Later immediately after filtering or upon recovery, then frozen at -80 degrees C until nucleic acid extractions. B. Orcutt provided a frozen sample of drilling mud from U1382A from IODP Exp. 336.

Sterivex filters and 47 mm flat filters were cut into two equal pieces using sterile technique. Total genomic DNA was extracted from one half using a phenol chloroform method as previously described in:
Sogin, M. L. et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proceedings of the National Academy of Sciences of the United States of America 103, 12115-12120, doi:10.1073/pnas.0605127103

RNA was extracted from the other half with a mirVana miRNA isolation kit (Ambion Inc) preceded by a bead beating step using RNA Powersoil beads (MoBio). Extracted RNA was treated with Turbo DNase (Ambion Turbo DNA-free kit) and converted to cDNA with an Applied Biosystems (ABI) High Capacity RNA to cDNA kit prior to amplicon library preparation. Total genomic DNA was extracted from approximately 1 g of drilling mud using a MoBio UltraClean® Soil DNA Isolation Kit. The V6 region of 16S rRNA genes was amplified in triplicate for each sample with previously reported primers designed for archaea and bacteria (Huber, J. A. et al. Microbial population structures in the deep marine biosphere. Science (New York, N.Y.) 318, 97-100, doi:10.1126/science.1146689 (2007)) that were modified to include indices and barcodes compatible with the Illumina HiSeq1000 platform rather than 454 Life Sciences Adapters (Eren, A. M., Vineis, J. H., Morrison, H. G. & Sogin, M. L. A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology. PLoS ONE 8, 6-11, doi:10.1371/journal.pone.0066643 (2013)). Triplicate PCR amplifications were pooled for each sample, cleaned with a Qiagen MinElute kit, and quanitified by PicoGreen assay on a Turner Biosystems spectrophotometer. Fifty nanograms of each cleaned amplicon library was then size selected with a 2% agarose PippinPrep cassette to produce a narrow range of fragment sizes from 200 to 240 bp for sequencing and cleaned again to remove agarose. Equimolar amounts of pooled amplicon libraries and a metagenomic library were run in the same lane to avoid known difficulties of sequencing low-complexity amplicon libraries with Illumina (Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal 6, 1621-1624, doi:10.1038/ismej.2012.8 (2012)).

Processing Description

Paired Illumina sequencing reads were quality filtered to remove any reads containing ambiguous nucleotides and only pairs with perfectly overlapping reads were used for further analysis. Quality-filtered reads and raw reads are publicly available through the NCBI under BioProject PRJNA280201 at http://www.ncbi.nlm.nih.gov/bioproject/PRJNA280201/

BCO-DMO Data Processing:
– separated lat/lon into separate columns;
– changed lon from positive degrees west to negative degrees east;
– created depth min and max columns; reformatted depth range column;
– replaced ‘na’ with ‘nd’ to indicate “no data”.



sample [sample]
Sample name.

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

description [unknown]
Description of the sample.
association with a community-wide standard parameter is not yet defined
bioproject_id [accession number]

NCBI BioProject ID number and link.

Database identifier assigned by repository and linked to GenBank or other repository.
collection_date [date]

Date sample was collected.

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)

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

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

lon [longitude]
Longitude of sample collection. Negative = West.

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

depth_mbsf_range [meters below seafloor]

Depth range of sample.

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.

depth_mbsf_min [meters below seafloor]

Minimum depth of sample.

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.

depth_mbsf_max [meters below seafloor]

Maximum depth of sample.

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.

Dataset Maintainers

Julie A. HuberMarine Biological Laboratory (MBL)
Peter R. GirguisMarine Biological Laboratory (MBL)
Brian T. GlazerHarvard University
Shannon RauchHarvard University
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