v6 16S rRNA from IODP boreholes, seawater, and drilling mud at North Pond collected from Maria S. Merian cruise MSM20-5 in 2012 (North Pond Microbes project)

Website: https://www.bco-dmo.org/dataset/573508
Version: 28 Sept 2015
Version Date: 2015-09-28

» Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling (North Pond Microbes)

» Center for Dark Energy Biosphere Investigations (C-DEBI)
» International Ocean Discovery Program (IODP)
Huber, JulieMarine Biological Laboratory (MBL)Principal Investigator
Girguis, PeterHarvard UniversityCo-Principal Investigator
Glazer, BrianUniversity of Hawaii at Manoa (SOEST)Co-Principal Investigator
Rauch, ShannonWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Methods & Sampling

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)).

Data 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".

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Data Files

(Comma Separated Values (.csv), 1.24 KB)
Primary data file for dataset ID 573508

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sampleSample name. text
descriptionDescription of the sample. text
bioproject_idNCBI BioProject ID number and link. text
collection_dateDate sample was collected. mm/dd/yyyy
latLatitude of sample collection. Positive = North. decimal degrees
lonLongitude of sample collection. Negative = West. decimal degrees
depth_mbsf_rangeDepth range of sample. meters below seafloor (mbsf)
depth_mbsf_minMinimum depth of sample. meters below seafloor (mbsf)
depth_mbsf_maxMaximum depth of sample. meters below seafloor (mbsf)

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R/V Maria S. Merian
Start Date
End Date

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Project Information

Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling (North Pond Microbes)

Coverage: North Pond, mid-Atlantic Ridge

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.

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Program Information

Center for Dark Energy Biosphere Investigations (C-DEBI)

Coverage: Global

The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?

C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.

Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.

Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.

To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.

International Ocean Discovery Program (IODP)

Coverage: Global

The International Ocean Discovery Program (IODP) is an international marine research collaboration that explores Earth's history and dynamics using ocean-going research platforms to recover data recorded in seafloor sediments and rocks and to monitor subseafloor environments. IODP depends on facilities funded by three platform providers with financial contributions from five additional partner agencies. Together, these entities represent 26 nations whose scientists are selected to staff IODP research expeditions conducted throughout the world's oceans.

IODP expeditions are developed from hypothesis-driven science proposals aligned with the program's science plan Illuminating Earth's Past, Present, and Future. The science plan identifies 14 challenge questions in the four areas of climate change, deep life, planetary dynamics, and geohazards. 

IODP's three platform providers include:

  • The U.S. National Science Foundation (NSF
  • Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT
  • The European Consortium for Ocean Research Drilling (ECORD)

More information on IODP, including the Science Plan and Policies/Procedures, can be found on their website at http://www.iodp.org/program-documents.

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Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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