URLhttps://www.bco-dmo.org/dataset/782058
Download URLhttps://www.bco-dmo.org/dataset/782058/data/download
Media Typetext/tab-separated-values
CreatedNovember 19, 2019
ModifiedDecember 2, 2019
StateFinal no updates expected
Brief DescriptionReconstructed genomes from North Pond

Acquisition Description

Ribosomal rRNA identification and relative abundance
From the high-quality paired-end Illumina sequencing reads, 16S rRNA gene fragments were identified using Meta-RNA (Huang et al., 2009; v.H3; -e 1e-10). Putative rRNA fragments and associated mate pairs from each sample were processed through EMIRGE (Miller et al., 2011, 2013); emirge_amplicon.py; -l 113 -i 163 -s 33 -a 32 —phred33) to generate full-length sequences using the SILVA (Quast et al., 2012) SSURef111 reference database (https://github.com/csmiller/EMIRGE). Reconstructed 16S rRNA genes were assigned taxonomy using mothur (v1.34.4) by first aligning the sequences to the SILVA SSURef123 database (align.seqs; flip=T), removing sequences that failed to align, if necessary (remove.seqs), and classifying the sequences (classify.seqs; cutoff=80, iters=1000).

Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions

 

Instruments

Details
Instance Description (CTD)

Deep bottom water was sampled in 2012 and 2014 via a CTD at 100 m above the seafloor and filtered in the same manner as the crustal fluids onto Sterivex filters.

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.
Aanderaa sensor [Aanderaa Oxygen Optodes]
Details
Instance Description (Aanderaa sensor)

Fluid systems were flushed and allowed to equilibrate before sampling, and dissolved oxygen concentrations were measured during pumping using an Aanderaa sensor (Meyer et al., 2016).

Aanderaa Oxygen Optodes are instrument for monitoring oxygen in the environment. For instrument information see the Aanderaa Oxygen Optodes Product Brochure.
GeoMICROBE sled [GeoMICROBE]
Details
Instance Description (GeoMICROBE sled)

After sampling in 2012, a battery-powered GeoMICROBE sled was left at each CORK for time series autonomous sampling of the fluid delivery lines (Cowen et al., 2012).

Integrated Ocean Drilling Program borehole CORK (Circulation Obviation Retrofit Kit) observatories provide long-term access to hydrothermal fluids circulating within the basaltic crust (basement), providing invaluable opportunities to study the deep biosphere. We describe the design and application parameters of the GeoMICROBE instrumented sled, an autonomous sensor and fluid sampling system. The GeoMICROBE system couples with CORK fluid delivery lines to draw large volumes of fluids from crustal aquifers to the seafloor. These fluids pass a series of in-line sensors and an in situ filtration and collection system. GeoMICROBE’s major components include a primary valve manifold system, a positive displacement primary pump, sensors (e.g., fluid flow rate, temperature, dissolved O2, electrochemistry-voltammetry analyzer), a 48-port in situ filtration and fluid collection system, computerized controller, seven 24 V-40 A batteries and wet-mateable (ODI) communications with submersibles. This constantly evolving system has been successfully connected to IODP Hole 1301A on the eastern flank of the Juan de Fuca Ridge. 

Reference: Cowen, J.P., Copson, D., Jolly, J., Hsieh, C.-C., Matsumoto, R., Glazer, B.T. et al. (2012) Advanced instrument system for real-time and time-series microbial geochemical sampling of the deep (basaltic) crustal biosphere., Deep-Sea Research I, 61: 43-56 doi:10.1016/j.dsr.2011.11.004

epifluorescent microscopy [Microscope-Fluorescence]
Details
Instance Description (epifluorescent microscopy)

Total microbial biomass in fluids was enumerated with DAPI (4′,6′-diamidino-2-phenylindole; Sigma-Aldrich, St Louis, MO, USA) and epifluorescent microscopy (Porter and Feig, 1980). 

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.

automated colorimetric analysis [Automatic titrator]
Details
Instance Description (automated colorimetric analysis)

Fluids also were analyzed for dissolved silicon and nitrate using automated colorimetric analysis and pH was measured with an electrode before a potentiometric titration for the determination of alkalinity (Wheat et al., 2017).

Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.

Parameters

bioproject_id [accession number]
Details
bioproject_id
NIH bioproject term
Database identifier assigned by repository and linked to GenBank or other repository.
Assembly [unknown]
Details
Assembly
GenBank assembly accession
association with a community-wide standard parameter is not yet defined
Level [unknown]
Details
Level
contig or scaffold
association with a community-wide standard parameter is not yet defined
WGS [unknown]
Details
WGS
Whole Genome Shotgun Submission
association with a community-wide standard parameter is not yet defined
BioSample [accession number]
Details
BioSample
BioSample accession numbers
Database identifier assigned by repository and linked to GenBank or other repository.
Isolate [unknown]
Details
Isolate
Genome designation (eg. NORP is NORthPond)
association with a community-wide standard parameter is not yet defined
Taxonomy [taxon]
Details
Taxonomy
Sepcies assigned with mothur for reconstructed 16SrRNA genes

taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.

Dataset Maintainers

NameAffiliationContact
Julie A. HuberMarine Biological Laboratory (MBL)
Peter R. GirguisHarvard University
Brian T. GlazerUniversity of Hawaii at Manoa (SOEST)

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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