URLhttps://www.bco-dmo.org/dataset/660802
Download URLhttps://www.bco-dmo.org/dataset/660802/data/download
Media Typetext/tab-separated-values
CreatedOctober 5, 2016
ModifiedApril 18, 2019
StateFinal no updates expected
Brief DescriptionSingle amplified genomes (SAGs) of microbial cells isolated from Crab Spa, East Pacific Rise

Acquisition Description

AT15-38: Samples for SAGs were obtained using the so-called 'titanium major samplers' (von Damm et al, 1985). Replicate samples of 1 ml aliquots of water were cryopreserved with 6% glycine betaine (Sigma) or 15% glycerol and stored at -80 ºC for the ”Single Cell” aliquot.

AT26-10:  Background samples were obtained from the IGTs, in which the incubations were carried out. Just in this case, an aliquot was removed after sample retrieval and before starting the incubation. During AT26-10, samples were preserved with Gly-TE and stored at -80. 

Cells were sorted, identified and sequenced by the Bigelow Laboratory Single Cell Genomics FacilityCenter (SCGC), following  SCGCthe facilities’s standard practices: SCGC_Services_Description.pdf

Processing Description

On average, at least 5 million 2x150 bp or longer paired-end reads were generated per SAG using in-house MiSeq and NextSeq (Illumina) instruments. The obtained reads were pre-processed and, de novo, assembled and quality-controlled using algorithms SCGC's standard protocols that are optimized for single cell MDA products . A combination of tetramer homogeneity tests and blast searches against reference databases is used to detect potential DNA contaminants among the assembled contigs. Benchmark data demonstrating SCGC SAG WGS whole genome sequencing pipeline performance is available from the SCGC website http://data.bigelow.org/~scgc/WGS_benchmark_data/.

Genome annotation was performed through IMG (http://img-stage.jgi-psf.org/cgi-bin/submit/main.cgi).

Additional related references (pdf)

Instruments

Details
The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.
Instance Description

MiSeq and NextSeq (Illumina) sequencers

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Isobaric Gas Tight (IGT) samplers, designed and built by scientists and engineers at WHOI, are titanium instruments designed to be used with deep submergence vehicles to sample corrosive hydrothermal vent fluids at high temperature and high pressure. The IGT prevents the sampled fluid from degassing as pressure decreases during the vehicle’s ascent to the surface.

Parameters

taxon_oid [taxon_code]
Details
taxon_oid
Identification number of the Single Amplified Genome (SAG) in IMG

taxonomic group or entity code, such as the ten digit number from the NODC Taxonomic List, v. 8.

SAG_id [sample]
Details
SAG_id
The identifier of the SAG

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

taxon [taxon]
Details
taxon
Taxonomic affiliation of the SAG

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

source [treatment]
Details
source

The origin of the sample used for the single cell sorting:
Background: Cell sorted from the natural water samples
Control: Cell sorted from the natural water samples incubated in isobaric chambers without any amendments
NO3-/H2, ~24C: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of NO3- (nitrate) and hydrogen (H2)
H2 only: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of hydrogen (H2)
NO3- only: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of NO3- (nitrate)hydrogen (H2)
O2, ~110uM: Cell sorted from the natural water samples incubated at 24oC in isobaric chambers with the addition of 110uM of O2 (oxygen)
NO3-/H2, ~50C: Cell sorted from the natural water samples incubated at 50oC in isobaric chambers with the addition of NO3- (nitrate) and hydrogen (H2)

Experimental conditions applied to experimental units.  In comparative experiments, members of the complementary group, the control group, receive either no treatment or a standard treatment.

deployment [dive_id]
Details
deployment
J denotes "Jason dive" followed by the nember of dive
Unique dive id or number for ROV, AUV or HOV type system dive or deployment
accession_IMG [accession number]
Details
accession_IMG
The accession number in IMG
Database identifier assigned by repository and linked to GenBank or other repository.
GOLD_Analysis_project_id [accession number]
Details
GOLD_Analysis_project_id
The project identification number in the GOLD Database; accession number for the metadata
Database identifier assigned by repository and linked to GenBank or other repository.
GOLD_sequencing_strategy [sampling_method]
Details
GOLD_sequencing_strategy
The strategy used for sequencing (whole genome sequencing vs amplicon sequencing)
Method used to collect sample, for example Bongo net or Methot trawl.
latitude [latitude]
Details
latitude
Latitude of the sampling site

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

longitude [longitude]
Details
longitude
Longitude of the sampling site

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

assembly_size [unknown]
Details
assembly_size
The total size of the assembled contigs
association with a community-wide standard parameter is not yet defined
gene_count [count]
Details
gene_count
Number of identified genes
Number of individuals counted in sample or sample fraction
accession_link [external_link]
Details
accession_link
Link to taxon_oid at IMG database

Link to an external data entry.

study_name [exp_id]
Details
study_name
The name of the study
Experiment Id

Dataset Maintainers

NameAffiliationContact
Ramunas StepanauskasBigelow Laboratory for Ocean Sciences
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project TitleAn Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
AcronymMicrobial Communities at Deep-Sea Vents
URLhttps://www.bco-dmo.org/project/2216
CreatedJune 11, 2012
ModifiedJune 11, 2012
Project Description

Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives: 1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities. 2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents. 3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents. 4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms.

Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts.

Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context.

Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)

Project Maintainers
NameAffiliationRoleContact
Stefan M. SievertWoods Hole Oceanographic Institution (WHOI)Lead Principal Investigator
Costantino VetrianiRutgers UniversityPrincipal Investigator
Dionysis I. FoustoukosCarnegie Institution for Science (CIS)Principal Investigator
Ramunas StepanauskasBigelow Laboratory for Ocean SciencesPrincipal Investigator
Craig TaylorWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Jeffrey S. SeewaldWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Nadine Le BrisLaboratoire d'Écogéochimie des Environnements Benthiques (LECOB)International Collaborator
Niculina MusatMax Planck Institute for Marine Microbiology (MPI)International Collaborator
Thomas SchwederUniversity of GreifswaldInternational Collaborator
Fengping WangShanghai Jiao Tong University (SJTU)International Collaborator
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