URLhttps://www.bco-dmo.org/dataset/549138
Download URLhttps://www.bco-dmo.org/dataset/549138/data/download
Media Typetext/tab-separated-values
CreatedFebruary 5, 2015
ModifiedAugust 19, 2016
StateFinal no updates expected
Brief DescriptionSamples sequenced from chemosynthetic biofilm communities from deep-sea hydrothermal vents

Acquisition Description

Samples were collected at several sites along the East Pacific Rise hydrothermal vent zone.  They included ROV/Jason deployments J2-758, J2-759, J2-760, J2-761, J2-762.

About 1 GB of raw sequence data (bacterial ssrRNA) was obtained using the Ion Torrent platform from total RNA extracted from sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes. Samples included background references. Sequence data are currently being analyzed and will be deposited in GenBank prior to publication and will be made available to the scientific community. [2015-02-04]

The use of rRNA transcripts instead of DNA will allow us to identify the fraction of the population actively transcribing in situ. Sixteen microbial biofilm samples characterized by different temperature, redox and biological regimes were used. These samples included biofilm formed on experimental colonizers deployed at selected vents to obtain early stage biofilm. A comparison of early stage and established biofilms will help to understand how the community changes in relation to biofilm age and geochemical regimes. 

Processing Description

We have optimized a RNA extraction protocol from biofilm biomass using the RNeasy kit (Qiagen). Following extraction and DNase treatment, we generated cDNA using random primers (SuperScript III First-Strand kit).  cDNA from biolfilm and fluid samples was used to amplify the 16S rRNA gene with tagged primers and subjected to sequencing. Obtained sequences are currently being analyzed using the QIIME pipeline. The reads are being dereplicated, denoised, screened for chimeric sequences and taxonomically classified using the RDP and GreenGenes databases. Multivariate ordination techniques will be used to discriminate among samples with similar community structures.

Instruments

Automated Sequencer [Automated DNA Sequencer]
Details
Instance Description (Automated Sequencer)

Ion Torrent next-generation sequencing platform

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.

ROV Jason [ROV Jason]
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.
McLane Pump [McLane Pump]
Details
Instance Description (McLane Pump)

Large Volume Pump (LVP): McLane WTS 6-1-142LV

McLane pumps sample large volumes of seawater at depth. They are attached to a wire and lowered to different depths in the ocean. As the water is pumped through the filter, particles suspended in the ocean are collected on the filters. The pumps are then retrieved and the contents of the filters are analyzed in a lab.

Parameters

sample_num [sample]
Details
sample_num
sample number

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

cruise_id [cruise_id]
Details
cruise_id
cruise identification
cruise designation; name
dive [dive_id]
Details
dive
Alvin or Jason dive number
Unique dive id or number for ROV, AUV or HOV type system dive or deployment
lat [latitude]
Details
lat
latitude; north is positive

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

lon [longitude]
Details
lon
longitude; east is positive

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

date [date]
Details
date
date of collection

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)

habitat [site_descrip]
Details
habitat
habitat at collection site

Description or characteristics of a sampling site

site [site]
Details
site
name of collection site
Sampling site identification.
sample [sample]
Details
sample
sample identification

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

sample_description [sample_descrip]
Details
sample_description
sample description
text description of sample collected
collection_method [sampling_method]
Details
collection_method
how sample was collected
Method used to collect sample, for example Bongo net or Methot trawl.
nucleic_acid [unknown]
Details
nucleic_acid
type of nucleic acid measured
association with a community-wide standard parameter is not yet defined
nucleic_acid_conc [unknown]
Details
nucleic_acid_conc

total concentration of the nucleic acid

association with a community-wide standard parameter is not yet defined
cDNA [unknown]
Details
cDNA

concentration of cDNA

association with a community-wide standard parameter is not yet defined

Dataset Maintainers

NameAffiliationContact
Costantino VetrianiRutgers University (Rutgers IMCS)
Nancy CopleyWoods Hole Oceanographic Institution (WHOI BCO-DMO)
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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