| URL | https://www.bco-dmo.org/dataset/674781 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/674781/data/download |
| Media Type | text/tab-separated-values |
| Created | January 13, 2017 |
| Modified | July 24, 2017 |
| State | Preliminary and in progress |
| Brief Description | Vent fluid chemistry from AT26-10 and AT26-23 |
– All fluids were collected using isobaric gas-tight fluid samplers (Seewald et al., 2002).
– Temperature was measured during sample collection using a type-J thermocouple attached to the inlet snorkel. Reported values are maximums observed during sample collection.
Analytical methods:
pH: Ag/AgCl combination reference electrode
Na+, K+, Ca2+, Mg2+, Cl-, Br-, SO42- : ion chromatography with suppressed conductivity detectionCH4: gas chromatography with flame ionization detection
H2: gas chromatography with thermal conductivity detection
Reference:
Seewald, J.S., Doherty K.W., Hammar T.R. and Liberatore S.P. (2002). A new gas-tight isobaric sampler for hydrothermal fluids, Deep-Sea Research 49, 189-196. http://dx.doi.org/10.1016/S0967-0637(01)00046-2
BCO-DMO Processing:
– Added conventional header with dataset name, PI name, version date
– Modified parameter names to conform with BCO-DMO naming conventions
– Replaced blanks (missing data) and ‘nd’ to indicate ‘no data’
– Added cruise_id column
Used for sample collection
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.
Used to measure in-situ temperature.
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
pH: The measure of the acidity or basicity of an aqueous solution
Sodium (Na). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
K (potassium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Mg (magnesium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Calcium (Ca). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Concentration of sulfate (SO4) per unit volume
| Name | Affiliation | Contact |
|---|---|---|
| Jeffrey S. Seewald | Woods Hole Oceanographic Institution (WHOI) | ✓ |
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | ✓ |
| Nancy Copley | Woods Hole Oceanographic Institution (WHOI) | |
| Nancy Copley | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents |
|---|---|
| Acronym | Microbial Communities at Deep-Sea Vents |
| URL | https://www.bco-dmo.org/project/2216 |
| Created | June 11, 2012 |
| Modified | June 11, 2012 |
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)
| Name | Affiliation | Role |
|---|---|---|
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | Lead Principal Investigator |
| Costantino Vetriani | Rutgers University | Principal Investigator |
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | Principal Investigator |
| Ramunas Stepanauskas | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
| Craig Taylor | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Jeffrey S. Seewald | Max Planck Institute for Marine Microbiology (MPI) | International Collaborator |
| Nadine Le Bris | University of Greifswald | International Collaborator |
| Niculina Musat | Shanghai Jiao Tong University (SJTU) | International Collaborator |
| Thomas Schweder | Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB) | International Collaborator |
| Fengping Wang | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/660802 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/660802/data/download |
| Media Type | text/tab-separated-values |
| Created | October 5, 2016 |
| Modified | April 18, 2019 |
| State | Final no updates expected |
| Brief Description | Single amplified genomes (SAGs) of microbial cells isolated from Crab Spa, East Pacific Rise |
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
On average, at least 5 million 2×150 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).
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.
taxonomic group or entity code, such as the ten digit number from the NODC Taxonomic List, v. 8.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.
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.
Method used to collect sample.
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Link to an external data entry.
| Name | Affiliation | Contact |
|---|---|---|
| Ramunas Stepanauskas | Bigelow Laboratory for Ocean Sciences | ✓ |
| Nancy Copley | Bigelow Laboratory for Ocean Sciences | ✓ |
| Project Title | An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents |
|---|---|
| Acronym | Microbial Communities at Deep-Sea Vents |
| URL | https://www.bco-dmo.org/project/2216 |
| Created | June 11, 2012 |
| Modified | June 11, 2012 |
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)
| Name | Affiliation | Role |
|---|---|---|
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | Lead Principal Investigator |
| Costantino Vetriani | Rutgers University | Principal Investigator |
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | Principal Investigator |
| Ramunas Stepanauskas | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
| Craig Taylor | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Jeffrey S. Seewald | Max Planck Institute for Marine Microbiology (MPI) | International Collaborator |
| Nadine Le Bris | University of Greifswald | International Collaborator |
| Niculina Musat | Shanghai Jiao Tong University (SJTU) | International Collaborator |
| Thomas Schweder | Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB) | International Collaborator |
| Fengping Wang | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/628993 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/628993/data/download |
| Media Type | text/tab-separated-values |
| Created | December 16, 2015 |
| Modified | February 13, 2017 |
| State | Final no updates expected |
| Brief Description | Results of on-board incubations of microbes in diffuse flow vent fluids collected from Crab Spa and Alvinella patch |
From AT26-10 cruise report (01/29/2014):
DOB: An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents
Cruise Report by the CIW research team: Dr. Ileana Perez-Rodriguez, Mr. Matt Rawls and Dr. Dionysis I. Foustoukos
The CIW team was responsible for the shipboard continuous culturing incubations of vent fluids collected from Crab Spa and Tica hot springs during the AT26-10 expedition at 9oN EPR by utilizing our high-pressure bioreactor (Fig. 1). This was accomplished through a collaborative effort with Jeff Seewald and Sean Sylva (WHOI), who deployed isobaric gas-tight samplers (IGTs) to collect hydrothermal vent fluids at the diffuse flow sites. Experiments were designed to study the cycling to N through the metabolic processes of denitrification and dissimilatory nitrate reduction to ammonia (DNRA) under in-situ deep-sea vent temperature and pressure conditions.
We studied the evolution of nitrate reducing microorganisms at mesophilic (30oC) and thermophilic (50oC) conditions at pressures ranging from 5 to 250 bar. Vent fluids (16 IGTs) were delivered in the bioreactor and homogeneously mixed with aqueous media solution enriched in dissolved nitrate, hydrogen and 13C labeled bicarbonate to facilitate the growth of nitrate reducing microorganisms (Fig. 2). The two distinct sets of experiments were lasted for 356 and 100 hours. In short, experimental results constrained the function and metabolic rates of the denitrifying microbial communities in the Crab Spa fluids, while DNRA metabolic pathways were identified for the populations residing in the moderate temperature vent fluids (60oC) of the Alvinella colony at Tica.
During the course of the experiments we monitored the growth of deep-sea microbial communities by measuring the concentrations of dissolved aqueous species directly involved in nitrate based metabolism, such as NO3, NH4, H2 and H2S. We also monitored cell densities by utilizing an epi-fluorescence microscope (Sievert, WHOI). Dissolved gas and NH4+ concentrations were attained by gas and ion chromatography (Seewald – Sylva, WHOI). Subsamples were also collected for a number of offshore analysis to determine: i) the 15N/14N isotope composition of NO3-,/NH4+ and constrain kinetic isotope effects associated with denitrification/DNRA (Perez-Rodriguez, CIW), ii) to study the rates of autotrophic carbon fixation by NanoSIMS (Musat, UFZ), iii) to perform single cell genomics on the microbial populations grown in the bioreactor (Ramunas, Bigelow) and (iv) to isolate and characterize novel microogranisms from the communities cultured in our experiments (Perez-Rodriguez, CIW and Vetriani, Rutgers).
BCO-DMO Processing:
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.
The integrated system allows for the culturing of microorganisms under hydrostatic pressures from 0.1 to 69 MPa (and up to 138 MPa with ongoing developments) and at temperatures ranging from 25 to 120°C. For full description, see Foustoukos and Perez-Rodriguez (2015), Applied and Environmental Microbiology, 81, 6850
A device mounted on a ship that holds water samples under conditions of controlled temperature or controlled temperature and illumination.
Olympus BX61 microscope with a UPlanF1 100x (numerical aperture, 1.3) oil immersion objective
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".
JSM-6500F field emission scanning electron microscope (JEOL)
Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of electrons behaving as waves.
start date of incubation in yyyy-mm-dd format
date sampling starts such as YYYYMMDD
end date of incubation in yyyy-mm-dd format
water pressure at measurement; depth reported as pressure; positive number increasing with water depth
ammonium concentration
Ammonium and ammonia concentration parameters in any body of fresh or salt water.
hydrogen concentration
methane concentration
cell_concentration
Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.
d15N_NO3_ppt
delta 15N (d15N) is a measure of the ratio of stable isotopes 15N:14N. It is commonly reported in parts per thousand (per mil, 0/00).
| Name | Affiliation | Contact |
|---|---|---|
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | ✓ |
| Nancy Copley | Carnegie Institution for Science (CIS) | ✓ |
| Project Title | An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents |
|---|---|
| Acronym | Microbial Communities at Deep-Sea Vents |
| URL | https://www.bco-dmo.org/project/2216 |
| Created | June 11, 2012 |
| Modified | June 11, 2012 |
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)
| Name | Affiliation | Role |
|---|---|---|
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | Lead Principal Investigator |
| Costantino Vetriani | Rutgers University | Principal Investigator |
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | Principal Investigator |
| Ramunas Stepanauskas | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
| Craig Taylor | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Jeffrey S. Seewald | Max Planck Institute for Marine Microbiology (MPI) | International Collaborator |
| Nadine Le Bris | University of Greifswald | International Collaborator |
| Niculina Musat | Shanghai Jiao Tong University (SJTU) | International Collaborator |
| Thomas Schweder | Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB) | International Collaborator |
| Fengping Wang | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/529026 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/529026/data/download |
| Media Type | text/tab-separated-values |
| Created | September 30, 2014 |
| Modified | February 13, 2017 |
| State | Final no updates expected |
| Brief Description | Chemical composition of diffuse flow vent fluids collected from Crab Spa, 9N on the East Pacific Rise |
These samples were collected with Isobaric-Gas-Tight samplers and processed onboard R/V Atlantis. The IGT samplers were deployed by Dr. Jeff Seewald from WHOI. Chemical analysis of the major cation/anion species was conducted at the Geophysical Lab, Carnegie Institution of Washington
BCO-DMO Processing:
Metrohm/Dionex, for cation and anion species.
Ion chromatography is a form of liquid chromatography that measures concentrations of ionic species by separating them based on their interaction with a resin. Ionic species separate differently depending on species type and size. Ion chromatographs are able to measure concentrations of major anions, such as fluoride, chloride, nitrate, nitrite, and sulfate, as well as major cations such as lithium, sodium, ammonium, potassium, calcium, and magnesium in the parts-per-billion (ppb) range. (from http://serc.carleton.edu/microbelife/research_methods/biogeochemical/ic.html)
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.
sampling date. Format: YYYY-MM-DD
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)
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Sodium (Na). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
K (potassium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Mg (magnesium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Calcium (Ca). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
depth where sample was taken
Observation/sample depth below the sea surface. Units often reported as: meters, feet.
When used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.
| Name | Affiliation | Contact |
|---|---|---|
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | ✓ |
| Nancy Copley | Carnegie Institution for Science (CIS) | ✓ |
| Project Title | An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents |
|---|---|
| Acronym | Microbial Communities at Deep-Sea Vents |
| URL | https://www.bco-dmo.org/project/2216 |
| Created | June 11, 2012 |
| Modified | June 11, 2012 |
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)
| Name | Affiliation | Role |
|---|---|---|
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | Lead Principal Investigator |
| Costantino Vetriani | Rutgers University | Principal Investigator |
| Dionysis I. Foustoukos | Carnegie Institution for Science (CIS) | Principal Investigator |
| Ramunas Stepanauskas | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
| Craig Taylor | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Jeffrey S. Seewald | Max Planck Institute for Marine Microbiology (MPI) | International Collaborator |
| Nadine Le Bris | University of Greifswald | International Collaborator |
| Niculina Musat | Shanghai Jiao Tong University (SJTU) | International Collaborator |
| Thomas Schweder | Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB) | International Collaborator |
| Fengping Wang | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
