Download URLhttps://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

Acquisition Description

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).

Processing Description

BCO-DMO Processing:

  • added conventional header with dataset name, PI name, version date
  • renamed parameters to BCO-DMO standard
  • concatenated the 2 datasets: Crab Spa and Alvinella patch
  • blank cells replaced with ‘nd’
  • added columns for description, date_start and date_end
  • version 2017-02-07 replaced version 2015-12-17: added cell concentration, d15N_NO3_ppt, and d15N_Biomass_ppt



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.

custom high pressure bioreactor [Shipboard Incubator]
Instance Description (custom high pressure bioreactor)

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.

Instance Description

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".

Instance Description

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.


description [exp_id]
description of experimental incubation
Experiment Id
date_start [date_start]

start date of incubation in yyyy-mm-dd format

date sampling starts such as YYYYMMDD

date_end [date_end]

end date of incubation in yyyy-mm-dd format

date sampling ends; as YYYYMMDD
flow_rate [unknown]
flow rate
association with a community-wide standard parameter is not yet defined
temp [temperature]
water temperature at measurement depth
press [pressure]

water pressure at measurement; depth reported as pressure; positive number increasing with water depth

time_elapsed [time_elapsed]
time since start of incubation
Elapsed time. Typically found in CTD profile data. Units can be seconds, minutes, etc.
NO3_uM [NO3]

nitrate concentration

Nitrate concentration in the water column

NH4_uM [Ammonium]

ammonium concentration

Ammonium and ammonia concentration parameters in any body of fresh or salt water.

H2_uM [unknown]

hydrogen concentration

association with a community-wide standard parameter is not yet defined
H2S_uM [sulfide]

hydrogen sulfide concentration

concentration of sulfide

CH4_uM [unknown]

methane concentration

association with a community-wide standard parameter is not yet defined
pH [pH]
pH at 25 C

pH: The measure of the acidity or basicity of an aqueous solution

cell_concentration [cell_concentration]


Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.

d15N_NO3_ppt [d15N]

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).

d15N_Biomass_ppt [d15N]

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).

Dataset Maintainers

Dionysis I. FoustoukosCarnegie Institution for Science (CIS)
Nancy CopleyCarnegie Institution for Science (CIS)

BCO-DMO Project Info

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
Created June 11, 2012
Modified June 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)

Data Project Maintainers
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. SeewaldMax Planck Institute for Marine Microbiology (MPI)International Collaborator
Nadine Le BrisUniversity of GreifswaldInternational Collaborator
Niculina MusatShanghai Jiao Tong University (SJTU)International Collaborator
Thomas SchwederLaboratoire d'Écogéochimie des Environnements Benthiques (LECOB)International Collaborator
Fengping WangWoods Hole Oceanographic Institution (WHOI)Co-Principal Investigator