Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.
|Created||December 12, 2019|
|Modified||February 11, 2020|
|State||Final no updates expected|
|Brief Description||delta 15N values from sediment cores P6, P10, P11, P12, and P13, collected on the Guaymas Basin Ridge flanks and the Sonora Margin|
All coring operations were performed using a the piston-coring system onboard the R/V El Puma. See http://www.buques.unam.mx for additional information.
Bulk sediment δ¹⁵N and elemental ratio data were collected using 20mg samples in Sn capsules; organic δ¹³C and elemental composition data were collected using 2.5mg samples of acidified sediment in Sn capsules. All samples were measured by Dumas combustion performed on a Carlo Erba 1108 elemental analyzer coupled to a ThermoFinnigan Delt Plus XP isotope ratio mass spectrometer (EA-IRMS). An in-house gelatin standard, Acetanilide, and an in-house bulk sediment standard, "Monterey Bay Sediment Standard", were used in all runs. Reproducibility of an in-house matrix-matched sediment standard is <0.1‰ VPDB for δ¹³C and <0.2‰ AIR for δ¹⁵N. Data is corrected for blank, and for drift when appropriate. Carbon and nitrogen elemental composition was estimated based on standards of known composition, for which analytical precision is determined to be better than 1%.
- modified parameter names (removed units in parens);
- added dates provided by submitter.
core number/identification, to be used with ice, rock and sediment cores
Latitude at sampling location; positive = north
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Longitude at sampling location; negative = west
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Water depth at sampling location
water depth, in meters
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
depth below seafloor. Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).
del15N values for organic matter
|Andreas P. Teske||University of North Carolina at Chapel Hill (UNC-Chapel Hill)||✓|
|Ivano Aiello||Moss Landing Marine Laboratories (MLML)|
|Ana Christina Ravelo||University of California-Santa Cruz (UC Santa Cruz)|
|Shannon Rauch||Woods Hole Oceanographic Institution (WHOI BCO-DMO)|
BCO-DMO Project Info
|Project Title||RAPID proposal: Site characterization cruise to document the active and extensive subsurface biosphere in the Guaymas Basin|
|Acronym||RAPID Guaymas Basin|
|Created||November 5, 2015|
|Modified||March 13, 2019|
Description from NSF project abstract:
The Guaymas Basin in the central Gulf of California is an active tectonic spreading center overlain with thick, organic-rich sediments. In contrast to typical deep-water, mid-ocean ridge spreading centers that have very focused magmatism and little or no sediment, magmatism in the Guaymas Basis is more broadly distributed. This broadly-distributed magmatism significantly expands the fraction of organic-rich sediments that may be subject to alteration by the magmatic heat and thus it greatly expands the range of environments that support hydrocarbon generation and microbial populations in the sediments. Recognition that magmatism is not confined to the spreading axis, but instead is distributed throughout Guaymas Basin, suggests that models for the natural sequestration of carbon, the formation of oceanic crust, and life in the subsurface in marginal rift basins should be reconsidered as this has implications for the long-term removal of atmospheric carbon dioxide (and hence potential climatic implications). The Principal Investigator of this RAPID proposal is a lead proponent on an International Ocean Discovery Program (IODP) proposal to study this system in depth through scientific ocean drilling. To properly plan this expensive IODP expedition, additional site characterization gained from sediment sampling and seismic data is required. This proposal requests funds for the Principal Investigator to participate on an already planned site survey cruise aboard the Mexican Research Vessel (RV) El Puma. The results from this cruise will provide valuable data, at an exceptionally low investment, to guide decisions about potential future scientific drilling in the Guaymas Basin.
This RAPID proposal requests funds for the Principal Investigator to participate on a Mexican site survey cruise in October 2014 on RV El Puma to collect five-meter gravity cores of an extensive sediment transect across the Guaymas Basin and to integrate sequencing-based microbial community analyses of subsurface bacteria and archaea with biogechemical characterizations of these subsurface sediments. Gravity coring and microbial community analysis will target cold non-hydrothermal sediments as well as off-axis hydrothermally-influenced sediments. The gravity coring campaign and the geochemistry/microbiology studies are coordinated with heatflow measurements and extensive 2D seismic analysis and high-resolution 3D seismic mapping by other planned Mexican and German cruises. This multi-pronged strategy will deliver the additional data and complete the site characterizations that are required to properly plan a potential IODP drilling expedition by the JOIDES Resolution.
|Andreas P. Teske||University of North Carolina at Chapel Hill (UNC-Chapel Hill)||Principal Investigator||✓|
|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).
- 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.
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".
start date of incubation in yyyy-mm-dd format
date sampling starts such as YYYYMMDD
end date of incubation in yyyy-mm-dd format
Ammonium and ammonia concentration parameters in any body of fresh or salt water.
Concentration of cells; often determined by spectrophotometry, flow cytometry, or using a microscope.
|Dionysis I. Foustoukos||Carnegie Institution for Science (CIS)||✓|
|Nancy Copley||Woods Hole Oceanographic Institution (WHOI BCO-DMO)|
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|
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)
|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||Woods Hole Oceanographic Institution (WHOI)||Co-Principal Investigator|
|Nadine Le Bris||Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB)||International Collaborator|
|Niculina Musat||Max Planck Institute for Marine Microbiology (MPI)||International Collaborator|
|Thomas Schweder||University of Greifswald||International Collaborator|
|Fengping Wang||Shanghai Jiao Tong University (SJTU)||International Collaborator|