| URL | https://www.bco-dmo.org/dataset/820188 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/820188/data/download |
| Media Type | text/tab-separated-values |
| Created | August 7, 2020 |
| Modified | October 14, 2020 |
| State | Final no updates expected |
Once on deck, OsmoSamplers were sectioned. Individual coils of Teflon tubing (each ~300 m long) were removed, sealed, and labeled. Each coil was then sectioned into 1.2 m lengths and the fluid expelled into acid washed (60C for 14 hours in 10%HCl) and rinsed (18 mega ohm water) micro centrifuge tubes. Centrifuge tubes were labeled and packaged for shipment.
In the laboratory aliquots from these centrifuge tubes were diluted before being analyzed using an inductively coupled plasma optical emission spectrometer (ICPOES). In addition the fresh water reservoir for each of the OsmoSampler pumps was analyzed for salinity to asses if the samplers over pumped and if so, by how much.
Additional descriptions for the recovered samplers can be found at Edwards et al. (2012) and Wheat et al. (2011).
Fluids were analyzed with an inductively coupled plasma optical emission spectrometer (ICPOES) as described in Wheat et al. (2020). Analytical precision is listed as 2%, but individual runs were ofter lower.
BCO-DMO processing notes:
Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
OsmoSamplers that were recovered on R/V Atlantis Expedition AT39-01 with the ROV Jason-II
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)
Ba (Barium). May be reported in parts per million, nanomoles per Liter, or other units. Refer to dataset metadata for units.
B (Boron) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Manganese (Mn). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Iron (Fe). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Li (Lithium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Silicon (Si). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Sampling location - longitude, west is negative
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF) | ✓ |
| Karen Soenen | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| URL | https://www.bco-dmo.org/dataset/764875 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/764875/data/download |
| Media Type | text/tab-separated-values |
| Created | April 11, 2019 |
| Modified | April 18, 2019 |
| State | Final no updates expected |
| Brief Description | Pore water chemical concentration data and location from push cores collected by the ROV Jason II on dive J2-773 |
Push cores were collected by the ROV Jason II on dive J2-773 on 11-April-2014.
Pore waters were extracted in a cold room at 4C using acid-rinsed, washed and dried rhizomes. The first 2 ml of fluid was discarded, then the remaining fluid was filtered through a 0.45 micron membrane and stored in hot acid (60C) washed high-density polyethylene bottles. Fluids were analyzed by electrode (pH), titration (chlorinate, calcium, and alkalinity), colorimetric (nitrate), inductively coupled optical emission spectroscopy (ICPOES), and inductively coupled mass spectroscopy (ICPMS). Precision was generally 0.2% for chlorinate and calcium titrations, 2% for alkalinity titrations, 0.01 for pH, 5% for nitrate determinations, 2% for ICPOES measurements and 5% for ICPMS measurements. All measurements were above detection limits with the exception of Mn (0.1 umol/kg) and Fe (0.01 mol/kg).
Careful consideration of these data should examine the potential of sampling artifacts for many of the solutes. We believe, for example, the Ca difference from bottom seawater values is an artifact of sample handling, resulting from the movement of sediment with carbonate present to the ship where the sediment was handled. Other solutes are likewise probably affected.
BCO-DMO Processing:
– copied core ID number from header row to all corresponding data rows;
– moved notes into new “notes” column for all corresponding data rows;
– deleted empty rows;
– created lat/lon columns using info from the notes column;
– replaced “—” and blank cells with “nd” for “no data”.
Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
Also referred to as an Inductively coupled plasma atomic emission spectroscope (ICP-AES). These instruments pass nebulised samples into an inductively-coupled gas plasma (8-10000 K) where they are atomised and excited. The de-excitation optical emissions at characteristic wavelengths are spectroscopically analysed. It is often used in the detection of trace metals.
Core identification number
Core identification number or label; often used with ice, rock, sediment, or coral cores.
Depth below seafloor, in centimeters
pH: The measure of the acidity or basicity of an aqueous solution
A measure of chloride content (Cl).
Calcium (Ca). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
B (Boron) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Manganese (Mn). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Iron (Fe). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Silicon (Si). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Sr (Strontium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Li (Lithium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Sodium (Na). Concentrations may be reported in parts per million, nanomoles per 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.
K (potassium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
V (Vanadium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Rb (rubidium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Molybdenum (Mo). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.
Cs (Cesium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Ba (Barium). May be reported in parts per million, nanomoles per Liter, or other units. Refer to dataset metadata for units.
U (Uranium) concentration. May be reported in parts per million, nanomoles/Liter, or other units. Refer to dataset metadata for units.
Latitude in decimal degrees; calculated from position described in Notes column
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Longitude in decimal degrees; calculated from position described in Notes column; Negative values = West
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | Monterey Bay Aquarium Research Institute (MBARI) | ✓ |
| Shannon Rauch | Monterey Bay Aquarium Research Institute (MBARI) | ✓ |
| Project Title | Collaborative Research: Characterization of Microbial Transformations in Basement Fluids, from Genes to Geochemical Cycling |
|---|---|
| Acronym | North Pond Microbes |
| URL | https://www.bco-dmo.org/project/554914 |
| Created | April 3, 2015 |
| Modified | August 29, 2019 |
Description from NSF award abstract:
Current estimates suggest that the volume of ocean crust capable of sustaining life is comparable in magnitude to that of the oceans. To date, there is little understanding of the composition or functional capacity of microbial communities in the sub-seafloor, or their influence on the chemistry of the oceans and subsequent consequences for global biogeochemical cycles. This project focuses on understanding the relationship between microbial communities and fluid chemistry in young crustal fluids that are responsible for the transport of energy, nutrients, and organisms in the crust. Specifically, the PIs will couple microbial activity measurements, including autotrophic carbon, nitrogen and sulfur metabolisms as well as mineral oxide reduction, with quantitative assessments of functional gene expression and geochemical transformations in basement fluids. Through a comprehensive suite of in situ and shipboard analyses, this research will yield cross-disciplinary advances in our understanding of the microbial ecology and geochemistry of the sub-seafloor biosphere. The focus of the effort is at North Pond, an isolated sediment pond located on ridge flank oceanic crust 7-8 million years old on the western side of the Mid-Atlantic Ridge. North Pond is currently the target for drilling on IODP expedition 336, during which it will be instrumented with three sub-seafloor basement observatories.
The project will leverage this opportunity for targeted and distinct sampling at North Pond on two German-US research cruises to accomplish three main objectives:
1. to determine if different basement fluid horizons across North Pond host distinct microbial communities and chemical milieus and the degree to which they change over a two-year post-drilling period.
2. to quantify the extent of autotrophic metabolism via microbially-mediated transformations in carbon, nitrogen, and sulfur species in basement fluids at North Pond.
3. to determine the extent of suspended particulate mineral oxides in basement fluids at North Pond and to characterize their role as oxidants for fluid-hosted microbial communities.
Specific outcomes include quantitative assessments of microbial activity and gene expression as well as geochemical transformations. The program builds on the integrative research goals for North Pond and will provide important data for guiding the development of that and future deep biosphere research programs. Results will increase understanding of microbial life and chemistry in young oceanic crust as well as provide new insights into controls on the distribution and activity of marine microbial communities throughout the worlds oceans.
There are no data about microbial communities in ubiquitous cold, oceanic crust, the emphasis of the proposed work. This is an interdisciplinary project at the interface of microbial ecology, chemistry, and deep-sea oceanography with direct links to international and national research and educational organizations.
| Name | Affiliation | Role |
|---|---|---|
| Julie A. Huber | Marine Biological Laboratory (MBL) | Lead Principal Investigator |
| Peter R. Girguis | Harvard University | Principal Investigator |
| Brian T. Glazer | University of Hawaii at Manoa (SOEST) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/660792 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/660792/data/download |
| Media Type | text/tab-separated-values |
| Created | October 5, 2016 |
| Modified | October 11, 2016 |
| State | Final no updates expected |
| Brief Description | Stable carbon isotopic composition of organic matter from seafloor basalts incubated with labeled bicarbonate |
Acquisition methods are described in the following publication:
Orcutt, B.N., Sylvan, J.B., Rogers, D.R., Delaney, J., Lee, R.W., & Girguis, P.R. 2015. Carbon fixation by basalt-hosted microbial communities. Front. Microbiol. doi:10.3389/fmicb.2015.00904
In summary (excerpted from above):
Basalt samples used in this study were collected from three different crustal formation areas. One glassy, seafloor-exposed basalt came from the ASHES vent field in the Axial Seamount volcano caldera on the Juan de Fuca Ridge off the western coast of North America. The sample was collected in 2009 with the Alvin submersible during dive AD-4527 on RV Atlantis cruise AT15-51 (Sample JdF2009). The basalt piece had a thick (up to 1 cm depth) glassy rim overlying moderately to sparsely vesicular cryptocrystalline groundmass. A film of iron oxide discoloration was evident in the contact between the glass and groundmass. Two altered, seafloor-exposed basalts were collected from the Loihi Seamount off the coast of the big island of Hawai’i in October 2009 by ROV Jason-II during R/V Kilo Moana cruise KM0923: one from “Marker 2” in Pele’s Pit on the summit of the Loihi Seamount, and one from the Ula Nui vent field at the base of the Loihi Seamount. Sample Ula Nui, collected on dive J2-477, was glassy, highly vesicular, and friable, contained ∼3 mm olivine phenocrysts, and displayed visible iron oxide staining. Sample Marker 2, collected on dive J2-481 from an area away from diffuse venting, was pillow basalt with an altered rind Finally, two seafloor-exposed rocks were collected from outcrops surrounding North Pond in April 2012 by ROV Jason-II on dives J2-626 and J2-627 during the MSM20-5 cruise on the R/V Maria S. Merian. The J2-626-R1 rock was a breccia of mm- to cm-sized clasts of aphanitic basalt in a greenish-gray matrix, while the J2-627-R3 rock was a highly serpentinized harzburgite (25–30% orthopyroxene surrounded by completely serpentinized olivine and with chrysotile-filled veins.
Upon retrieval of the samples, all seafloor-exposed rocks and surrounding water from the plastic sampling containers were immediately transferred to glass jars and placed at 4 degrees C until processing. Basalts were then transferred to ethanol- and flame-sterilized steel processing trays and subsampled with ethanol- and flame-sterilized chisels and tweezers. The experiments utilized the glassy rims of the basalts, which were removed, broken into smaller pieces (<1 cm diameter) and transferred to sterile glass serum vials (30–100 ml volume, depending on experiment) containing 0.2-mm-mesh filter-sterilized oxic bottom seawater. All samples were maintained at 4 degrees C.
Basalt fragments (5–20 cm3) were transferred to sterile and baked glass serum vials (to remove organics, vials had been heated to 500 degrees C for 2 h), which were filled to overflowing with sterile oxic seawater then sealed with autoclaved butyl rubber septa and aluminum crimp seals. Multiple replicate bottles were prepared for each sample to enable as many time series as possible with the limited sample volume, including a no-tracer-addition control.
Time series samples were injected with a small volume of 0.2-um filter-sterilized 13C-bicarbonate-labeled solution (in sterile filtered seawater) to achieve the following starting concentrations: JdF2009 incubations received a final concentration of 0.75 mM 13C-labeled bicarbonate against a background of seawater bicarbonate (∼2 mM, or, 27% 13C label); the Ula Nui and Marker 2 rock incubations received a final concentration of 2.7 mM 13C-labeled bicarbonate in background bottom seawater (57% 13C label); and the seafloor-exposed North Pond basalt incubations contained a final concentration of 4.5 mM 13C-labeled bicarbonate in surface seawater (69% 13C label). Vials were incubated in the dark at 4 degrees C until sampling. At each time point, the vials were opened and rock fragments were transferred to sterile plastic centrifuge tubes and frozen for shore-based DNA and organic carbon extraction and analysis. For the JdF2009, Marker 2, and Ula Nui samples, time series were stopped after 1 h, 1 day, and 1 week of incubation. The North Pond samples were incubated for 2-weeks, 2-months, and 4-months intervals. Final concentrations of dissolved inorganic carbon were not measured, as rates of carbon consumption were presumed to be significantly slow compared to the bulk pool size.
The carbon content and stable carbon isotopic composition of biofilms on the incubated basalts were determined by IRMS analysis of subsamples of the basalts that had been stored frozen. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer. Results are presented in the standard δ notation, where isotopic ratios (R) are expressed in per mil (‰) differences relative to the conventional standard, the PeeDee Belemnite limestone. Although the instrument precision was established as 0.3‰, rates of change were conservatively assumed to be robust if there was more than a 2‰ difference between samples; values less than 2‰ difference are reported as below the detection limit (BDL).
BCO-DMO Processing:
– Added the following columns from information Orcutt et al. (2015) paper: cruise, dive, date, water_depth, depth_mbsf, lat, lon;
– replaced “b.d.l.” with “BDL” (below detection limit), “n.a.” with “na”, “n.d.” and blanks with “nd” (no data);
– replaced spaces with underscores in sample names.
Dried samples of basalt (20–70 mg) were placed into tin foil capsules for isotopic analysis of 13C/12C ratios. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer.
Dried samples of basalt (20–70 mg) were placed into tin foil capsules for isotopic analysis of 13C/12C ratios. Samples were analyzed using a Costech elemental analyzer in line with a Micromass Isoprime continuous flow stable isotope mass spectrometer.
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.
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
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)
Meters below seafloor (mbsf); convention used for depths below the seabed in geology, oceanography, petrology and ocean drilling; often used in reporting measurements made from sediment cores.
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
Duration of sample incubation; used in laboratory experiments. Refer to dataset for units of measure.
| Name | Affiliation | Contact |
|---|---|---|
| Beth N. Orcutt | Bigelow Laboratory for Ocean Sciences | ✓ |
| Shannon Rauch | Bigelow Laboratory for Ocean Sciences | ✓ |
| Project Title | Primary productivity in young, oxic oceanic crust: rates of activity and autotrophic groups in subsurface and seafloor-exposed basalts from North Pond, Mid-Atlantic Ridge |
|---|---|
| Acronym | Basalt carbon fixation |
| URL | https://www.bco-dmo.org/project/660300 |
| Created | September 30, 2016 |
| Modified | October 5, 2016 |
Project description obtained from C-DEBI:
We conducted stable carbon isotope incubations with four subsurface rocks and two seafloor-exposed rocks collected from the North Pond major program site during IODP Expedition 336 in 2011 and the MSM20-5 cruise in 2012, respectively. In combination with similar experiments done with basalts from the Loihi Seamount and the Juan de Fuca Ridge, our experiments document the potential for carbon fixation by basalt biofilm communities, providing the first empirical assessment of potential rates for this process. When scaled to the global production of oceanic crust, our results suggest carbon fixation rates that match earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this vast, dark environment.
Related Publications:
Orcutt, B.N., Sylvan, J.B., Rogers, D.R., Delaney, J., Lee, R.W. Girguis, P.R. 2015. Carbon fixation by basalt-hosted microbial communities. Frontiers in Microbiology, 6: 904.C-DEBI Contribution 277. doi:10.3389/fmicb.2015.00904
Note: This project was funded by a C-DEBI Research Grant.
| Name | Affiliation | Role |
|---|---|---|
| Beth N. Orcutt | Bigelow Laboratory for Ocean Sciences | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/632784 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/632784/data/download |
| Media Type | text/tab-separated-values |
| Created | January 18, 2016 |
| Modified | August 19, 2016 |
| State | Final no updates expected |
| Brief Description | Whole genome sequence data from bacterial isolates from venting fluids at NW Rota Seamount, collected in 2009 and 2010. |
Diffuse hydrothermal vent fluids were collected at several vent sites on NW Rota-1 seamount in 2009 and 2010 using the ROV Jason 2 and the hydrothermal fluid and particle sampler. Anaerobic enrichment media previously used for the isolation of Caminibacter profundus was inoculated with 1 ml of unfiltered diffuse flow fluids and incubated at 55 degrees C. Enrichments with positive microbial growth were isolated by three sets of dilution-to-extinction. The growth of Lebetimonas under varying conditions including alternative electron donor/acceptor pairs and with N2 gas as the sole nitrogen source was evaluated as described in the Supplementary Material of Meyer & Huber (2014). Growth of Lebetimonas strain JH369 with N2 gas as the sole nitrogen source was evaluated using anaerobic seawater media without yeast extract or ammonia and containing formate and elemental sulfur with an 80% N2 and 20% CO2 headspace.
Genomic DNA was extracted from pure cultures at log phase using a CTAB extraction. Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina). In the case of strains sequenced with multiple platforms, the same genomic DNA extraction was used for all library preparations, with the exception of strain JS085. Genomes were assembled using several tools as described in the Supplementary material of Meyer and Huber 2014.
Related references:
Meyer, J.L. and J.A. Huber. 2014. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME Journal. 8:867–880. doi:10.1038/ismej.2013.206
Prior to assembly, Illumina sequences were quality filtered using adaptive window trimming and a quality threshold of 30 using the script Trim.pl (http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.pl). All reads were screened for adaptor, barcorde, primer, and transposan sequences and trimmed as needed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). De novo genome assembly was performed with several assembly programs. Sequences generated through the 454 platform were first assembled with Roche’s GS De Novo Assembler v 2.6 (“Newbler”) 2 using default parameters. De novo assemblies of 454 reads were also performed using mira 3 with the default settings for normal quality de novo genome assembly. De novo assembly of subsets of Illumina reads was performed with velvet 4, using an estimated coverage of 1000x, kmer size of 21, and a coverage cutoff of 5). Large contigs from Newbler , mira, and velvet were consolidated using Geneious Pro v 5.6.6 (Biomatters, Ltd, http://www.geneious.com) and aligned with progressiveMauve 5 to visualize the relationship of large contigs from different assemblies and to identify gaps to close. Primers were designed at the ends of contigs using either Geneious Pro or CLC Genomics Workbench v 5.1 (CLCbio, http://www.clcbio.com) to amplify gaps between contigs. Positive PCR amplification products linking contigs were cleaned using a Min-Elute PCR Purification kit (Qiagen) and Sanger sequenced. A nearly complete draft genome from strain JS085 served as a reference genome for the remaining five strains. Both Illumina and 454 reads were mapped to the reference genome with CLC Genomics Workbench. Unmapped reads were then assembled de novo to ensure that novel genomic content in the mapped strains was not overlooked. De novo assembly of 454 and/or Illumina reads for each strain was also performed in CLC Genomics Workbench and compared to the mapped assemblies using progressiveMauve.
Four of the strains were sequenced using both 454 and Illumina and two strains were sequenced only with Illumina. The sequencing coverage depth of quality-filtered reads ranged from 22X to 50X for 454 and up to 3618X for Illumina. Lebetimonas strain JS085 had the highest coverage of 454 reads and was assembled into 33 large contigs with Newbler and 1747 contigs with mira. The 20 largest contigs from each of these assemblies were consolidated using de novo assembly in Geneious to 10 contigs. An additional round of assembly in Geneious with the 10 consolidated contigs and velvet contigs greater than 10 Kbp further consolidated the draft genome to 6 contigs. Primers were designed for all possible combinations between the 6 contigs. One gap was closed using Sanger-sequenced positive pcr products. Finally, all 454 and Illumina reads for strain JS085 were mapped to the draft genome consisting of 5 contigs and the resulting consensus was used as the final draft genome. The five remaining genomes were assembled by mapping 454 and Illumina reads to the JS085 reference genome in CLC Genomics Workbench. Hybrid de novo assemblies in CLC Genomics Workbench of each strain did not extend contigs or close gaps between the 5 contigs of the draft genomes. Assemblies of unmapped reads produced only short contigs with no significant similarities using nucleotide BLAST 6.
BCO-DMO Processing:
– modified parameter names to conform with BCO-DMO naming conventions;
– added hyperlinks;
– removed “m” (meters) in depth column.
Libraries were prepared using Nextera DNA sample prep kits (Illumina, San Diego, CA, USA) and sequenced by Roche 454 GS FLX Titanium (454 Life Sciences, Branford, CT, USA) and/or using Illumina HiSeq 2000 paired reads (Illumina).
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.
phylum, organism taxonomic level. May include super-phylum and sub-phylum
order, organism taxonomic level; may include super-order and sub-order
Family. One of the levels in the taxonomic system of classification; typically ends in 'ae'. . May include super-family and sub-family.
a taxonomic binomial that consists of a genus name followed by the species name of an organism
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.
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
| Name | Affiliation | Contact |
|---|---|---|
| Julie A. Huber | Marine Biological Laboratory (MBL) | ✓ |
| Shannon Rauch | Marine Biological Laboratory (MBL) | ✓ |
| Project Title | Functional gene diversity and expression in ocean crust microbial communities |
|---|---|
| Acronym | NP Functional Gene Div |
| URL | https://www.bco-dmo.org/project/637566 |
| Created | February 1, 2016 |
| Modified | February 1, 2016 |
Project description from C-DEBI:
The objective of this project is to determine the diversity, phylogeny, and expression of functional genes involved in carbon, hydrogen, and sulfur cycling in North Pond crustal fluids. These formation fluids are expected to be representative of the ubiquitous cold ocean crust habitat, where reactions between the water and mineral rock surfaces create substrates suitable for sustaining a potentially large reservoir of microbial life. Information regarding crustal microbial communities and the energy sources available for microbial metabolism has been limited by the inaccessibility of samples. IODP Expedition 336 will provide a unique opportunity to access deep subsurface formation fluids from North Pond, including sampling from multiple depth horizons within oceanic crust. My goal is to develop quantitative polymerase chain reaction assays to determine the expression of functional genes in order to increase our understanding of microbial metabolisms in deep subsurface environments.
This project was funded by a C-DEBI Postdoctoral Fellowship to Julie Meyer (formerly at the Marine Biological Laboratory).
| Name | Affiliation | Role |
|---|---|---|
| Julie L. Meyer | University of Florida (UF) | Principal Investigator |
| Julie A. Huber | Marine Biological Laboratory (MBL) | Co-Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/664422 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/664422/data/download |
| Media Type | text/tab-separated-values |
| Created | November 10, 2016 |
| Modified | July 3, 2017 |
| State | Final no updates expected |
| Brief Description | DO of pore water from sediment gravity and push cores |
Sampling took place at Dorado Outcrop off the west coast of Costa Rica in the Pacific Ocean during the R/V Atlantis cruises AT26-09 and AT26-24. For more information about operations of this cruise see the cruise pages which contain links to cruise reports ( AT26-09, AT26-24).
Dissolved oxygen (DO) was measured at-sea in pore waters from sediment gravity cores and cores collected by the submersible ALVIN with a needle-type oxygen optode inserted radially into sediment cores, following published protocols (e.g., Orcutt et al., 2013).
Reference:
Orcutt, B. N., Wheat, C. G., Rouxel, O., Hulme, S., Edwards, K. J., Bach, W., 2013. Oxygen Consumption rates in subseafloor basaltic crust derived from a reaction transport model, Nature Comm., published 27 Sep 2013, pg. 1-8, doi:10.1038/ncomms3539.
The data have not been processed further.
BCO-DMO Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values replaced with no data value ‘nd’
* added approximate lat/lon values for Dorado Outcrop sample site
Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
Approximate latitude of Dorado Outcrop
latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes
Approximate longitude of Dorado Outcrop
longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes
Core identifier
Core identification number or label; often used with ice, rock, sediment, or coral cores.
Depth in core sample
Dissolved oxygen
Oxygen; dissolved; reported in units of micromoles/liter
| Name | Affiliation | Contact |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF) | ✓ |
| James McManus | University of Alaska Fairbanks (UAF) | ✓ |
| Beth N. Orcutt | University of Akron (UAkron) | |
| Andrew T. Fisher | University of Akron (UAkron) | |
| Samuel M. Hulme | Bigelow Laboratory for Ocean Sciences | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | |
| Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
| Project Title | Discovery, sampling, and quantification of flows from cool yet massive ridge-flank hydrothermal springs on Dorado Outcrop, eastern Pacific Ocean |
|---|---|
| Acronym | Dorado Outcrop |
| URL | https://www.bco-dmo.org/project/627844 |
| Created | November 30, 2015 |
| Modified | December 1, 2015 |
Description from NSF award abstract:
Pristine fluids from a typical ridge-flank hydrothermal system have never been sampled, mainly because it has not been possible to locate a site of focused discharge where representative samples could be collected. The PIs have located a small basement feature, Dorado outcrop, on 23 m.y.-old seafloor on the eastern flank of the East Pacific Rise that they plan to sample to determine the fluid composition, and to assess the rate of discharge from the outcrop, so that they can quantify the chemical impact of this hydrothermal system. They plan an 18-day expedition that combines the surveying capabilities of the AUV Sentry (bathymetric, sub-bottom sonar, photo mosaics, water column anomalies) and an ocean-class vessel capable of collecting high-quality multi-beam data and CTD samples, and supporting the survey and sampling capabilities of the ROV Jason II for collection of spring and plume fluids, heat flow data, sediment push cores, and still and video photography. These data and samples will be combined hopefully to generate the first well-constrained estimates of hydrothermal flows from Dorado outcrop. This expedition will result in the collection of samples and data from a “fire hose” of ridge-flank, hydrothermal system, challenging the commonly held view that discharge from ridge flank hydrothermal systems occurs primarily from diffuse seeps.
| Name | Affiliation | Role |
|---|---|---|
| Charles Geoffrey Wheat | University of Alaska Fairbanks (UAF-IMS) | Principal Investigator |
| Andrew T. Fisher | University of California-Santa Cruz (UC Santa Cruz) | Principal Investigator |
| Samuel M. Hulme | Moss Landing Marine Laboratories (MLML) | Principal Investigator |
| URL | https://www.bco-dmo.org/dataset/616326 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/616326/data/download |
| Media Type | text/tab-separated-values |
| Created | October 23, 2015 |
| Modified | August 19, 2016 |
| State | Final no updates expected |
| Brief Description | Assembled metagenome sequences > 500 bp from EPR, Lo'ihi, and control |
Methodology:
EPR: Rock material was collected from the EPR at 9.725 N, 104.16 W (2,674 m depth) aboard the R/V Atlantis using the submarine Alvin (cruise AT11-07, dive 3968) in 2004. DNA was extracted from basalt chips using a phenol-chloroform extraction including a negative control. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA samples and the control were sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).
Loi’hi: Two seafloor basalt samples (J2-243 R2-F, J-246 R2) were collected from the Lō’ihi Seamount (18.47 N, 155.18 W) at a depth of 5,000 m aboard the R/V Melville using the ROV Jason II in 2006. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA samples and the control were sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).
Negative control: DNA was extracted from sterile MilliQ water using a phenol-chloroform extraction. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA was sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).
All seafloor basalts were stored frozen at -80°C for XRD analysis and DNA extraction. Bulk mineralogy analysis, i.e. quantitative determination of rock-forming minerals and total clay minerals, was determined on all three seafloor basalts via X-ray Diffraction (XRD) analysis at KT GeoServices, Inc. Detection limits were at 1-5 wt%. For the two Lō’ihi seafloor basalts, average values were used.
Raw sequence reads were evaluated with FastQC version 0.11.3 (Schmieder and Edwards, 2011a), quality trimmed (minimum quality score – 25, maximum length – 450 bp, maximum homopolymer length – 9 bp, max N-tail – 1 bp), and filtered (removal of technical duplicates, minimum length – 60 bp) with Prinseq 0.20.4 (Schmieder and Edwards, 2011b) and MG-RAST (Meyer et al., 2008). We obtained 1,191,651 sequences in the EPR dataset; 1,102,191 sequences in the Lo’ihi dataset; and 58,188 sequences in the negative control dataset. Quality-filtered reads were assembled denovo using standard 454 settings in mira 3.4.1.1 (Chevreux et al., 1999). Padded (i.e. including potential gaps) contigs > 500 bp were filtered using mira 3.4.1.1 (convert_project) (Chevreux et al., 1999). Seafloor basalt contigs were screened for contamination using a combination of BBMap (bbduk.sh with parameters mcf=0.25, k=31) and the BLASTN algorithm (Altschul et al., 1990). The BBMap algorithm identified 4 potentially contaminant contigs in the EPR metagenome dataset (total of 4,290 bp) and 10 potentially contaminant contigs in the Lo’ihi (total of 12,423 bp). Community richness was estimated using the Chao1 index, diversity analysis was calculated using the Shannon index in QIIME 1.9.1 (alpha_diversity.py) based on BLASTX assignments of contigs. Phylosift was used to assess community diversity using the core molecular marker set of genes, which includes ~40 three-domain protein coding genes, single-copy eukaryote specific nuclear orthologs, ribosomal RNA genes (16S/18S), mitochondrial genes (mtDNA markers), and plastid and viral markers identified through Markov-clustering algorithms applied to genome datasets (Darling et al., 2014).
BCO-DMO Processing:
version 2015-11-06: replaced version 2015-10-23. Added site, lat, lon, and date columns.
Jason dives 243 and 246 (18.47 N, 155.18 W).
DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA)
General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA) at the core genomics center at University of Pennsylvania.
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.
X-ray Diffraction (XRD) analysis at KT GeoServices, Inc.
Instruments that identify crystalline solids by measuring the characteristic spaces between layers of atoms or molecules in a crystal.
Site name: EPR = East Pacific Rise: Loihi = Loi'hi Seamount Hawaii.
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 file (such as a data file or document).
link to NCBI GenBank accession page
| Name | Affiliation | Contact |
|---|---|---|
| Katrina J. Edwards | University of Southern California (USC) | |
| Esther Singer | University of Southern California (USC) | |
| Nancy Copley | University of Southern California (USC) | ✓ |
| Project Title | Metagenomic signatures in seafloor rocks and subsurface sediments: East Pacific Rise and Loihi Seamount |
|---|---|
| Acronym | EPR and Loihi basalt genomes |
| URL | https://www.bco-dmo.org/project/616350 |
| Created | October 23, 2015 |
| Modified | November 6, 2015 |
The seafloor and subsurface microbial world represents a significant portion of life on our planet. The influence on its proximate ambience and global processes, such as element cycles, has potentially been largely underestimated and not always been precisely evaluated. I am interested in the nature of deep biosphere microorganisms in rocks from the Loihi seamount, Hawai’i, the East Pacific Rise, and the Juan de Fuca Ridge, as well as in sediments from North Pond (Mid-Atlantic). In order to assess microbial diversity, metabolic activity, adaptation strategies and biogeographical signatures in the deep subseafloor biosphere, metagenomics by pyrosequencing will be used to complement previous research efforts with the most in-depth and precise data that is available to date.
This project is a C-DEBI Graduate Student Fellowship award (2011)
| Name | Affiliation | Role |
|---|---|---|
| Esther Singer | University of Southern California (USC) | Principal Investigator |
| 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/559780 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/559780/data/download |
| Media Type | text/tab-separated-values |
| Created | June 3, 2015 |
| Modified | February 10, 2017 |
| State | Final no updates expected |
| Brief Description | sample log from Jason-II dives for Sievert |
Samples were collected at several sites at the 9ºN deep-sea hydrothermal vent field on the East Pacific Rise. They included ROV Jason-II deployments J2-758, J2-759, J2-760, J2-761, J2-762. DNA was extracted following established protocols. We were able to successfully sequence 16S rRNA amplicons for Bacteria and Archaea from a total of 17 shipbaord incubations, 10 LVP samples, and one basalt rock sample. Sequence data are currently being analyzed and will be deposited in GenBank prior to publication and will be made available to the scientific community. From the incubations, the following analyses have been completed: total cell numbers, NanoSIMS analyses, 13C-bulk organic carbon analysis, and chemical measurements. These data are currently being prepared for a manuscript and data will be publically released with the publication. Metagenomic sequencing, metaproteomic analyses, and lipid biomarker analysis of the LVP samples are currently underway. Data will be made available to the scientific community once the data processing is complete and data are published. This is expected to be the case in the first half of 2016.
16S rRNA amplicons for Bacteria and Archaea were generated using 454 sequence technology. 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 are being used to discriminate among samples with similar community structures. Total sulfide was determined by combining a 2mL sample with sulfide antioxidant buffer and measuring voltage with a sulfide-selective electrode. The electrode was calibrated daily with a serial dilution of a standard sodium sulfide solution. To account for oxidation of the sulfide solution, the solution was titrated daily with lead nitrate to determine the actual sulfide concentration. pH was measured using an electrode, which was calibrated daily. Methane and hydrogen were determined by quantitative headspace extraction of a known volume of sample and measured on a GC-FID (for methane and concentrations of hydrogen > 5μM) or GC-TCD (for concentrations of hydrogen <5μM). Oxygen was determined by passing hydrothermal fluid through a specially designed flow-through cell fitted with a commercially available oxygen optode (Pts3, Presens, Germany). Fluorescence lifetime decay was measured every second using a computerized system corrected for temperature effects (Fibox 3, Presens, Germany), and the most stable final oxygen value was used. The oxygen optode spot was calibrated once with oxygen-free water (treated with sodium dithionate) and air-saturated water to make a two-point calibration. Prior to measurements, the optode flow-through cell was flushed with N2-purged FBSW to remove air bubbles and connected to the IGT sample valve while both were dripping liquid to avoid entrainment of air bubbles in the sample chamber. For subsequent nutrient analysis, fluids were filtered through a 0.2µm GTTP membrane and stored frozen at -20oC. Total nitrate+nitrite was determined by conversion to NO and chemiluminescent determination using the NoxBox instrument (Teledyne, San Diego CA, USA) following the original protocol (Garside 1982). Similarly, filtered samples were analyzed shipboard for total ammonium+ammonia by flow injection as previously described. All standards were pure chemicals made up in distilled water. All analytes, with the exception of oxygen, were measured in analytical duplicates. Cells were prepared for counting by preserving 1.5mL of fluids with 40µL of borate-buffered formalin, and subsequently adding 200µL of 0.1% acridine orange solution. The fixed and stained sample was then filtered under gentle vacuum onto a black 0.2µm polycarbonate filter, and enumerated aboard the ship by fluorescence microscopy. 10 grids were counted per sample and extrapolated using the area filtered to determine cell concentrations. All counts were done in analytical duplicates.
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.
Fibox 3/Pts3, Presens, Germany
For nitrate+nitrite measurement. Teledyne, San Diego CA, USA
The chemiluminescence method for gas analysis of oxides of nitrogen relies on the measurement of light produced by the gas-phase titration of nitric oxide and ozone. A chemiluminescence analyzer can measure the concentration of NO/NO2/NOX.
One example is the Teledyne Model T200: http://www.teledyne-api.com/products/T200.asp
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
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
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.
sampling date, UTC
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)
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
collection method: IGT=Isobaric Gastight Sampler ; LVP=Large Volume Pump
Method used to collect sample.
| Name | Affiliation | Contact |
|---|---|---|
| Stefan M. Sievert | Woods Hole Oceanographic Institution (WHOI) | ✓ |
| Craig Taylor | Woods Hole Oceanographic Institution (WHOI) | ✓ |
| Jeffrey S. Seewald | Woods Hole Oceanographic Institution (WHOI) | |
| Nancy Copley | Woods Hole Oceanographic Institution (WHOI) | |
| Fengping Wang | Woods Hole Oceanographic Institution (WHOI) | |
| Fengping Wang | 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/549138 |
|---|---|
| Download URL | https://www.bco-dmo.org/dataset/549138/data/download |
| Media Type | text/tab-separated-values |
| Created | February 5, 2015 |
| Modified | August 19, 2016 |
| State | Final no updates expected |
| Brief Description | Samples sequenced from chemosynthetic biofilm communities from deep-sea hydrothermal vents |
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.
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.
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.
Large Volume Pump (LVP): McLane WTS 6-1-142LV
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
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
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)
Description or characteristics of a sampling site
unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent
Method used to collect sample.
total concentration of the nucleic acid
| Name | Affiliation | Contact |
|---|---|---|
| Costantino Vetriani | Rutgers University (Rutgers IMCS) | ✓ |
| Nancy Copley | Rutgers University (Rutgers IMCS) | ✓ |
| 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 |
