Award: OCE-0939564

Award Title: Center for Dark Energy Biosphere Investigations (C-DEBI)
Funding Source: NSF Division of Ocean Sciences (NSF OCE)
Program Manager: David L. Garrison

Outcomes Report

C-DEBI's mission was to greatly expand our fundamental knowledge of the deep subsurface biosphere on Earth, with a particular focus on the igneous ocean crust and the overlying sediments. Our approach combined research efforts with the training of early career scholars, a range of knowledge transfer activities, and programs that integrated outreach and diversity. C-DEBI research in the initial phase primarily focused on exploration and discovery of subseafloor ecosystems anchored firmly in three major field programs: Juan de Fuca Ridge Flank, South Pacific Gyre, and North Pond. These field sites globally span a range of subseafloor environments, e.g., seafloor below oligotrophic ocean gyres, ridge systems and ridge flanks, and seamounts where fluids flow into or discharge from the subseafloor, with characteristics along the continuum of field habitats in sediment cover, rock type, crustal age, and fluid temperatures, among other environmental conditions that impact the deep biosphere. The overall goal was to investigate microbial life, geochemistry, and hydrology in the sediment and igneous crust of the subseafloor, beginning with a small set of focused study sites. These studies relied on a variety of truly innovative methods and tools, using numerous oceanographic technologies, including ships, submersibles, drilling, and observatories, capitalizing on the unprecedented scheduling of three ocean drilling expeditions within 18 months of each other, all with subseafloor microbiology as a major focus. As we moved forward into the second phase of C-DEBI, our exploratory and discovery-based science from multiple compelling seafloor settings was balanced with ongoing and new elements of hypothesis testing, data integration, laboratory experimentation, and modeling to develop an integrated understanding of subseafloor microbial habitats, communities, and adaptations maintaining highly multidisciplinary and interdisciplinary approaches. We had our greatest emphasis on microbial ecology, with three overarching research themes and associated research objectives: Theme 1: Fluxes, Connectivity, and Energy-centering on subseafloor environmental conditions; Theme 2: Activities, Communities, and Ecosystems-emphasizing resident microbial communities; and Theme 3: Metabolism, Survival, and Adaptation-concentrating on the actions and traits of individual microbial species. C-DEBI facilitated and encouraged the synthesis and broad understanding of submarine microbiological processes within geochemical, geophysical, and hydrogeologic contexts. This was largely accomplished by funding scientific and technical activities, coordinating and hosting meetings and workshops, and supporting researchers and graduate students (in over 100 grant projects at nearly 50 institutions including graduate student and postdoctoral research fellowships). These research endeavors generated a vast array of diverse data types and products that were managed, integrated and archived for the long term, as well as a vast array of important scientific discoveries and technical advances that were disseminated to the scientific community and the broader population through journal publications (over 500 community contributions), worldwide access to data and new technologies, exchanges of personnel, lectures and presentations, professional development activities, conferences and workshops, and targeted courses for students and educators. C-DEBI incorporated deep biosphere research into all facets of its education, outreach, and professional development programs, with a keen focus on targeting and engaging underrepresented students at all levels. We have trained and mentored hundreds of undergraduate and K-12 students, instilling enthusiasm for scientific discovery in future subseafloor research and fostering the next generation of deep subseafloor biosphere researchers. C-DEBI has nurtured a growing multidisciplinary scientific community, and coordinated a broad range of complementary activities in research and training, thereby establishing a vibrant international community of scientists in a field that barely existed before C-DEBI. In C-DEBI's short decade of existence, we have trained, mentored, and financially supported >50 graduate students and postdoctoral fellows. Through C-DEBI, almost 100 graduate students and postdoctoral scholars, dominated by women (63%) and many underrepresented minorities (20%), have transitioned (or are in the process of transitioning) to permanent career appointments with opportunities for leadership in their chosen professions. Those women and underrepresented minorities include a Nature journal editor, a number of research scientists, and 50 faculty members at universities in the USA and elsewhere. Our legacy has spawned from our scientific community of subseafloor biosphere researchers into new related programs (e.g., NASA Astrobiology Institute: Life Underground, International Center for Deep Life Investigation, Accel-Net: Crustal Ocean Biosphere Research Accelerator, International Earth 4D program through the Canadian Institute for Advanced Research). Last Modified: 03/06/2023 Submitted by: Jan P Amend
DatasetLatest Version DateCurrent State
Assembled metagenome sequences collected on the R/V Melville (MGLN10MV) and R/V Atlantis (Alvin AT11-07) cruises in the Loihi Seamount, Hawaiian archipelago and East Pacific Rise from 2011-2013 (EPR and Loihi basalt genomes project)2016-01-14Final no updates expected
Sub-seafloor metatranscriptomes from anaerobic Peru Margin sediments collected on R/V JOIDES Resolution Leg 201 in 20022015-11-05Final no updates expected
Sub-seafloor sediment eukaryotic rRNA collected on R/V JOIDES Resolution Legs 201 and 204, R/V Maria Merian cruise MSM11-1 at North Pond, and R/V Meteor cruise M76-1a at the Benguela Upwelling System from 2002-20092015-11-06Final no updates expected
Accession numbers for raw sequence reads; samples collected on R/V Roger Revelle cruise KNOX02RR in the South Pacific Gyre from 2006-2007 (Microbial Diversity SPG project)2015-11-10Final no updates expected
Elemental composition for 16S rRNA gene amplicon and metagenomic sequences collected on the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project)2015-12-02Final no updates expected
NCBI accession numbers for metagenomic sequences collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project)2015-12-02Final no updates expected
16S rRNA gene amplicon sequence accessions collected from the R/V JOIDES Resolution (JRES-204) cruise in the Cascadia Continental Margin during 2002 (Methane-Hydrate Sediment Omics project)2015-12-02Final no updates expected
Iberian Margin Anaerobic Sediment 18S rRNA amplicons from R/V JOIDES Resolution cruise JRES-339 in the West Iberian margin from 2011-2012 (Subseafloor Microbial Ecology project)2015-12-02Final no updates expected
Iberian Margin Anaerobic Sediment Metagenomes from R/V JOIDES Resolution cruise JRES-339 in the West Iberian margin from 2011-2012 (Subseafloor Microbial Ecology project)2015-12-02Final no updates expected
Metagenomes from Delaware estuarine riverbank sediments obtained by push corer in July 20122015-12-04Final no updates expected
Microbial cell counts derived from the formation fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruises MSM20-5 and MSM37 from 2012-2014 (North Pond Microbes project)2015-12-29Final no updates expected
Net oxygen consumption rates of the fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM37 in 2014 2015-12-29Final no updates expected
Particulate organic carbon from the formation fluids recovered from the CORKs installed at North Pond; collected on Maria S. Merian cruise MSM20-5 in 20122015-12-30Final no updates expected
Dissolved organic carbon and total dissolved nitrogen from the formation fluids recovered from the CORKs installed at the North Pond; collected on Maria S. Merian cruise MSM20-5 in 2012 2015-12-30Final no updates expected
Raw LC-MS/MS data with list of identified peptides in xml format from a proteomic analysis performed on protein extracts of M. ferrooxydans2016-01-27Final no updates expected
Raw LC-MS/MS data, with list of identified peptides, and DNA sequences from a proteomic profile of Mariprofundus ferrooxydans2016-01-28Final no updates expected
16S rRNA Sequences from cathode-oxidizing lithoprophic isolates (COLI) from Catalina Harbor Marine sediments2016-01-28Final no updates expected
454 pyrotag sequencing of 16S rRNA genes from R/V Atlantis cruise AT15-35 in the Cascadia Basin and Juan de Fuca Ridge in 20082016-01-28Preliminary and in progress
The acetate and inorganic carbon uptake rates as determined via stable isotopic tracers from Maria S. Merian cruise MSM20-5 in 2012; data generated using the formation fluids recovered from CORKs installed at North Pond2016-02-03Final no updates expected
Sub-seafloor single amplified genomes (SAGs) from anaerobic Peru Margin sediment collected on R/V JOIDES Resolution cruise JRES-201 in 20022016-02-04Final no updates expected
Porewater measurements of nitrate concentration and N and O isotopic ratios (d15N and d18O) from bore holes at North Pond; collected during IODP expedition 336 on R/V JOIDES Resolution in the Mid-Atlantic Ridge in 20112016-02-04Final no updates expected
Porewater geochemistry (sulfate, methane, and DIC) from sediments of the White Oak River (WOR), NC, Station H in 2013 (SEDpep project)2016-03-11Preliminary and in progress
Activities of extracellular peptidases at Station H of the White Oak River (WOR) Station H in 2013 (SEDpep project)2016-03-14Preliminary and in progress
Inhibition data for 3 peptidases at Bogue Sound NC and Tennessee River at Knoxville (SEDpep project)2016-03-14Preliminary and in progress
Microbial diversity and geochemistry of marine sediment mesocosm, Cape Lookout Bight, North Carolina2016-07-27Final no updates expected
Sequence accession numbers for archaeal and bacterial clone libraries from Guaymas Basin sediments collected from R/V Atlantis cruise AT15-56 in 20092016-08-10Final no updates expected
Fungal iTAG analyses on Peru Margin sediment core samples from R/V JOIDES Resolution cruise JRES-201 in the Peru Margin from January to March 20022016-08-15Final no updates expected
40 16S amplicon libraries collected from sediments of the Adelie Basin from R/V JOIDES Resolution JRES-318 from Wellington, New Zealand to Hobart, Australia from January to March 20102016-08-16Preliminary and in progress
The manually curated genome of the SAG SCGC AD-561-N23; collected from R/V JOIDES Resolution JRES-318 from Wellington, New Zealand to Hobart, Australia from January to March 20102016-08-16Preliminary and in progress
Whole community (3 domain) metatranscriptomes for subsurface sediment core samples from R/V JOIDES Resolution cruises JRES-201 and JRES-317 in the Peru Margin and Canterbury Basin in 2002 and 2009-102016-08-16Final no updates expected
Bacterial 16S rRNA sequences from hydrothermal plume particles sampled at 9 degrees North, East Pacific Rise, depth 2500m, on R/V Atlantis cruise AT15-06 in July 2006.2016-08-16Final no updates expected
Bacterial 16S rRNA sequences from inactive sulfide chimneys from R/V Atlantis cruise AT11-20 in the North East Pacific Rise in November 20042016-08-18Final no updates expected
The eukaryotic (poly-A) metatranscriptome for Canterbury Basin from R/V JOIDES Resolution cruise JRES-317 in the Canterbury Basin from 2009-20102016-08-19Final no updates expected
Bacterial 16S rRNA sequences from seafloor rocks (silicates and sulfides) collected on R/V Thomas G. Thompson cruise TN235 in the Eastern Lau Spreading Center from May to June 20092016-08-24Final no updates expected
SSU rRNA gene sequences from marine sediments, marine subseafloor, and deep seawater sampled from the Juan de Fuca Ridge Flank from various R/V Atlantis cruises from 2008-2011 (microJdFR project)2016-10-07Final no updates expected
Stable carbon isotopic composition of organic matter from seafloor basalts incubated with labeled bicarbonate from R/V Atlantis AT15-51, R/V Kilo Moana KM0923, and Maria S. Merian MSM20-5 cruises2016-10-05Final no updates expected
Accession numbers for clone and Illumina amplicon sequence libraries from Dorado Outcrop basalts collected on R/V Atlantic cruise AT26-09 in December 20132016-10-06Final no updates expected
Porewater DIC concentrations and d13C isotopic values from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma in October 2014 2016-10-13Final no updates expected
Porewater methane concentrations from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin in 2014 from R/V El Puma in October 2014 2016-10-14Final no updates expected
Porewater sulfate concentrations from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin in 2014 from R/V El Puma in October 20142016-10-14Final no updates expected
Porewater sulfide concentrations from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin in 2014 from R/V El Puma in October 20142016-10-14Final no updates expected
16S rRNA gene sequences of cells in marine methane seep sediments from R/V Atlantis and R/V Western Flyer cruises off the Pacific Northwest, USA in 2010 and 20132016-10-25Final no updates expected
Carbon geochemistry of Santa Elena (Costa Rica) ultramafics and bulk rock carbonate samples from expeditions 149, 173, and 209 on R/V JOIDES Resolution in the Iberia Abyssal Plain, Iberian Margin, and Mid-Atlantic Ridge from 1993-20032016-11-03Final no updates expected
Description and isotopic composition of the carbonate deposits in the Santa Elena Ophiolite (Costa Rica) and expeditions 149, 173, and 209 on R/V JOIDES Resolution in the Iberia Abyssal Plain, Iberian Margin, and Mid-Atlantic Ridge from 1993-20032016-11-03Final no updates expected
Sulfur geochemistry of the Santa Elena (Costa Rica) ultramafics; R/V JOIDES Resolution JRES-149, JRES-173, JRES-209 cruises in the Iberia Abyssal Plain, Iberian Margin, and Mid-Atlantic Ridge from 1993-20032016-11-03Final no updates expected
Polysaccharide hydrolysis rates for Marmara Sea, Guaymas Basin, and Eastern Mediterranean Sea sediments collected from R/V El Puma and R/V Meteor cruises2016-12-09Final no updates expected
Geochemistry measurements from the Strytan Hydrothermal Field collected by SCUBA July 15-8 2012 (C-DEBI, Lost City-type hydrothermal system project) 2017-03-22Preliminary and in progress
Organic acid concentrations from the Strytan Hydrothermal Field collected by SCUBA July 15-8 2012 (C-DEBI, Lost City-type hydrothermal system project) 2017-03-22Preliminary and in progress
Dissolved inorganic carbon concentrations from the Strytan Hydrothermal Field collected by SCUBA July 15-8 2012 (C-DEBI, Lost City-type hydrothermal system project) 2017-03-22Preliminary and in progress
CH4, H2, CO, and d13C concentrations from the Strytan Hydrothermal Field collected by SCUBA July 15-8 2012 (C-DEBI, Lost City-type hydrothermal system project) 2017-03-22Preliminary and in progress
3H-leucine and thymidine incorporation of North Atlantic subseafloor sediments from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 20142017-03-27Final no updates expected
North Atlantic subseafloor sediment viable microbe numbers/metabolisms from cruise KN223 on R/V Knorr in the North and West Atlantic Ocean in November 2014 2017-03-28Final no updates expected
Single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N. 12C12C, 12C13C from Chikyu-337 (IODP 337)2017-08-10Final no updates expected
Geochemistry summary data: single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N, 12C12C, 12C13C ions from Chikyu-337 (IODP 337)2017-08-10Final no updates expected
Siderophore-enhanced olivine dissolution experiments from the University of Southern California (Microbial Olivine Dissolution project)2017-08-17Preliminary and in progress
Lake surface sediment and submarine canyon sediment bacterial V1-V3 iTag sequence libraries collected from CA and MN in 2012.2017-10-19Final no updates expected
Collection information and genetic accession identifiers for Single Amplified Virus Genomes from hydrothermal fluids at IODP HOLE U1362B CORK observatory from R/V Atlantis cruise AT18-07 ROV Jason dives at the Juan de Fuca Ridge Flank in July of 20112022-05-23Final no updates expected
Presence/absence of taxa detected with the Phylochip in a sediment core collected in the Ulleng Basin in 20112018-06-14Final no updates expected
16S gene sequencing of microbial communities in South China Sea sediments from January to March 20142018-09-05Final no updates expected
Porewater measurements of nitrate and nitrite concentration and N and O isotopic ratios (d15N and d18O) collected from sites 3 and 10 on the North Atlantic Long Core Cruise R/V Knorr KN223 from October to December 20142018-10-26Final no updates expected
d13C and d18O isotopic data for carbonate nodules and sedimentary carbonates in Guaymas Basin and Sonora Margin sediments collected from R/V El Puma, leaving Guaymas on October 14, 2014 and returning to Mazatlan on October 27, 20142019-03-13Final no updates expected
Radiocarbon [14C] ages of sedimentary organic matter and sedimentation rates for Guaymas Basin and Sonora Margin sediments collected from R/V El Puma, leaving Guaymas on October 14, 2014 and returning to Mazatlan on October 27, 20142019-03-13Final no updates expected
Pore water chemical concentration data and location from push cores collected by the ROV Jason II on dive J2-773 from cruise MSM37 on R/V Maria S. Merian from March to April 20142019-04-11Final no updates expected
Modeling bio-energetics for South Pacific Gyre marine sediment at site U13702019-12-20Final no updates expected
16S rRNA gene (from DNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 20102019-11-05Final no updates expected
16S rRNA gene (from RNA) from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 20102019-11-05Final no updates expected
Metagenomic data from samples collected on cruise Chikyu-331 in the Okinawa Trough, Japan from September to October 20102019-11-05Final no updates expected
Organic carbon, d13C, and total nitrogen content of pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223, KNOX02RR, and ODP leg 201 between 2002 and 20132020-06-15Final no updates expected
Protein assay of proteinaceous material in pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223, KNOX02RR, and ODP leg 201 between 2002 and 20132020-06-15Final no updates expected
TOC concentrations from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma during October 20142019-12-12Final no updates expected
Porewater Si concentrations from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma during October 20142019-12-12Final no updates expected
delta 15N values from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma during October 20142019-12-12Final no updates expected
delta 13C values from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma during October 20142019-12-12Final no updates expected
Organic matter C:N ratios from sediment cores collected on the Guaymas Basin Ridge flanks and the Sonora Margin from R/V El Puma during October 20142019-12-12Final no updates expected
Calculated power from the oxidation of necromass that is produced in marine sediment on a global scale.2019-12-20Final no updates expected
Calculated power from the oxidation of biomolecules with oxygen at South Pacific Gyre (hole U1370, IODP Expedition 329)2019-12-20Final no updates expected
Solution 31P NMR spectra files from sediment samples collected during cruises in the Arctic Ocean, California Margin, and Equatorial Pacific from 1992-19982020-02-28Final no updates expected
Molybdate reactive phosphorus concentrations in NMR pretreatment extracts from sediment samples collected during cruises in the Arctic Ocean, California Margin, and Equatorial Pacific from 1992-19982020-04-13Final no updates expected
16S rRNA gene datasets, metagenomes, and metatranscriptomes from cores collected on R/V Knorr cruise KN223 in the North and West Atlantic Ocean from October to December 20142020-02-28Final no updates expected
Total molybdate reactive and unreactive phosphorus concentrations from sediment extracts from sediment samples collected during cruises in the Arctic Ocean, California Margin, and Equatorial Pacific from 1992-19982020-06-23Final no updates expected
Total phosphorus and metal concentrations from sediment extracts from samples collected during cruises in the Arctic Ocean, California Margin, and Equatorial Pacific from 1992-19982020-06-23Final no updates expected
Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during cruises in the Arctic Ocean, California Margin, and Equatorial Pacific from 1992-19982020-06-23Final no updates expected
Table 1: Experimental conditions and fluid carbonate chemistry for RPI-3 run where only aragonite precipitated2020-03-25Final no updates expected
Table 2. Elemental ratios and partition coefficients for CaCO3 in deepsea conditions: Mg, S, Sr, and Ba between crystallized solids and fluid.2020-03-25Final no updates expected
Thermovibrio ammonificans HB1 genome manual curation2020-04-13Final no updates expected
Metagenomic data from site U1382B at North Pond (IODP 336), western flank of the mid-Atlantic Ridge from core samples collected in November of 20112020-04-22Final no updates expected
Carbon isotopic compositions and fractionation factors of M. jannaschii in high and low hydrogen (H2) environments2020-05-25Final no updates expected
Carbon near edge X-ray absorption fine structure (NEXAFS) spectra of standard compounds2020-06-15Final no updates expected
Carbon near edge X-ray absorption fine structure (NEXAFS) spectra from pelagic sediment from the North Atlantic gyre, South Pacific gyre, and Peru Basin from cruises KN223 (R/V Knorr), KNOX02RR (R/V Roger Revelle), and ODP leg 201 between 2002 and 20142020-07-22Final no updates expected
Molybdate reactive phosphorus concentrations in NMR pretreatment extracts from sediment samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 20112020-06-23Preliminary and in progress
Total phosphorus concentrations in NMR sediment pretreatment extracts from samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 20112020-06-23Final no updates expected
Solution 31P NMR spectra files from sediment samples collected during R/V JOIDES Resolution cruise JRES-336 (IODP336, North Pond) to the western flank of the mid-Atlantic Ridge in November of 20112020-06-23Final no updates expected
Geochemical data collected from Whillans Subglacial Lake sediment cores in West Antarctica2020-08-27Data not available
pmoA sequences amplified from DNA extracted from Whillans Subglacial Lake sediment in West Antarctica2020-09-02Preliminary and in progress
High throughput tag-sequencing accessions (18S rRNA gene region) and environmental metadata from Axial Seamount, 2013-20152020-11-05Final no updates expected
High throughput tag-sequencing data from Gorda Ridge Hydrothermal vent field, including 16S and 18S rRNA gene sequences, and environmental metadata from Gorda Ridge Seamount, May/June 20192020-11-09Final no updates expected
Major catabolic pathway of organic carbon oxidation in Quaternary-age sediment quantified from bio-energetic modeling of subseafloor parameters on a 0.25°×0.25° resolution global grid2020-11-13Preliminary and in progress
Power produced by microbial POC degradation in Quaternary-age sediment quantified from bio-energetic modeling of subseafloor parameters on a 0.25°×0.25° resolution global grid2020-11-13Preliminary and in progress
Microbial power production per cell in Quaternary-age sediment quantified from bio-energetic modeling of subseafloor parameters on a 0.25°×0.25° resolution global grid2020-11-13Preliminary and in progress
Cell-specific power utilization (power per cell) in methanogenic, oxic, and sulfate-reducing sediments quantified from bio-energetic modeling of subseafloor parameters on a 0.25°×0.25° resolution global grid2020-11-13Preliminary and in progress
POC concentration at the sediment water interface quantified from bio-energetic modeling on a 0.25°×0.25° resolution global grid2020-11-13Preliminary and in progress
Summary geochemistry and radiotracer rates for 30 marine sediment cores covering eight sites and four geochemical regimes2020-11-19Final no updates expected
Costa Rica Margin Subseafloor Microbial Community Analysis2017-10-17Preliminary and in progress
16S rRNA sequences from subsurface microbial communities (Blackwood Sinkhole)2021-05-25Final no updates expected
18S rRNA amplicon sequencing of microbial eukaryotes from the Mid-Cayman Rise acquired Jan-Feb, 20202023-11-06Final with updates expected

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People

Principal Investigator: Jan P. Amend (University of Southern California)

Co-Principal Investigator: Andrew T Fisher

Co-Principal Investigator: Steven L D'Hondt

Co-Principal Investigator: Charles G Wheat

Co-Principal Investigator: Julie A Huber