A new series of DCO webinars focusing on big data modeling and visualization will launch Wednesday, 17 May 2017 at 2 pm EDT. Called “DCO Webinar Wednesdays,” this webinar series builds on the successful workshop program at the Third DCO International Science Meeting and will take place monthly over the summer. We hope you join in to learn from DCO experts in data science, modeling, and data visualization, who will guide you through a series of available modeling tools and software packages that you can integrate into your research now. Synthesis Group 2019 and the DCO Engagement Team are hosting this series. You can join the webinars live, and follow along on Twitter on the hashtag #DCOWebWed. All webinars will begin with a 30-minute presentation, followed by 15 minutes for open discussion and Q&A. We will archive the webinars as they happen, so don’t worry if you miss one! The final webinar of this series on 12 October 2017 will bring together the presenters for a live Q&A, giving you plenty of opportunity to view the archive and have your questions answered by our panel of experts. Contact Katie Pratt (firstname.lastname@example.org) or Darlene Trew Crist (email@example.com) with any questions about the webinar series, or if you would like to propose a future series.
The Deep Carbon Observatory, in collaboration with the Department of Earth Sciences of Sapienza University (Rome), is hosting its third Early Career Scientist Workshop in Nicolosi (Etna), Italy, 28 August-2 September 2017. This workshop will bring together the next generation of researchers active in deep carbon studies from around the world. Building on the success of the first and second DCO Early Career Scientist Workshops, this third workshop (~50 scientists) of early career researchers will continue to foster collaboration and community within the ever expanding DCO Science Network. The workshop is funded by the Alfred P. Sloan Foundation and aims to financially support as many participants as possible. There is no registration fee for this workshop (accommodation and meals will be provided). Successful applicants will be eligible for up to 100% reimbursement of travel costs. Senior graduate students, postdoctoral researchers, fellows, and newly appointed assistant professors, are encouraged to apply. The application window is open through April 14, 2017.
The NSF Continental Scientific Drilling Coordination Office (CSDCO) at the University of Minnesota requests participation in the development of a community Long Range Science Plan. If you plan to core or drill on Earth’s continents in the next 10 years, your ideas should be included in the Science Plan. This workshop is for scientific disciplines other than Paleorecords requiring continental drilling and coring: Critical Zone, Deep Biosphere, Tectonics/Magmatism, Fault Zone, Impact Structures, Hydrology, Geothermal, Geochemistry, and others. Travel is supported through CSDCO funding from NSF. The goal of this workshop is to identify and prioritize for each discipline the compelling science drivers, drilling/coring targets, strategic frameworks, and timelines focusing on continental localities in the coming decade. Projects include, but are not limited to, collaborative efforts and co-funding with international partners. Investigators with committed funding from the International Continental Scientific Drilling Program (ICDP), or those who will seek such support, are particularly encouraged to participate. Application deadline: April 14, 2017.
|Project Title||An Integrated Study of Energy Metabolism, Carbon Fixation, and Colonization Mechanisms in Chemosynthetic Microbial Communities at Deep-Sea Vents|
|Acronym||Microbial Communities at Deep-Sea Vents|
|Created||June 11, 2012|
|Modified||June 11, 2012|
Deep-sea hydrothermal vents, first discovered in 1977, are poster child ecosystems where microbial chemosynthesis rather than photosynthesis is the primary source of organic carbon. Significant gaps remain in our understanding of the underlying microbiology and biogeochemistry of these fascinating ecosystems. Missing are the identification of specific microorganisms mediating critical reactions in various geothermal systems, metabolic pathways used by the microbes, rates of the catalyzed reactions, amounts of organic carbon being produced, and the larger role of these ecosystems in global biogeochemical cycles. To fill these gaps, the investigators will conduct a 3-year interdisciplinary, international hypothesis-driven research program to understand microbial processes and their quantitative importance at deep-sea vents. Specifically, the investigators will address the following objectives: 1. Determine key relationships between the taxonomic, genetic and functional diversity, as well as the mechanisms of energy and carbon transfer, in deep-sea hydrothermal vent microbial communities. 2. Identify the predominant metabolic pathways and thus the main energy sources driving chemoautotrophic production in high and low temperature diffuse flow vents. 3. Determine energy conservation efficiency and rates of aerobic and anaerobic chemosynthetic primary productivity in high and low temperature diffuse flow vents. 4. Determine gene expression patterns in diffuse-flow vent microbial communities during attachment to substrates and the development of biofilms.
Integration: To address these objectives and to characterize the complexity of microbially-catalyzed processes at deep-sea vents at a qualitatively new level, we will pursue an integrated approach that couples an assessment of taxonomic diversity using cultivation-dependent and -independent approaches with methodologies that address genetic diversity, including a) metagenomics (genetic potential and diversity of community), b) single cell genomics (genetic potential and diversity of uncultured single cells), c) meta-transcriptomics and -proteomics (identification and function of active community members, realized potential of the community). To assess function and response to the environment, these approaches will be combined with 1) measurement of in situ rates of chemoautotrophic production, 2) geochemical characterization of microbial habitats, and 3) shipboard incubations under simulated in situ conditions (hypothesis testing under controlled physicochemical conditions). Network approaches and mathematical simulation will be used to reconstruct the metabolic network of the natural communities. A 3-day long project meeting towards the end of the second year will take place in Woods Hole. This Data Integration and Synthesis meeting will allow for progress reports and presentations from each PI, postdoc, and/or student, with the aim of synthesizing data generated to facilitate the preparation of manuscripts.
Intellectual Merit. Combining the community expression profile with diversity and metagenomic analyses as well as process and habitat characterization will be unique to hydrothermal vent microbiology. The approach will provide new insights into the functioning of deep-sea vent microbial communities and the constraints regulating the interactions between the microbes and their abiotic and biotic environment, ultimately enabling us to put these systems into a quantitative framework and thus a larger global context.
Broader Impacts. This is an interdisciplinary and collaborative effort between 4 US and 4 foreign institutions, creating unique opportunities for networking and fostering international collaborations. This will also benefit the involved students (2 graduate, several undergraduate) and 2 postdoctoral associates. This project will directly contribute to many educational and public outreach activities of the involved PIs, including the WHOI Dive & Discover program; single cell genomics workshops and Cafe Scientifique (Bigelow); REU (WHOI, Bigelow, CIW); COSEE and RIOS (Rutgers), and others. The proposed research fits with the focus of a number of multidisciplinary and international initiatives, in which PIs are active members (SCOR working group on Hydrothermal energy and the ocean carbon cycle, http://www.scorint. org/Working_Groups/wg135.htm; Deep Carbon Observatory at CIW, https://dco.gl.ciw.edu/; Global Biogeochemical Flux (GBF) component of the Ocean Observatories Initiative (OOI), http://www.whoi.edu/GBF-OOI/page.do?pid=41475)
|Stefan M. Sievert||Woods Hole Oceanographic Institution (WHOI)||Lead Principal Investigator|
|Costantino Vetriani||Rutgers University||Principal Investigator|
|Dionysis I. Foustoukos||Carnegie Institution for Science (CIS)||Principal Investigator|
|Ramunas Stepanauskas||Bigelow Laboratory for Ocean Sciences||Principal Investigator|
|Craig Taylor||Woods Hole Oceanographic Institution (WHOI)||Co-Principal Investigator|
|Jeffrey S. Seewald||Woods Hole Oceanographic Institution (WHOI)||Co-Principal Investigator|
|Nadine Le Bris||Laboratoire d'Écogéochimie des Environnements Benthiques (LECOB)||International Collaborator|
|Niculina Musat||Max Planck Institute for Marine Microbiology (MPI)||International Collaborator|
|Thomas Schweder||University of Greifswald||International Collaborator|
|Fengping Wang||Shanghai Jiao Tong University (SJTU)||International Collaborator|
Since its inception, the Deep Carbon Observatory (DCO) has coalesced a multidisciplinary and international group of researchers focused on understanding and quantifying Earth's deep carbon budget. Carbon is the fourth most abundant element in the universe, and understanding carbon chemistry under a variety of environmental conditions impacts all aspects of planetary sciences. DCO recognizes that contributions of early career scientists are integral to the advancement of knowledge regarding the quantities, movements, origins, and forms of Earth's deep carbon. This research topic highlights the contributions of the DCO Early Career Scientist community.
|Project Title||Edginess in the subsurface: Microbial diversity of deep subseafloor ecotones|
|Acronym||Edginess in the subsurface|
|Created||September 5, 2018|
|Modified||September 5, 2018|
For subseafloor microorganisms, defined geological and chemical gradients affect population sizes and community structure. We examined how distinct sediment types influence microbial diversity and community composition and the factors that drive deep-subsurface microbial community structure (e.g., depth, interstitial water chemistry, sample location). During IODP Expedition 349 (South China Sea Tectonics), either coupled ash/clay or turbidite/clay boundaries were sampled, DNA extracted, and the 16S rRNA gene analyzed on an Illumina MiSeq platform. Microbial communities in sediments were distinct from communities in drilling fluid, indicating that drilling-based contamination was unlikely. Illumina sequencing of the 16S rRNA gene yielded 5,453 OTUs (97% identity) representing 44 bacterial phyla and 3 archaeal phyla. Members of the Atribacteria dominated all microbial communities among all sites. Sulfate-reducing bacteria were relatively rare within sulfate-replete sediments in all cores. Ordination of the microbial communities using weighted UniFrac distances revealed significant differences in communities both between sites and between the sulfate reduction zone and methanogenic zone at two of the sites. The number of observed taxa followed an exponential decline with sediment age only in the sulfate reduction zone. Species evenness increased linearly with sediment age regardless of geochemical zonation in the sediment column. Our investigation helps to characterize the factors that drive microbial community structure of the subseafloor and highlights the need to focus on habitat heterogeneity at a scale pertinent to bacteria and archaea in studies of microbial ecology.
This project is funded with:
Center for Dark Energy Biosphere Investigations (C-DEBI); subaward number: 59209190
Deep Carbon Observatory (DCO) /Deep Life Community (DLC); subaward number: 53587
Consortium for Ocean Leadership; award number: IUSSP410
|Frederick S. Colwell||Oregon State University (OSU)||Principal Investigator||✓|
|Andrew R. Thurber||Oregon State University (OSU)||Co-Principal Investigator|
AbstractThe emplacement of subaqueous gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical and biological signatures of turbidite deposition, the response of bacteria and archaea within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and those attached to allochthonous material must respond to substantially altered environmental conditions and selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine (i) the microbial community response to rapid sedimentation and (ii) the preservation and identification of displaced micro-organisms. We collected Illumina MiSeq sequence libraries across turbidite boundaries at ~26 cm sediment depth in La Jolla Canyon off the coast of California, and at ~50 cm depth in meromictic Twin Lake, Hennepin County, MN. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, both the marine and lacustrine turbidite boundaries are sharply demarcated by the abundance and diversity of Chloroflexi, suggesting a characteristic sensitivity to sediment disturbance history or to differences in organic substrates across turbidite profiles. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the buried La Jolla Canyon sediment–water interface reflect turbidite-induced changes to the geochemical environment. Species-level distinctions within the Deltaproteobacteria clearly conform to the sedimentological boundary, suggesting a continuing impact of genetic inheritance distinguishable from broader trends attributable to selective pressure. Abrupt, <1-cm scale changes in bacterial diversity across the Twin Lake turbidite contact are consistent with previous studies showing that relict DNA signatures attributable to sediment transport may be more easily preserved in low-energy, anoxic environments. This work raises the possibility that deep subsurface microbial communities may inherit variations in microbial diversity from sediment flow and deformation events.
AbstractDiscrete biological community signatures were identified in individual sub‐annually deposited sedimentary laminae of anoxic lake sediments from two lakes in the Minneapolis–St. Paul (Minnesota, U.S.A.) urban area. Recognizing variation in microbial communities associated with discrete millimeter scale sedimentary horizons was made possible using a freeze‐coring method to recover bacterial DNA for amplicon iTag sequencing and Terminal Restriction Fragment Length Polymorphism analyses. Variation in 16S rRNA gene composition between laminae suggests that seasonal changes in cell transport from the water column impart a residual molecular signature on subsurface communities. Direct comparison of frozen‐in‐situ core samples to ambient temperature sediment indicates that freeze coring methodology imposes no significant bias on DNA‐based community fingerprints. This work further supports previous observations demonstrating the efficacy of freeze coring for high‐resolution analysis of microbial communities, but here it is applied to resolving molecular signatures derived from sedimentary laminae.
Since 2011, the Deep Carbon Observatory’s (DCO; http://deepcarbon.net/) Deep Life Community has sponsored the Census of Deep Life (CoDL) that has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of diversity of subsurface microbial communities at numerous sites worldwide including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples can also be performed. This call for proposals aims to support sequencing that represents expanded analyses from ongoing Deep Life Community projects or projects that represent sites and investigators new to the DCO’s Deep Life Community. The proposal deadline is July 15, 2018.
The Deep Life Modeling and Visualization (DLMV) network of the Deep Life community of the Deep Carbon Observatory (DCO) is looking to fund postdoctoral fellows to develop interdisciplinary models that produce fundamental new insights or hypotheses regarding the carbon cycle on Earth. Themes may include but are not limited to (1) biosphere-geosphere coupling in the deep carbon cycle, (2) integration of microbiological data and data on (bio)geochemical rates, processes, or fluxes, (3) integration of quantitative microbiological data with physical and geochemical data to identify the limits of life and distribution of microbial biomass throughout the biosphere, and/or (4) modeling of interactions between deep life and continental evolution. Proposals may involve the (1) synthesis of insights and data produced by members of the Deep Life community, and (2) integration of these insights and data with insights and data produced by other communities within and outside the DCO. Ideal candidates will have a proven track record in interdisciplinary and quantitative biological, geochemical, and/or geological sciences that includes modeling and visualization, and demonstrated ability to work in a team of multi-disciplinary scientists. Proposal submission deadline: January 20, 2018.
Experience the Fall 2017 National Science Foundation (NSF) Grants Conference virtually. We are pleased to announce that the upcoming conference in Phoenix, AZ on November 13-14, will be webcast live to the research community. View the plenary sessions to gain key insights into a wide range of current issues at NSF including: the state of current funding, new and current policies and procedures, and pertinent administrative issues. Please click here to register. Check out the webcast agenda for more information on the sessions that will be covered. These sessions will be recorded for on-demand viewing once the conference has concluded. Presentations will also be available on the conference website.
Since 2011, the Deep Carbon Observatory’s (DCO) Deep Life Community has sponsored the Census of Deep Life (CoDL) that has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of diversity of subsurface microbial communities at numerous sites worldwide including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples can also be performed. This call for proposals aims to support sequencing that represents expanded analyses from ongoing Deep Life Community projects or projects that represent sites and investigators new to the DCO’s Deep Life Community. Proposal deadline: April 30, 2017.
Eight members of the DCO science network volunteered to become Wikipedia Fellows and to improve the content of science material on the free online encyclopedia. Through their efforts, they improved 23 articles and contributed more that 13,000 words to this widely read resource.
The sampling expedition Biology Meets Subduction: A Collaborative and Multidisciplinary Deep Carbon Field Initiative was designed to develop novel connections between microbiology, volcanic systems, and the cycling of living and dead (biotic and abiotic) carbon as Earth’s plates move and subduct past each other. With the fieldwork complete, the team, led by DCO early career scientists has started to publish their findings. Join Peter Barry (University of Oxford, UK), Karen Lloyd (University of Tennessee Knoxville, USA), and Donato Giovannelli (CNR-IRBIM, Italy and Rutgers University, USA) as they discuss their fieldwork in Costa Rica and Panama and share the value added and problems created by conducting a multidisciplinary scientific investigation in the field. The live webinar will be held January 23, 2019 at 11am PT / 2pm ET.
Message from the Director:
Proposals for C-DEBI Research Grants and Fellowships are due today! If you miss these annual calls, don’t forget we also support C-DEBI Community Workshops and Research Exchanges in a year-round call.
NSF Geoscience is again seeking input on exciting research to call out for support in their next report. Please comment on your perspective of deep biosphere research as an area to continue to fund by 2/1/18.
At last month’s C-DEBI Annual Meeting, our presently-funded research and education community met to discuss our current activities. The meeting was preceded by a graduate student and postdoctoral professional development workshop “Key steps to landing a job and what to do once you’ve been offered the position.” See the agenda.
Another season of our Networked Speaker Series is over and we thank the presenters for their great talks connecting all of us interested “deeply” or broadly in the deep biosphere (watch the archived talks online). Nominate an early career investigator doing exciting research with effective communication for next season’s series!
Going to the 2017 AGU Fall meeting this month? Join DCO and C-DEBI for a poster swarm of Session B11G “Unearthing the Metabolic Potential of Microorganisms in the Deep Subsurface Biosphere II Posters” on Monday December 11. Gather at poster B11G-1729 at 10AM to hear short presentations of posters in the session followed by questions and discussion. See additional sessions of interest. While you are at the meeting, share your photos, scientific ponderings, and new found knowledge with us on Twitter! Please tag any NSF-funded C-DEBI research with #NSFfunded, @NSF_GEO and @deepbiosphere. Both C-DEBI and NSF are prepared to share your Tweets!”
- Maps and Contacts (Final)
- Agenda (Final)
- Participant List (Final)
- Poster List (Final)
- Site Visit Presentations
2016 Annual Report
- 2016 C-DEBI Annual Report – revised (revised final including budget)
- Appendix A – References Cited
- Appendix B – Active Grants and Fellowships
- Appendix C – CC-RISE and C4 Student Evaluation
- Appendix D – CC Instructor Workshop Evaluations
- Appendix E – GGURE Student Evaluation
- Appendix F – GEM Student Evaluation
- Appendix G – GeoBio Student Evaluation
- Appendix H – Diversity Director Noda CV
- Appendix I – External Advisor Kaye CV
- Appendix J – Center-wide Outputs
- Appendix K – Current Award Year Budget
- Appendix L – USC Account Status
- Appendix M – Requested Award Year Budget
- Appendix N – Institutional Commitment