C-DEBI Newsletter – May 1, 2019

Publications

mBio
Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments – NEW!
Jordan T. Bird, Eric D. Tague, Laura A. Zinke*, Jenna M. Schmidt, Andrew D. Steen*, Brandi Kiel Reese*, Ian P.G. Marshall, Gordon Webster, Andrew Weightman, Hector F. Castro, Shawn R. Campagna, Karen G. Lloyd*
*C-DEBI Contribution 471

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD⁺-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.

Nature
Forearc carbon sink reduces long-term volatile recycling into the mantle – NEW!
P. H. Barry, J. M. de Moor, D. Giovannelli, M. Schrenk, D. R. Hummer, T. Lopez, C. A. Pratt, Y. Alpízar Segura, A. Battaglia, P. Beaudry, G. Bini, M. Cascante, G. d’Errico, M. di Carlo, D. Fattorini, K. Fullerton, E. Gazel, G. González, S. A. Halldórsson, K. Iacovino, J. T. Kulongoski, E. Manini, M. Martínez, H. Miller, M. Nakagawa, S. Ono, S. Patwardhan, C. J. Ramírez, F. Regoli, F. Smedile, S. Turner, C. Vetriani, M. Yücel, C. J. Ballentine, T. P. Fischer, D. R. Hilton & K. G. Lloyd

Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth’s surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth’s deep mantle and shallow crustal reservoirs, as well as Earth’s oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 10⁸ and 1.3 × 10¹⁰ moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth’s deep mantle than previously estimated.
 

IODP Workshop Report
Scientific Exploration of the Arctic and North Pacific: Community-driven Priorities for Ocean Drilling – NEW!
The Northern Pacific, Bering Sea and Western Arctic regions contain important records of linked tectonic and paleoceanographic histories. The primary goal of this workshop was to develop new proposals and reinvigorate existing proposals for scientific ocean drilling in the region. By focusing on regional coordination across scientific themes, our breakout groups and working sessions encouraged new collaborations to develop coordinated drilling strategies.

Proposal Calls

NOAA: Ocean Exploration and Research FFO Announcement
The deadline for the pre-proposal submission is May 24, 2019.

NSF: Research Experiences for Undergraduates (REU) – NEW!
The Research Experiences for Undergraduates (REU) program supports active research participation by undergraduate students in any of the areas of research funded by the National Science Foundation. REU projects involve students in meaningful ways in ongoing research programs or in research projects specifically designed for the REU program. This solicitation features two mechanisms for support of student research: (1) REU Sites are based on independent proposals to initiate and conduct projects that engage a number of students in research. REU Sites may be based in a single discipline or academic department or may offer interdisciplinary or multi-department research opportunities with a coherent intellectual theme. Proposals with an international dimension are welcome. (2) REU Supplements may be included as a component of proposals for new or renewal NSF grants or cooperative agreements or may be requested for ongoing NSF-funded research projects. Full Proposal Deadlines: May 24, 2019 and August 28, 2019.

Simons Foundation: Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 14, 2019.

NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.

NSF: Biological Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Chemical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Physical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet)
Letter of intent due date: October 30, 2019.

NSF: Research Traineeship (NRT) Program
Next letter of intent window: November 25, 2019 – December 6, 2019.

Rolling Calls:

• C-DEBI: Rolling call for Research Exchange proposals
• DCO: Deep Life Cultivation Internship Program
• IODP-USSSP: Proposals for Pre-Drilling Activities
• NSF: Arctic Sciences Program Solicitation
• NSF: Division of Environmental Biology (core programs) (DEB)
• NSF: Infrastructure Innovation for Biological Research (IIBR)
• NSF: Instrument Capacity for Biological Research (ICBR)
• NSF: Non-Academic Research Internships for Graduate Students (INTERN) Supplemental Funding Opportunity
• NSF: Research Assistantships for High School Students (RAHSS): Funding to Broaden Participation in the Biological Sciences
• NSF: Research Experience for Teachers (RET): Funding Opportunity in the Biological Sciences
• NSF: Tribal Colleges and Universities Program (TCUP)

Employment

TAMU: Instructional Assistant Professor
Application deadline: June 1, 2019.

MBL: Computational Postdoctoral Scientist – NEW!
A computational postdoctoral position in Ocean Biogeochemical Modeling is available at the Marine Biological Laboratory, Woods Hole. This NSF-funded, collaborative project with the Massachusetts Institute of Technology will focus on combining thermodynamics and trait-based biogeochemical models to augment an existing marine ecosystem modeling framework (“Darwin model”) developed at MIT. We are seeking an individual with a PhD in oceanography, engineering, applied math or related field who has interest or experience in marine biogeochemical modeling. While not required, knowledge in thermodynamics, numerical analysis and/or optimal control theory will be considered advantageous. The successful candidate will be expected to work collaboratively with teams at both MBL and MIT, but will be employed at MBL. Review of applications will begin July 1, 2019 and continue until the position is filled.

LMU: Professorship of Geological Earth Surface Processes