C-DEBI Newsletter – January 15, 2020

Publications & Press

Limnology and Oceanography
Impacts of deep‐sea mining on microbial ecosystem services – NEW!
Beth N. Orcutt, James A. Bradley, William J. Brazelton, Emily R. Estes, Jacqueline Goordial, Julie A. Huber, Rose M. Jones, Nagissa Mahmoudi, Jeffrey J. Marlow, Sheryl Murdock, Maria G. Pachiadaki
C-DEBI Contribution 481

Interest in extracting mineral resources from the seafloor through deep‐sea mining has accelerated in the past decade, driven by consumer demand for various metals like zinc, cobalt, and rare earth elements. While there are ongoing studies evaluating potential environmental impacts of deep‐sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of seafloor life and the services that this life provides in the deep sea are rarely considered explicitly. In April 2018, scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep‐sea mining, and to provide recommendations for how to evaluate and safeguard these services. Here, we indicate that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to loss of services that cannot be remedied by protected area offsets. For example, we (1) describe potential major losses of microbial ecosystem services at active hydrothermal vent habitats impacted by mining, (2) speculate that there could be major ecosystem service degradation at inactive massive sulfide deposits without extensive mitigation efforts, (3) suggest minor impacts to carbon sequestration within manganese nodule fields coupled with potentially important impacts to primary production capacity, and (4) surmise that assessment of impacts to microbial ecosystem services at seamounts with ferromanganese crusts is too poorly understood to be definitive. We conclude by recommending that baseline assessments of microbial diversity, biomass, and, importantly, biogeochemical function need to be considered in environmental impact assessments of deep‐sea mining.

See also Bigelow Laboratory’s press release about the paper, an outcome of the April 2018 Deep Sea Mining Impacts on Microbial Ecosystem Services Workshop, supported in part by C-DEBI.

mBio
A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index – NEW!
Roman A. Barco*, G. M. Garrity, Jarrod J. Scott, Jan P. Amend*, Kenneth H. Nealson, David Emerson
*C-DEBI Contribution 498

Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.

Geochemistry, Geophysics, Geosystems
Subseafloor Cross‐Hole Tracer Experiment Reveals Hydrologic Properties, Heterogeneities, and Reactions in Slow Spreading Oceanic Crust – NEW!
Charles Geoffrey Wheat*, Keir Becker, Heinrich W. Villinger, Beth N. Orcutt*, Trevor Fournier, Anne M. Hartwell, Claudia Paul
*C-DEBI Contribution 518

The permeability, connectivity, and reactivity of fluid reservoirs in oceanic crust are poorly constrained, yet these reservoirs are pathways for about a quarter of the Earth’s heat loss and seawater‐rock exchange within them impact ocean chemical cycles. We present results from the second‐ever cross‐hole tracer experiment within oceanic crust and the first conducted during a single expedition and in slow‐spreading crust west of the Mid‐Atlantic Ridge at North Pond. Here we employed boreholes that were drilled by the Integrated Ocean Drilling Program (IODP Sites U1382 and U1383) that were instrumented and sealed. A cesium‐salt solution and bottom seawater tracer experiment provided a measure of the minimum Darcy fluid velocity (2 to 41 m d^‐1) within the upper volcanic crust, constraining the minimum permeability of 10^‐11 to 10^‐9 m². We also document chemical heterogeneities in crustal fluid compositions, rebound from drilling disturbances, and nitrification within the basaltic crust, based on systematic differences in borehole fluid compositions over a 5‐year period. These results also show heterogeneous fluid compositions with depth in the borehole, indicating that hydrothermal circulation is not vigorous enough to homogenize the fluid composition in the upper permeable basaltic basement, at least not on the time scale of 5 years. Our work verifies the potential for future manipulative experiments to characterize hydrologic, biogeochemical, and microbial process within the upper basaltic crust.

The ISME Journal
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment – NEW!
Bennett J. Kapili, Samuel E. Barnett, Andrew Buckley, Anne E. Dekas*
*C-DEBI Contribution 520

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using ¹⁵N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.

Astrobiology
Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration – NEW!
T.C. Onstott, B.L. Ehlmann, H. Sapers, M. Coleman, M. Ivarsson, J.J. Marlow, A. Neubeck, P. Niles

Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth’s history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.

Have an upcoming manuscript about the deep subseafloor biosphere and want to increase your press coverage? NSF’s Office of Legislative and Public Affairs is looking to coordinate press releases between your home institution and the NSF to coincide with the date of publication. Please contact us as soon as your publication is accepted!

Meetings & Activities

Goldschmidt: Hawai’i 2020, June 21-26 – UPDATED!
Goldschmidt is the foremost annual, international conference on geochemistry and related subjects, organized by the Geochemical Society and the European Association of Geochemistry. Planning on attending? Consider submitting your abstracts to:

Abstract submission deadline: February 14, 2020.

UNOLS: SCOAR Town Hall at 2020 Ocean Sciences – NEW!
The UNOLS Science Committee for Oceanographic Aircraft Research (SCOAR) will host a Town Hall at the 2020 Ocean Sciences on “Expanding the Reach of the Research Fleet: Autonomous (and Piloted) Airborne Systems in Support of Ocean Sciences.” The Town Hall is scheduled for Wednesday, February 19 from 12:45 pm to 1:45 pm at at the San Diego Convention Center, Room 9, UL. The community will have the opportunity to hear the latest information about the use of airborne resources to enhance oceanographic research. The Town Hall will include a series of lightning presentations where scientists are invited to present one slide in one-three minutes explaining how s/he has used aircraft in her/his respective research. We hope you will consider presenting a slide in the lightning session. If you will/have used airborne resources in your oceanographic work and wish to present a lightning talk please sign up here by February 14, 2020.

UNOLS: Quality of Life at Sea Survey – NEW!
The UNOLS Council has the standing goal of improving the quality and capability of existing ocean science facilities and the quality, reliability and safety of their operation. Many improvements have been made over the past decade, including the addition of new research vessels. UNOLS Council would also now like to turn attention to improving the quality of life and morale while working at sea, for both the permanent crew and itinerant scientists. For example, technological improvements in satellite internet connections have changed and enhanced life at sea, enabling those onboard to attend to personal business and maintain family connections, but these technological improvements often come with high financial costs. Simpler, less expensive efforts can also improve morale and quality of life at sea, such as cook outs on the deck or swim calls (long ago …). Please help us improve the quality of life at sea by filling out this brief three question survey. Please complete the survey by February 28, 2020.

AGU: Nominate Your Peers for 2020 Honors
Nominations are now open for 2020 AGU honors, including the Asahiko Taira International Scientific Ocean Drilling Research Prize. Deadline: March 15, 2020.

USC: 17th Annual Southern California Geobiology Symposium
The symposium will be held on April 4, 2020. Information about registration/abstract submissions, program details, and specific location will be available in January 2020.

GRC: Exploring Fluxes, Forms and Origins of Deep Carbon in Earth and Other Terrestrial Planets, June 28-July 3, 2020, Lewiston, ME, USA
Applications for this meeting must be submitted by May 31, 2020.

Serpentine Days: 5th Workshop, September 21-24, Sestri Levante (Genova, Italy)
Registration will close June 30, 2020.

UNOLS: Science in the Abyss Workshops – NEW!
In 2020, HOV Alvin will undergo the final steps to achieve a depth rating of 6500m that will allow the workhorse human-occupied submersible to reach 97% of the ocean floor. We will be hosting a series of online and in-person workshops to allow the community to discuss the science priorities at abyssal depths for Alvin and other deep-diving vehicles. The outcomes of the workshops will include a manuscript defining abyssal research priorities and a white-paper guiding science verification activities for the newly-capable submarine (anticipated for 2021). Please take a few minutes to complete the survey linked below. In addition to helping set the agenda for the workshop, your input will enable us to ensure that you are kept informed as the timing of the workshops solidifies. We are eagerly anticipating the opportunity to convene our community for interdisciplinary discussions of deep submergence science, and hope that we will see you there!

Ongoing Activities:

Education & Outreach

MARUM: ECORD Training Course, April 20-24, 2020, Bremen, Germany
The application deadline is January, 17 2020.

IODP-USSSP: Apply to sail on the JR as an Onboard Outreach Officer for Expeditions 391 and 392 – NEW!
The USSSP Onboard Outreach Program gives formal and informal educators, artists, writers, videographers and other participants the opportunity to spend an entire expedition with an IODP shipboard party and translate their experiences for students and the general public via blogs, videos, social networking sites, live ship-to-shore video events and development of educational resources. Onboard Outreach Program participants are selected through a competitive application and interview process. All expenses for Onboard Outreach Program participants, such as travel to and from the ports of call, and a $10,000 stipend, are paid by USSSP. The selected individual(s) will also be flown to a three-day training session prior to their expedition. Non-US applicants will be directed to their country’s IODP Program Member Office but are still encouraged to apply. Deadline: February 10, 2020.

USC Wrigley Institute: Summer REU: Coastal Ocean Processes
Applications are due by February 14, 2020.

RPI: School of Earth and Environmental Sciences: Graduate School Applications
Applications are welcome at any time.

Proposal Calls

NSF: Understanding the Rules of Life: Microbiome Theory and Mechanisms (URoL:MTM)
Letter of Intent due date: January 17, 2020.

NSF: Research Coordination Networks in Undergraduate Biology Education (RCN-UBE)
Full proposal deadline: January 21, 2020.

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet) – NEW!
The goals of the Accelerating Research through International Network-to-Network Collaborations (AccelNet) program are to accelerate the process of scientific discovery and prepare the next generation of U.S. researchers for multiteam international collaborations. The AccelNet program supports strategic linkages among U.S. research networks and complementary networks abroad that will leverage research and educational resources to tackle grand scientific challenges that require significant coordinated international efforts. The program seeks to foster high-impact science and engineering by providing opportunities to create new collaborations and new combinations of resources and ideas among linked global networks. This solicitation invites proposals for the creation of international networks of networks in research areas aligned either with one of the NSF Big Ideas or a community-identified scientific challenge with international dimensions. AccelNet awards are meant to support the connections among research networks, rather than supporting fundamental research as the primary activity. Each network of networks is expected to engage in innovative collaborative activities that promote synergy of efforts across the networks and provide professional development for students, postdoctoral scholars, and early-career researchers. There are two proposal categories covered by this solicitation: Catalytic and Full-Scale Implementation. Full proposal deadline date: January 31, 2020.

NSF: Growing Convergence Research (GCR) – NEW!
Growing Convergence Research (GCR)at the National Science Foundation was identified as one of 10 Big Ideas. Convergence research is a means for solving vexing research problems, in particular, complex problems focusing on societal needs. It entails integrating knowledge, methods, and expertise from different disciplines and forming novel frameworks to catalyze scientific discovery and innovation. GCR identifies Convergence Research as having two primary characteristics: 1) Research driven by a specific and compelling problem. Convergence Research is generally inspired by the need to address a specific challenge or opportunity, whether it arises from deep scientific questions or pressing societal needs. 2) Deep integration across disciplines. As experts from different disciplines pursue common research challenges, their knowledge, theories, methods, data, research communities and languages become increasingly intermingled or integrated. New frameworks, paradigms or even disciplines can form sustained interactions across multiple communities. A distinct characteristic of convergence research, in contrast to other forms of multidisciplinary research, is that from the inception, the convergence paradigm intentionally brings together intellectually diverse researchers and stakeholders to frame the research questions, develop effective ways of communicating across disciplines and sectors, adopt common frameworks for their solution, and, when appropriate, develop a new scientific vocabulary. Research teams practicing convergence aim at developing sustainable relationships that may not only create solutions to the problem that engendered the collaboration, but also develop novel ways of framing related research questions and open new research vistas. Full proposal deadline: February 3, 2020.

NSF: Frontier Research in Earth Sciences (FRES)
Full proposal deadline: February 5, 2020.

NSF: Understanding the Rules of Life: Epigenetics – NEW!
Understanding the Rules of Life (URoL): Predicting Phenotype is one of NSF’s 10 Big Ideas and is focused on predicting the set of observable characteristics (phenotype) from the genetic makeup of the individual and the nature of its environment. The development of new research tools has revolutionized our ability to manipulate and investigate the genome and to measure multiple aspects of biological, physical, and social environments. The opportunity now is to assimilate this new information into causal, mechanistic, and/or predictive relationships among the genomic and epigenetic makeup, the environmental experience, and the phenotypic characteristics of biological systems. These relationships are the basis for the Rules of Life – the theoretical constructs that explain and predict the characteristics of living systems, from molecular and sub-cellular components, to cells, whole organisms, communities and biomes. Successful projects of the URoL:Epigenetics Program are expected to use complementary, interdisciplinary approaches to investigate how epigenetic phenomena lead to emergent properties that explain the fundamental behavior of living systems. Full proposal deadline: February 6, 2020.

National Science Foundation Research Traineeship (NRT) Program – NEW!
The NSF Research Traineeship (NRT) program is designed to encourage the development and implementation of bold, new, and potentially transformative models for science, technology, engineering and mathematics (STEM) graduate education training. The NRT program seeks proposals that explore ways for graduate students in research-based master’s and doctoral degree programs to develop the skills, knowledge, and competencies needed to pursue a range of STEM careers. The program is dedicated to effective training of STEM graduate students in high priority interdisciplinary or convergent research areas, through the use of a comprehensive traineeship model that is innovative, evidence-based, and aligned with changing workforce and research needs. The NRT program addresses workforce development, emphasizing broad participation, and institutional capacity building needs in graduate education. Strategic collaborations with the private sector, non-governmental organizations (NGOs), government agencies, national laboratories, field stations, teaching and learning centers, informal science centers, and academic partners are encouraged. NRT especially welcomes proposals that will pair well with the efforts of NSF Inclusion across the Nation of Communities of Learners of Underrepresented Discoverers in Engineering and Science (INCLUDES) to develop STEM talent from all sectors and groups in our society. Collaborations are encouraged between NRT proposals and existing NSF INCLUDES projects, provided the collaboration strengthens both projects. Full Proposal Deadline Date: February 6, 2020; February 6, Annually Thereafter.

NSF: EarthCube
Full proposal deadline: March 12, 2020.

NSF: Dimensions of Biodiversity
The 2020 program is restricted to projects supported by international partnerships with the National Natural Science Foundation of China (NSFC), the São Paulo Research Foundation (FAPESP) of Brazil, and the National Research Foundation (NRF) of South Africa. Full Proposal Deadline: March 27, 2020.

NSF: Facilitator of Marine Seismic Capabilities for the U. S. Research Community
The proposal submission deadline is April 10, 2020.

NSF: Faculty Early Career Development Program (CAREER)
Full proposal deadline: July 27, 2020.

NSF: Improving Undergraduate STEM Education: Pathways into the Earth, Ocean, Polar and Atmospheric & Geospace Sciences (IUSE:GEOPAths)
Letter of Intent Due Date: November 17, 2020.

Rolling Calls:

Employment

UCSD: International Ocean Discovery Program Data Manager – NEW!
The International Ocean Discovery Program (IODP) Data Manager (DM) is a technical leader with a high degree of knowledge in geo-sciences and recognized expert in scientific ocean drilling. The incumbent will apply extensive knowledge as a research professional with an in-depth understanding of scientific data, statistics and analysis of on site data recorded in seafloor sediments and rocks and will monitor sub-seafloor environments. As needed, act as a team lead in scientific ocean drilling and multidisciplinary research collaboration of broad scope and complexity. In addition, the position will support on-going efforts to improve data management procedures and the development of decision support tools. The position will contribute and lead scientific journal publications. In collaboration with the Executive Director/Principal Investigator of the Science Support Office, the DM serves a critical and visible role in the IODP management structure. Provide consultation, direction, and advice to research teams and proposal authors, who comprise over one thousand researchers affiliated with about 200 institutions worldwide, in developing and evaluating scientific data sets that support IODP drilling proposals. Formulate strategies to ensure the quality and timely review of site characterization data submitted to the IODP Site Survey Data Bank (SSDB) and serve as the primary Subject Matter Expert (SME) on data in meetings of the IODP Facility Boards and their subsidiaries. Formulate and administer policies and processes in the main Task Areas of the IODP Science Support Office and independently interact with the eight international IODP Program Member Offices to manage their participation in the IODP advisory structure. Filing Deadline: January 27, 2020.

WHOI: Tenure Track Scientist – Marine Chemistry & Geochemistry

U of Georgia: Assistant or Associate Professor – Biological Oceanography

U Akron: Post-Doctoral Position in Geochemistry/Astrobiology

WWU: Assistant Professor in Marine Molecular Biology

Don’t forget to email me with any items you’d like to share in future newsletters! We will also broadcast this information on our social media outlets, Twitter and Facebook. You are what makes our deep biosphere community!

Best,

Matt

—

Matthew Janicak

Data Manager

Center for Dark Energy Biosphere Investigations (C-DEBI)

University of Southern California
janicak@usc.edu

3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371

Phone: 708-691-9563, Fax: 213-740-2437

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