C-DEBI Newsletter – October 1, 2018

Publications & Press

mSystems
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes – NEW!
Karen G. Lloyd*, Andrew D. Steen*, Joshua Ladau, Junqi Yin, Lonnie Crosby
*C-DEBI Contribution 437

To describe a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly available metagenome and metatranscriptome databases, which we show have far less of the culture bias present in primer-amplified 16S rRNA gene surveys, to those of their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundances of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, and bioreactors (22% to 87% uncultured genera to classes and 0% to 64% uncultured phyla). The exceptions were human and human-associated environments, which were dominated by cultured genera (45% to 97%). We estimate that uncultured genera and phyla could comprise 7.3 × 10²⁹ (81%) and 2.2 × 10²⁹(25%) of microbial cells, respectively. Uncultured phyla were overrepresented in metatranscriptomes relative to metagenomes (46% to 84% of sequences in a given environment), suggesting that they are viable. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate nonhuman environments on Earth, and their undiscovered physiologies may matter for Earth systems.

Geobiology
Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time – NEW!
James A. Bradley*, Jan P. Amend*, Douglas E. LaRowe
*C-DEBI Contribution 438

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra‐low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

See DCO's feature article about the recent Geobiology publication, How Microbes Survive When Buried Alive.

Frontiers in Environmental Science
Using Maximum Entropy Production to Describe Microbial Biogeochemistry Over Time and Space in a Meromictic Pond – NEW!
Joseph J. Vallino, Julie A. Huber*
*C-DEBI Contribution 441

Determining how microbial communities organize and function at the ecosystem level is essential to understanding and predicting how they will respond to environmental change. Mathematical models can be used to describe these communities, but properly representing all the biological interactions in extremely diverse natural microbial ecosystems in a mathematical model is challenging. We examine a complementary approach based on the maximum entropy production (MEP) principle, which proposes that systems with many degrees of freedom will likely organize to maximize the rate of free energy dissipation. In this study, we develop an MEP model to describe biogeochemistry observed in Siders Pond, a phosphate limited meromictic system located in Falmouth, MA that exhibits steep chemical gradients due to density-driven stratification that supports anaerobic photosynthesis as well as microbial communities that catalyze redox cycles involving O, N, S, Fe, and Mn. The MEP model uses a metabolic network to represent microbial redox reactions, where biomass allocation and reaction rates are determined by solving an optimization problem that maximizes entropy production over time, and a 1D vertical profile constrained by an advection-dispersion-reaction model. We introduce a new approach for modeling phototrophy and explicitly represent oxygenic photoautotrophs, photoheterotrophs and anoxygenic photoautotrophs. The metabolic network also includes reactions for aerobic organoheterotrophic bacteria, sulfate reducing bacteria, sulfide oxidizing bacteria and aerobic and anaerobic grazers. Model results were compared to observations of biogeochemical constituents collected over a 24 h period at 8 depths at a single 15 m deep station in Siders Pond. Maximizing entropy production over long (3 day) intervals produced results more similar to field observations than short (0.25 day) interval optimizations, which support the importance of temporal strategies for maximizing entropy production over time. Furthermore, we found that entropy production must be maximized locally instead of globally where energy potentials are degraded quickly by abiotic processes, such as light absorption by water. This combination of field observations and modeling results indicate that natural microbial systems can be modeled by using the maximum entropy production principle applied over time and space using many fewer parameters than conventional models.

Lithos
Magmatism, serpentinization and life: Insights through drilling the Atlantis Massif (IODP Expedition 357) – NEW!
Gretchen L. Früh-Green, Beth N. Orcutt, Stéphane Rouméjon, Marvin D.Lilley, Yuki Morono, Carol Cotterill, Sophie Green, Javier Escartin, Barbara E. John, Andrew M. McCaig, Mathilde Cannat, Bénédicte Ménez, Esther M. Schwarzenbach, Morgan J. Williams, Sally Morgan, Susan Q. Lang, Matthew O. Schrenk, William J. Brazelton, Norikatsu Akizawa, Chiara Boschi, Kristina G. Dunkel, Marianne Quéméneur, Scott A. Whattam, Lisa Mayhew, Michelle Harris, Gaye Bayrakci, Jan-Hinrich Behrmann, Emilio Herrero-Bervera, Kirsten Hesse, Hai-Quan Liu, Amila Sandaruwan Ratnayake, Katrina Twing, Dominique Weis, Rui Zhao, Laura Bilenker

IODP Expedition 357 used two seabed drills to core 17 shallow holes at 9 sites across Atlantis Massif ocean core complex (Mid-Atlantic Ridge 30°N). The goals of this expedition were to investigate serpentinization processes and microbial activity in the shallow subsurface of highly altered ultramafic and mafic sequences that have been uplifted to the seafloor along a major detachment fault zone. More than 57 m of core were recovered, with borehole penetration ranging from 1.3 to 16.4 meters below seafloor, and core recovery as high as 75% of total penetration in one borehole. The cores show highly heterogeneous rock types and alteration associated with changes in bulk rock chemistry that reflect multiple phases of magmatism, fluid-rock interaction and mass transfer within the detachment fault zone. Recovered ultramafic rocks are dominated by pervasively serpentinized harzburgite with intervals of serpentinized dunite and minor pyroxenite veins; gabbroic rocks occur as melt impregnations and veins. Dolerite intrusions and basaltic rocks represent the latest magmatic activity. The proportion of mafic rocks is volumetrically less than the amount of mafic rocks recovered previously by drilling the central dome of Atlantis Massif at IODP Site U1309. This suggests a different mode of melt accumulation in the mantle peridotites at the ridge-transform intersection and/or a tectonic transposition of rock types within a complex detachment fault zone. The cores revealed a high degree of serpentinization and metasomatic alteration dominated by talc-amphibole-chlorite overprinting. Metasomatism is most prevalent at contacts between ultramafic and mafic domains (gabbroic and/or doleritic intrusions) and points to channeled fluid flow and silica mobility during exhumation along the detachment fault. The presence of the mafic lenses within the serpentinites and their alteration to mechanically weak talc, serpentine and chlorite may also be critical in the development of the detachment fault zone and may aid in continued unroofing of the upper mantle peridotite/gabbro sequences.

New technologies were also developed for the seabed drills to enable biogeochemical and microbiological characterization of the environment. An in situ sensor package and water sampling system recorded real-time variations in dissolved methane, oxygen, pH, oxidation reduction potential (Eh), and temperature and during drilling and sampled bottom water after drilling. Systematic excursions in these parameters together with elevated hydrogen and methane concentrations in post-drilling fluids provide evidence for active serpentinization at all sites. In addition, chemical tracers were delivered into the drilling fluids for contamination testing, and a borehole plug system was successfully deployed at some sites for future fluid sampling. A major achievement of IODP Expedition 357 was to obtain microbiological samples along a west–east profile, which will provide a better understanding of how microbial communities evolve as ultramafic and mafic rocks are altered and emplaced on the seafloor. Strict sampling handling protocols allowed for very low limits of microbial cell detection, and our results show that the Atlantis Massif subsurface contains a relatively low density of microbial life.

IODP-USSSP: JOIDES Resolution Assessment Report Now Available Online – NEW!
The JOIDES Resolution Assessment Report, representing the results of a multi-phase, year-long community review, is now available on the USSSP website. Thanks to everyone who participated in the community survey and the September ‘17 JR Assessment Workshop, both of which provided crucial input to this report!
 

Proposal Calls

Apply to sail now as an Onboard Outreach Officer on Expedition 385: Guaymas Basin Tectonics and Biosphere – 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. Application period ends on October 19, 2018.

NSF: Graduate Research Fellowship Program (GRFP)
Application deadlines: October 22-26, 2018.

IODP: Apply to Sail on IODP Expedition 389 – NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants on Expedition 389 Hawaiian Drowned Reefs aboard a Mission-Specific Platform (MSP) provided by the ECORD Science Operator. The overall goal of IODP Expedition 389 is to sample a unique succession of drowned coral reefs around Hawaii now at -134 to -1155 m below sea level. Scientific drilling through these reefs will generate a new record of sea-level and associated climate variability during several controversial and poorly understood periods over the last 500 kyr. Opportunities exist for researchers (including graduate students) in all specialties. While other expertise may be considered, specialists in the following fields are required: carbonate sedimentology, corals, sedimentology, paleontology, palynology, organic geochemistry, inorganic geochemistry, structural geology, paleomagnetics, microbiology, physical properties, geophysics, geodynamics, glacial isostatic adjustment, stratigraphic correlation and downhole logging. For the offshore phase of the expedition, we are particularly looking for the following fields: carbonate sedimentology, corals, sedimentology, paleontology, organic geochemistry, inorganic geochemistry, microbiology, physical properties, and petrophysics/downhole logging. The deadline to apply is November 23, 2018.

NSF: Graduate Research Fellowship Program (GRFP) – Graduate Research Internship Program (GRIP)
GRIP applications are due December 4, 2018.

NOPP: FY2019 Broad Agency Announcement – NEW!
There is a new National Oceanographic Partnership Program (NOPP) “Broad Agency Announcement” (ONR BAA # N000014-18-S-B007) posted that includes seven ocean research and technology topics that may be of interest. Up to $27.3 million over three (3) years may be available for this solicitation, subject to appropriation, availability of funds, and final approval by the participating NOPP agencies. The BAA provides research opportunities for the following seven topics: Topic 1 – CubeSat Sensors for Investigating Littoral Ocean & Atmosphere Dynamics; Topic 2 – Sustained observations of marine biodiversity for improved understanding of marine ecosystem responses to changing environmental conditions; Topic 3 – Advanced Sensor Technology; Topic 4 – Autonomous Profiling Floats for Investigating Tropical Pacific Ocean Biogeochemistry; Topic 5 – Improving Arctic Operational Forecasts Arctic Observing System Simulation Experiments using Year of Polar Prediction data (Arctic OSSE); Topic 6 – New Approaches for Data Assimilation to Improve Operational Ocean Prediction; Topic 7 – Autonomous Mapping. Proposal deadlines of December 21, 2018 and January 18. 2019.

NSF: Infrastructure Innovation for Biological Research (IIBR) – NEW!
The Infrastructure Innovation for Biological Research (IIBR) program encourages new approaches to the acquisition and use of biological data to provide greater value to the scientific community. The IIBR program is especially interested in proposals that offer innovative and potentially transformative advances in the acquisition and use of biological data through the development of 1) informatics methods and resources for organizing, analyzing, and displaying complex data sets, 2) novel instrumentation and associated methods for collection of new data, and 3) multidisciplinary approaches to innovative infrastructure solutions in data acquisition, management, or analysis. It is expected that awards made in the IIBR program will stimulate advances that impact a significant segment of the biological research community supported by the NSF Directorate for Biological Sciences (BIO). All fields of science supported by BIO are eligible for support under the IIBR program. Proposals accepted anytime.

More 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: 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

Bigelow: Postdoctoral Research Scientist in Microbial Ecology
Consideration of candidates will begin October 10, 2018; start dates will need to be several months prior to the 2019 field season.

U Cologne: Full Professor in Geobiology (Tenure Track) – NEW!
This call is part of the Federal Tenure Track Programme of the German Federal Government and the Federal States. It addresses researchers at an early career stage. The successful candidate is expected to develop research and teaching programs in the field of geobiology at the Institute of Geology and Mineralogy. Grounded in basic geoscientific research, the focus of a future geobiological research program may range from paleobiology through earth and life history to geomicrobiology. Research should rely on innovative, modern approaches and quantitative methodology. Links to other fields of research at the Institute of Geology and Mineralogy and to the guiding themes of the Department of Geosciences such as “Evolution of Life and Earth” or “Global change in Environmental Dynamics and the Atmosphere” are expected. The successful candidate will represent the field of geobiology in its entirety in the bachelor and master programs at the Institute Geology and Mineralogy. Contributions to basic undergraduate teaching are obligatory. We seek young researchers with an exceptional track record and the potential for establishing and advancing geobiological research at the Institute of Geology and Mineralogy. An excellent and internationally recognized publication record and proof of the successful acquisition of third-party funding and implementation of related projects are required. The successful candidate is expected to contribute to existing initiatives (e.g. Collaborative Research Center CRC 1211 “Earth Evolution at the Dry Limit” or Priority Programme 1833 “Building a Habitable Earth”) as well as establishing his/her own research program. Applications should be submitted no later than October 15, 2018.

U Edinburgh: Chancellor’s Fellowships
Applications due October 15, 2018.

Bigelow: Two Postdoctoral Researchers in Single Cell Genome-to-Phenome Studies of Environmental Microorganisms – NEW!
Bigelow Laboratory for Ocean Sciences is seeking two postdoctoral researchers to lead studies that tie cell-specific genome data to expressed functions (genome to phenome) such that rates of environmental processes can be coupled to specific microbial lineages. This work integrates cutting-edge approaches in field studies of marine and continental microbiomes, laboratory experimentation and bioinformatics. The primary focus of position #1, co-advised by Drs. Stepanauskas and Poulton, will be on the studies of marine bacterioplankton and the integration of flow cytometry and genomics of individual cells. The primary focus of position #2, co-advised by Drs. Orcutt and Emerson, will be on studies of the deep biosphere and the calibration of single cell activity and physiology measurements using laboratory cultures. Both hired scientists will be engaged in a collaborative, multi-institutional project that also includes the University of New Hampshire and the Desert Research Institute. Candidates must have a PhD degree in a relevant field and prior experience in environmental microbiology and genomics. Research will be conducted primarily at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine. Opportunities for fieldwork may be available but are not required. Applications due November 1, 2018.

Harvard: Tenure-Track Professor in Earth History – NEW!
The Department of Earth & Planetary Sciences (EPS) invites applications for an open faculty position spanning the broadly defined fields of Geology, Geobiology and/or Geochemistry as they pertain to reconstructing and understanding the history of the Earth. This is a tenure-track appointment at the assistant level. We seek to attract an outstanding individual to establish an innovative research program and teach both undergraduate and graduate students. We are especially interested in individuals whose work spans the intellectual interests of Harvard faculty, including – although not limited to – the interactions between life, evolution, (bio)geochemistry, tectonics, and marine or terrestrial environmental change over geologic time. There is also the opportunity to work with sister departments such as Organismic and Evolutionary Biology and the School of Engineering and Applied Sciences. Application Deadline: November 1, 2018.

Rice: Wiess and Pan Post-Doctoral Research Fellowships
The applications are due on November 1, 2018.

Bigelow: Senior Research Scientist – NEW!
Bigelow Laboratory for Ocean Sciences invites applications for a Senior Research Scientist (SRS) position to complement the mission of our non-profit research institution. Successful SRS candidates are expected to lead transformative, interdisciplinary research that aligns with, and expands, our research mission. Targeted research areas for this position are in any of the following research themes: (1) ocean microbiome, (2) ocean biogeochemistry, and (3) ocean health. Cross-cutting themes for these positions include human impacts, foundations of marine food webs and climate change. Minimum requirements include a Ph.D. degree in a relevant field and demonstrated capability to acquire external funding and lead scientific programs. We will consider candidates at all levels of their career progression. Bigelow Laboratory for Ocean Sciences is a “soft money” institution where SRSs are given the freedom to pursue their own funded research and entrepreneurial portfolio that advances the institutional mission. SRSs also have the opportunity to participate in the Laboratory’s sponsored education activities, such as our partnership with Colby College and an NSF REU internship program. SRSs are institutionally supported to engage in governance and administrative activities associated with the laboratory’s unique operational model. For full consideration, the application should be received by November 30, 2018.

BMSIS: Postdoctoral Scholar Position Available in Evolutionary and Isotopic Enzymology – NEW!
The Blue Marble Space Institute of Science has an opening for a postdoctoral scholar with interests in evolutionary protein biochemistry and geochemistry. The position is available immediately. The successful candidate will work in a collaborative and multi-institutional group which seeks to test and develop hypotheses related to the role of thioester chemistry in nascent life and the chemical networks that proceeded living systems. A primary target will be to determine enzyme specific kinetic isotope fractionation factors by purifying enzymes and conducting isotope ratio mass spectrometry measurements of substrate and product. Experience in anaerobic protein purification and manipulation is highly desirable. This project results from a recent NSF/NASA Ideas lab, and the position is made possible through the NSF Emerging Frontiers Crosscutting Activities Program (Award Abstract 1724300). The position is extendable beyond one year. The successful candidate will benefit from working together and sharing research results and ideas collaboratively within our diverse group. The primary workplace of the successful candidate will be the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology with supervision from Shawn McGlynn and regular interactions with group members including Betul Kacar (University of Arizona), Boswell Wing (CU Boulder), Chris Butch (BMSIS/ELSI), Chris House (Penn State) and Daniel Segrè (Boston University).

U Delaware: Postdoctoral positions in genetic markers and biochemistry of microbial Fe oxidation – NEW!
The Chan lab invites postdoctoral research applications to work on several newly funded projects on microbial Fe oxidation. The objectives of the projects are to: 1) Determine the key genes and proteins involved in neutrophilic microbial Fe oxidation; 2) Establish marker genes for monitoring microbial Fe oxidation in natural systems; 3) Better understand how cells interact with Fe minerals, both as electron donors, and as waste products. These projects are funded by NSF, and involve collaborations with Sharon Rozovsky (UD), Jeff Gralnick (University of Minnesota), Denise Akob (USGS), and Kirsten Küsel (FSU-Jena). Candidates should have a PhD in a relevant field (e.g. Microbiology, Biochemistry, Molecular/Cellular Biology), and be interested in microbial Fe oxidation and Fe biogeochemistry.  S/he should have experience in at least some subset of the following: Biochemistry of redox-active proteins (particularly membrane proteins); Microbial culturing and physiology (especially challenging organisms); Transcriptomics, genomics, bioinformatics; Fe metabolism and redox chemistry. Further information can be obtained by contacting Dr. Clara Chan (cschan@udel.edu).

BIOS: Postdoctoral Scholarship in Oceanography

U South Florida: Two Tenure-Track Faculty Positions in Chemical and Geological Oceanography

U Southern Mississippi: Three Positions (Postdoctoral Researcher, Graduate Student, Research Technician) in Marine Microbial Ecology

Karlsruhe Institute of Technology: Ph.D. and Postdoc position available