C-DEBI Newsletter – January 2, 2018

Publications & Press

mBio
Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes – NEW!
Holly L. Sewell, Anne-Kristin Kaster, Alfred M. Spormann*
*C-DEBI Contribution 410

The deep marine subsurface is one of the largest unexplored biospheres on Earth and is widely inhabited by members of the phylum Chloroflexi. In this report, we investigated genomes of single cells obtained from deep-sea sediments of the Peruvian Margin, which are enriched in such Chloroflexi. 16S rRNA gene sequence analysis placed two of these single-cell-derived genomes (DscP3 and Dsc4) in a clade of subphylum I Chloroflexi which were previously recovered from deep-sea sediment in the Okinawa Trough and a third (DscP2-2) as a member of the previously reported DscP2 population from Peruvian Margin site 1230. The presence of genes encoding enzymes of a complete Wood-Ljungdahl pathway, glycolysis/gluconeogenesis, a Rhodobacter nitrogen fixation (Rnf) complex, glyosyltransferases, and formate dehydrogenases in the single-cell genomes of DscP3 and Dsc4 and the presence of an NADH-dependent reduced ferredoxin:NADP oxidoreductase (Nfn) and Rnf in the genome of DscP2-2 imply a homoacetogenic lifestyle of these abundant marine Chloroflexi. We also report here the first complete pathway for anaerobic benzoate oxidation to acetyl coenzyme A (CoA) in the phylum Chloroflexi (DscP3 and Dsc4), including a class I benzoyl-CoA reductase. Of remarkable evolutionary significance, we discovered a gene encoding a formate dehydrogenase (FdnI) with reciprocal closest identity to the formate dehydrogenase-like protein (complex iron-sulfur molybdoenzyme [CISM], DET0187) of terrestrial Dehalococcoides/Dehalogenimonas spp. This formate dehydrogenase-like protein has been shown to lack formate dehydrogenase activity in Dehalococcoides/Dehalogenimonas spp. and is instead hypothesized to couple HupL hydrogenase to a reductive dehalogenase in the catabolic reductive dehalogenation pathway. This finding of a close functional homologue provides an important missing link for understanding the origin and the metabolic core of terrestrial Dehalococcoides/Dehalogenimonas spp. and of reductive dehalogenation, as well as the biology of abundant deep-sea Chloroflexi.

Tested: Awesome Jobs: Meet Julie Huber, Deep Sea Microbiologist – NEW!
There’s life in the deepest part of the ocean. And some of that life is microscopic. It’s not easy to find the world’s tiniest organisms on land and it’s even harder when they live in one of the most out of reach places on Earth. Julie Huber, a marine microbiologist at Woods Hole Oceanographic Institution, specializes in finding these itty bitty lifeforms. She talked to us about operating underwater ROVs, doing research off the side of a ship, how understanding the weirdest forms of life on Earth teaches us new lessons about our planet, and what it’s like to battle seasickness when your career requires you to spend your life among the waves.

Spiegel Online: Nine Hours in the Deep – NEW!
For the next two-and-a-half weeks, the Atlantis will now be on the high seas, first heading for the Guaymas Basin in the Gulf of California before then crisscrossing the gulf in search of hydrothermal vents, underwater hot springs that provide some of the most unique habitats on our planet. It will be a dream-come-true for many of the 18 scientists on board, even if they won’t be able to spend much time enjoying the warm climate, the sun and the sea breeze on the surface. Night after night, they will be working in the ship’s three laboratories and sleeping through the day. They will handle rare rock samples and examine deep-sea creatures pulled up from the depths, including crustaceans, bizarre tube worms and flocculent orange and yellow microbial mats. And mud. Kilos and kilos of dark-brown, slimy, stinky mud. Featuring C-DEBI researcher Andreas Teske.

Bigelow: Under Pressure: Studying Life Below the Sea Floor – NEW!
Deep at the bottom of the ocean, below thousands of feet of seawater, below even the rocky ocean crust that comprises the sea floor, lies something surprising: more water. “It’s unintuitive, because most people think of rock as being solid. But it’s not; it has pores, and fractures, and cracks in it,” said Jackie Goordial, a postdoctoral researcher at Bigelow Laboratory for Ocean Sciences. In fact, water percolating into the crust forms the largest aquifer on earth. This sub-seafloor system contains a whopping two percent of the ocean’s volume, and scientists believe it may be home to large amounts of microbial life. These tiny microbes are of global importance. Their activity in the sub-seafloor environment shapes the chemistry of the ocean and its influence on the atmosphere. Featuring C-DEBI researchers Jackie Goordial and Beth Orcutt.

Meetings & Activities

EGU: Deep biosphere session – call for abstracts
Please consider submitting an abstract to our session, due January 10, 2018.

3rd Ocean Worlds meeting, May 21–24, 2018, Houston, TX
Deadline for submitting indication of interest: January 12, 2018.

NSF: Call for Comments on Update to AC GEO Report on Dynamic Earth
Input can be sent to geovision@nsf.gov no later than Thursday, February 1, 2018.

C-DEBI: Nominations now open for the C-DEBI 2018 Networked Speaker Series
C-DEBI seeks nominations for three speakers for the 2018 program. C-DEBI is continuing the Networked Speaker Series (begun in Fall 2011) as a means to enhance communication and the exchange of ideas among our spatially distributed community. Potential speakers can be nominated by colleagues, mentors, or those mentored by C-DEBI participants; they can also self nominate. Selected C-DEBI Networked Speakers will make a presentation online, using video conferencing tools, with assistance from the C-DEBI main office at USC. Nominated C-DEBI Networked Speakers should be capable of combining compelling visual materials with the ability to communicate effectively to a broad audience. We are particularly enthusiastic about giving young researchers a chance to present work to the C-DEBI community. Being selected to be a C-DEBI Networked Speaker is an honor.

C-DEBI: Rolling call for Community Workshop support

C-DEBI: Protocols.io Group Page

C-DEBI: Subseafloor Cultures Database

C-DEBI Spotlight

Each newsletter, we’ll be featuring two, early-career, deep biosphere all-stars from our summer undergraduate programs. Meet the rest of our 2017 Global Enviromental Microbiology students and Community College Cultivation Cohort (C4) REU participants, or learn more about our undergraduate programs!

Education & Outreach

C-DEBI: USC students: apply now for the spring 2018 Genomics and Geobiology Undergraduate Research Experience – NEW!
The Genomics and Geobiology Undergraduate Research Experience (GGURE) is a research internship program for USC sophomores, juniors, and seniors majoring in the life sciences, earth and marine sciences, computational sciences, and engineering. There is both a part-time program during the academic year and a full-time program over 10 weeks during the summer break at the University of Southern California. The GGURE program offers USC undergraduates the opportunity to participate actively in a research group, with either an experimental or computational focus, and perform original research under the direct supervision of a faculty mentor. We will begin reviewing applications on Tuesday, January 2, 2018 but will continue to review applications until all positions are filled.

MARUM: ECORD Training Course: The Virtual Drillship Experience, April 23-27, 2018, Bremen, Germany
The application deadline is January 15, 2018.

Ocean Exploration Trust: Science Communication Fellowship
Applicationsare due by January 15, 2018.

Ocean Exploration Trust: Science & Engineering Internship Program
Application Deadline: January 26, 2018.

NOAA: Ernest F. Hollings Undergraduate Scholarship
Application deadline: January 31, 2018.

C-DEBI: Summer Undergraduate Global Environmental Microbiology (GEM) Course
Applications due: February 1, 2018.

Geobiology 2018: An International Training Course in a Rapidly Evolving Field
Application deadline: February 9, 2018.

ASM: Undergraduate Research Fellowship: Receive Summer Research Stipend – NEW!
The fellowship awards $4,000 to undergraduate, community college, and post-baccalaureate students to perform 10-12 weeks of summer research. Also, awardees submit their research for presentation at ASM Microbe 2019. If their abstract is accepted, they receive up to $2,000 in travel funds to attend the Microbe Academy for Professional Development prior to the meeting and present their research at the meeting. Application Deadline: February 15, 2018.

C-DEBI: NSF REU: Community College Cultivation Cohort (C4)
Applications due February 23, 2018.

ASM: Research Capstone Fellowship: Funding For Professional Development and Career Networking – NEW!
The Research Capstone Fellowship is available to underrepresented minority students at three different levels: 1) Community college, undergraduate, and post-baccalaureate students; 2) Master’s level and early-graduate students (prior to taking the preliminary exam); and 3_ Doctoral candidates (post-preliminary exam). All Fellows receive up to $2,000 to attend and present at the ASM Microbe Academy for Professional Development (MAPD) and the ASM Microbe Meeting (contingent upon abstract acceptance). Doctoral candidates receive up to $2,000 in additional funding during years two and three of the fellowship to participate in professional development courses/training and/or attend local or national meetings (contingent upon approval of progress report and annual budget plan). Application Deadline: March 1, 2018.

Mentoring365: Become an Earth and Space Science Mentor or Mentee

NOAA: Graduate Research & Training Scholarship Program

Proposal Calls

IODP: Apply to Sail on IODP Expedition 358
The deadline to apply is January 4, 2018.

DCO: Call for Postdoctoral Fellowship Proposals in Deep Life Modeling and Visualization – NEW!
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.

Duke: Mary Derrickson McCurdy Visiting Scholar
Application open until January 30, 2018.

NSF: International Research Experiences for Students (IRES)
Track I deadline: January 30, 2018; Track II deadline deadline: February 6, 2018; Track III deadline: February 13, 2018.

NSF: Major Research Instrumentation (MRI)
Submissions due February 5, 2018.

American Philosophical Society / NAI: Lewis and Clark Fund for Exploration and Field Research in Astrobiology
Deadline: February 15, 2018.

IODP: Apply to Sail on IODP Expedition 383
The deadline to apply is March 1, 2018.

DCO: Deep Life Cultivation Internship Program

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops, related to the International Ocean Discovery Program (IODP).

NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.

NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.

C-DEBI: Rolling call for Research Exchange proposals

Employment

WHOI: Tenure Track Research Scientist (Ocean Biogeochemical Modeler) – Marine Chemistry & Geochemistry (17-09-12)
Review of applications will begin on January 5, 2018.

University of Georgia: Two Faculty Vacancies (Assistant Professor) In Oceanography
Applications received by January 8, 2018 are assured full consideration.

UCSD / SIO: Assistant Professor – Marine Biogeochemist
Applications due January 8, 2018.

Aarhus University: Six Open Positions at Center for Electromicrobiology (CEM)
Application deadline: January 15, 2018.

UCSD / SIO: Assistant Professor – Low-Temperature Geochemistry – NEW!
We seek outstanding candidates for a tenure-track Assistant Professor position in low-temperature geochemistry. We are interested in candidates who will build a program of laboratory and field studies of international standing in low-temperature geochemical applications which strengthen the research portfolio of SIO and UC San Diego. The potential for academic excellence, rather than research area, will be the principal criterion for selection. Appropriate areas for specialization could span a wide range of surficial processes in the marine and terrestrial environments. The candidate’s area of research could include but is not limited to: sediment geochemistry, fluid geochemistry, paleoclimatology, paleoceanography, geochronology, fluid-rock interaction, low-temperature geochemical cycles, trace-element geochemistry, geochemical proxy development, or surficial inorganic geochemical process in the cryosphere, weathering systems, anthropological contexts, and the fossil record. Applications due January 31, 2018.

U Southern Mississippi: Two tenure-track positions in ocean engineering
Applicant review will begin February 1, 2018 and continue until the position is filled.

U Southern Mississippi: Endowed Chair, Division of Marine Science
Applicant review will begin February, 2018 and continue until the position is filled.

U Alaska Fairbanks: CFOS Assistant or Associate Professor
Applications due February 28, 2018.

U Penn: Two Graduate Research Assistant Positions

MBL: Postdoctoral Scientist – Molecular Microbial Ecology