|C-DEBI Newsletter – April 3, 2017
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Publications & Press
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids – NEW!
Sean P. Jungbluth*, Jan P. Amend*, Michael S. Rappé
*C-DEBI Contribution 357
The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.
Nature Microbiology Letters
Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea – NEW!
Blair G. Paul*, David Burstein, Cindy J. Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian C. Thomas, Partho Ghosh, Jeff F. Miller, Jillian F. Banfield & David L. Valentine
*C-DEBI Contribution 361
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence.
In situ electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring – NEW!
Annette R. Rowe*, Miho Yoshimura, Doug E. LaRowe, Lina J. Bird, Jan P. Amend*, Kazuhito Hashimoto, Kenneth H. Nealson, Akihiro Okamoto
*C-DEBI Contribution 364
Serpentinization is a geologic process that produces highly reduced, hydrogen-rich fluids that support microbial communities under high pH conditions. We investigated the activity of microbes capable of extracellular electron transfer in a terrestrial serpentinizing system known as “The Cedars”. Measuring current generation with an on-site two-electrode system, we observed daily oscillations in current with the current maxima and minima occurring during daylight hours. Distinct members of the microbial community were enriched. Current generation in lab-scale electrochemical reactors did not oscillate, but was correlated with carbohydrate amendment in Cedars-specific minimal media. Gammaproteobacteria and Firmicutes were consistently enriched from lab electrochemical systems on δ-MnO2 and amorphous Fe(OH)3 at pH 11. However, isolation of an electrogenic strain proved difficult as transfer cultures failed to grow after multiple rounds of media transfer. Lowering the bulk pH in the media allowed us to isolate a Firmicutes strain (Paenibacillus sp.). This strain was capable of electrode and mineral reduction (including magnetite) at pH 9. This report provides evidence of the in situ activity of microbes using extracellular substrates as sinks for electrons at The Cedars, but also highlights the potential importance of community dynamics for supporting microbial life through either carbon fixation and/or moderating pH stress.
Frontiers in Microbiology
Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH – NEW!
Katrina I. Twing, William J. Brazelton, Michael D. Y. Kubo, Alex J. Hyer, Dawn Cardace, Tori M. Hoehler, Tom M. McCollom and Matthew O. Schrenk
Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.
Frontiers Research Topic on Environmental Bioenergetics: Call for Manuscripts – NEW!
Topic Editors: Anke Marianne Herrman, Doug LaRowe, Alain F. Plante. Energy is continuously transformed in the environment through the metabolic activities of organisms. These transformations of energy, i.e. bioenergetics, underpin most biogeochemical cycles on Earth and allow the delivery of a wide range of life-supporting ecosystem services. The aim of this Research Topic is to gather contributions from scientists working in diverse disciplines who have a common interest in evaluating bioenergetics at various spatial and temporal scales in a variety of different environments. The spatial scales range from the process and organismal level up to ecosystems, the temporal scales range from the near-instantaneous to the millennial, and the scientific disciplines involved include: soil scientists, biogeochemists, organic geochemists, microbial and ecosystem ecologists etc. Articles can be original research, techniques, reviews or synthesis papers. We encourage manuscripts focusing on interdisciplinary interactions addressing both basic and applied research as well as associated theoretical work. The overarching goal of this Research Topic is to demonstrate the environmental breadth of bioenergetics, and foster understanding between different scientific communities who may not always be aware of one another’s work. Abstract submission deadline: June 30, 2017.
Marine Technology News: Uncharted Depths: Exploring the Marianas with SuBastian – NEW!
A crescent shaped scar on the earth’s crust marks the location of the deepest known part of the world’s ocean. With some areas reaching depths more than 36,000 feet, scientists rely on a range of pioneering deep-sea technologies to survey the unexplored regions of the Mariana Trench. In 1987, the submersible Alvin was the first to visit the nearby Mariana Back-arc, a zone of highly active submarine volcanism and hydrothermal vents hidden 13,000 feet below the ocean’s surface. After returning to the Back-arc 30 years later equipped with the Schmidt Ocean Institute’s new underwater vehicle SuBastian, scientists can now fill gaps in our understanding about the biogeography of these unique ecosystems and to identify possible new species thriving in this extreme deep-ocean environment.
IODP: Submit an IODP Drilling Proposal
Next Proposal Submission Deadline: TODAY, April 3, 2017.
DCO: Census of Deep Life Sequencing Opportunities: Request for Proposals
Proposal deadline: April 30, 2017.
DOE Office of Science Graduate Student Research (SCGSR) Program – NEW!
The goal of the Office of Science Graduate Student Research (SCGSR) program is to prepare graduate students for science, technology, engineering, or mathematics (STEM) careers critically important to the DOE Office of Science mission, by providing graduate thesis research opportunities at DOE laboratories. The SCGSR program provides supplemental awards to outstanding U.S. graduate students to pursue part of their graduate thesis research at a DOE laboratory in areas that address scientific challenges central to the Office of Science mission. The research opportunity is expected to advance the graduate students’ overall doctoral thesis while providing access to the expertise, resources, and capabilities available at the DOE laboratories. The SCGSR program is sponsored and managed by the DOE Office of Science’s Office of Workforce Development for Teachers and Scientists (WDTS), in collaboration with the 6 Office of Science research programs and the DOE national laboratories. Online application and awards administration support is provided by Oak Ridge Institute of Science and Education (ORISE) under Oak Ridge Associated Universities (ORAU). The SCGSR program provides supplemental funds for graduate awardees to conduct part of their thesis research at a host DOE laboratory in collaboration with a DOE laboratory scientist within a defined award period. The award period for the proposed research project at DOE laboratories may range from 3 to 12 consecutive months. Applications are due May 16, 2017.
DCO: Deep Life Cultivation Internship Program – NEW!
The Deep Life Community (DLC) within the Sloan Foundation supported Deep Carbon Observatory realizes that the majority of deep microbial life has been resistant to cultivation in the laboratory, which complicates the characterization of physiological characteristics of deep community members. However, recent studies using bioreactor-cultivation techniques, under high pressure and/or temperature, have resulted in successful enrichment of previously uncultivable archaeal and bacterial components that mediate biogeochemical carbon cycling in deep subsurface (1-7). In order to maintain and strengthen cultivation strategies in future deep life missions, the DLC will support early-carrier researchers to visit some key laboratories (Inagaki – Kochi, Japan, Bartlett – La Jolla, USA, and others) to learn and practice newly developed cultivation and cultivation-dependent molecular/biogeochemical techniques using samples from the DLC’s field missions. Financial support includes $5,400 per person for travel and lodging costs and host lab research supply reimbursement. Interested applicants should send their cv, a brief one page statement of their cultivation plans, and a letter of support from their intended host to Fumio Inagaki (email@example.com ) and Douglas Bartlett (firstname.lastname@example.org).
NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.
NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.
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).
Education & Outreach
Informational Webinars for NSF-UNOLS Early Career Scientist Training in Seismic Data Acquisition & Processing – NEW!
The National Science Foundation (NSF) has funded an Early Career Scientist Training Cruise in Seismic Data Acquisition and Processing to take place aboard the R/V Revelle in September 2017.The official announcement and application form for this opportunity will be forthcoming. As part of this effort, the program’s Principal Investigators will be hosting a three-part webinar series, which will provide participants with necessary information to complete the application package, including a 2-page (max) science proposal. The webinars will introduce the participants to the process of defining science goals, developing detailed cruise plans to meet those goals, and to fundamentals of active source marine seismology. The course will also cover the use of currently available data, open source processing, and interpretation tools to help develop a proposal. The cruise has been designed for (but is not limited to) graduate students and early career scientists who are “non-specialists” in active source seismic, but we welcome any interested parties for this webinar series! The program PIs are: Masako Tominaga (TAMU), Anne Trehu (OSU), Mitch Lyle (OSU), and Gregory Mountain (Rutgers), with additional support from Nathan Bangs (UTIG). Interested individuals can sign up for the free webinars, even if they do not intend to apply to the cruise opportunity. Please RVSP at the following link: https://www.surveymonkey.com/r/CSWSeismicWebinars and the UNOLS Office will send login and participation instructions prior to the start of the webinars. The deadline for webinar registration is TODAY, April 3, 2017.
IODP-USSSP: School of Rock: Hands-on Research Experiences for Earth and Ocean Science Educators – NEW!
USSSP periodically sponsors seagoing Earth systems research and education workshops—the “School of Rock”—aboard the JOIDES Resolution. During times when the ship is unavailable, the School of Rock is conducted at the Gulf Coast Repository, located at Texas A&M University in College Station, Texas, or other institutions. Over 150 formal and informal educators have participated in the School of Rock program since it was initiated in 2005. During the 7-14 day School of Rock workshop, educators have daily opportunities to conduct geological, physical and/or chemical analyses of sediment and hard-rock cores in laboratories on the ship or at the repository. Scientists who specialize in IODP research instruct participants on topics such as seafloor spreading, mid-ocean ridges, composition and structure of the oceanic crust, paleomagnetism, paleoceanography, biostratigraphy, sedimentology, hydrogeology, and methods for sampling the subseafloor environment. The workshop also provides educators with time to brainstorm and begin planning classroom activities based on their research and newly acquired knowledge. Application deadline: April 7, 2017.
NSF Advanced Training Program in Antarctica for Early-Career Scientists: Biological Adaptations to Environmental Change
Deadline for receipt of completed applications is April 17, 2017.
MARUM: ECORD Summer School: Current-Controlled Sea Floor Archives: Coral Mounds and Contourites, August 28 – September 1, 2017
The application deadline is May 5, 2017.
Meetings & Activities
IODP: Workshop Announcement: Australasian Regional Planning Workshop, June 13-16, 2017, Sydney, Australia
Applications due TODAY, April 3, 2017.
Third DCO Early Career Scientist Workshop to Study Mt. Etna – NEW!
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.
NSF Continental Scientific Drilling Coordination Office: Call for participation: CSDCO Science Planning Workshop 2, May 18-19, 2017, Minneapolis
Application deadline: April 14, 2017.
AGU 2017 Fall Meeting: Request for Session Proposals – NEW!
Proposals are invited from all fields of scientific interest to be represented at the most influential gathering of Earth and space scientists in the world. This year sessions on the topics of data and geohealth are of particular interest to the Fall Meeting Program Committee. Data & Emerging Technologies: Data is critical to scientific advancement and improving our understanding of how natural systems and phenomena operate and change. Data should be openly accessible and archived for reuse into the future. Emerging technologies are creating new instruments, sensor arrays, and platforms that enable the collection of new data types and/or improve the resolution, accuracy, and precision of data collection methodologies. Frontier computational techniques and visualization tools are rapidly influencing the way we collect data and conduct science, thus forming a fertile breeding ground for new ideas and never-before-attempted science. Geohealth: This rapidly growing science covers the interface between the Earth, health, ecosystem, and agricultural sciences. The topic connects and brings together talks on climate change and human health, medical geology, natural hazards and health, atmospheric science, air pollution, the health effects of fire, the interface between water quality and health, and much more. Submission deadline: April 19, 2017.
IODP-USSSP: Call for IODP-ICDP Session Conveners at AGU 2017 Fall Meeting
The provisional dates of the call for session proposal are February 15th – April 19th, 2017.
IODP: Workshop on Land-Ocean Interactions Across the Indian Ocean: Toward Regional Integration of Recent Drilling Results
The workshop is open to U.S. and international participants, and the deadline to apply is April 20, 2017.
ISSM 2017: Call for Abstracts
Abstracts due April 24, 2017.
NSF STC STROBE / UC Boulder: Education and Broadening Participation Manager – NEW!
We seek to fill a full time Education and Broadening Participation Manager position within the new National Science Foundation STROBE Science and Technology Center for Real-Time Functional Imaging. The successful candidate will serve as the day-to-day project manager for STROBE activities directed to education and broadening participation. STROBE is a partnership of University of Colorado Boulder, UC Berkley, UC Los Angeles, UC Irvine, Fort Lewis College, and Florida International University. The mission of Strobe is to create powerful and broadly-applicable real time nano-to-atomic scale imaging modalities to advance imaging science and increase access, that can be used to address grand challenges in science and technology, while building a diverse STEM workforce. In addition to research, STROBE emphasizes knowledge transfer, education and broadening participation in the STEM workforce. For more information about STROBE, visit STROBE.colorado.edu. The goals of STROBE’s Education and Broadening Participation efforts are to develop, implement, assess and disseminate new education programs, innovative instructional materials, and models for other programs that inspire and prepare a diverse group of students to be innovative and globally competitive in imaging science and technology. STROBE will create unique learning approaches and experiences in imaging science through four core and integrated programmatic approaches that focus on transforming graduate programs, developing new pathways for those underrepresented in our fields, efforts in communication and engaging the public, and developing models for transdisciplinary STEM education. The successful candidate will be an employee of CU Boulder. The initial appointment will be for 24 months, renewable subject to University policies and the availability of funding. Review of applications will begin April 14, 2017 and will continue until the position is filled.
SIO: Researcher Positions – BiologySection – NEW!
The Scripps Institution of Oceanography (SIO) at the University of California San Diego (http://scripps.ucsd.edu) invites applications for one or more full-time Researcher positions to be funded by extramural research grants and contracts. The Researcher series at SIO parallels the Professor series in terms of research and service, but carries no teaching requirements. Researchers receive nine-month appointments with 25% salary support from institutional sources. Researchers are expected to establish an externally funded research program that provides the remainder of their salary support, including an opportunity for summer salary. Researchers at SIO often obtain lecturer appointments in the SIO department and serve as graduate student advisors. Although the specific research area within ocean biosciences is open, candidates with interests and experience in marine genomics/bioinformatics, marine natural products, fisheries science, aquaculture, or marine resource policy are especially encouraged to apply. For full consideration, please apply by the April 18, 2017 deadline.
University of Southern Mississippi: PhD and MS Graduate Research Assistantship in Marine Microbial Ecology – NEW!
The Hamdan Lab, in the Division of Coastal Sciences at the University of Southern Mississippi seeks an exceptional student to participate in marine microbial ecology studies in deep-sea habitats. This funded position will support independent research on the effects of oil spills on benthic ecosystems in the Gulf of Mexico. The research assistantship will support (stipend, tuition, benefits) a highly motivated PhD or MS study for up to three years beginning in Fall 2017. A student is sought to conduct independent research that investigates microbial population structure, metabolic capability, biodiversity and biogeochemistry of benthic environments. This position will involve laboratory studies using molecular biological techniques (DNA extraction, amplification, sequencing), bioinformatics, classical approaches to environmental microbiology (microscopy, metabolic tracers), and analytical chemistry techniques (stable carbon isotope studies, elemental analysis, bulk carbon pool analysis). Individuals interested in this position should contact Dr. Leila Hamdan (email@example.com), and provide a cover letter outlining specific interests and experience in the study of marine microbial ecology or biogeochemistry and a curriculum vita. Application for Fall 2017 admission at USM is required.
University of Southern Mississippi: Postdoctoral Research Position in Marine Microbial Ecology – NEW!
The Hamdan Lab at the University of Southern Mississippi seeks a qualified and highly motivated individual for a Postdoctoral Research Scientist position. This position will support research on the effects of oil spills on benthic ecosystems in the Gulf of Mexico. Specifically sought is a Postdoc to investigate the long-term consequences of oil and chemical dispersant exposure on the preservation of 20th century historic steel shipwreck in the deep biosphere. The individual will design and implement ROV deployable seafloor experiments to monitor microbially induced corrosion. Individuals with experience with microbiology and biogeochemistry, with specific knowledge and molecular biological techniques (DNA extraction, amplification, sequencing) are encouraged to apply. Experience and proficiency in bioinformatics and statistical analysis is desired for this position as well as proficiency with analytical chemistry techniques, including hydrocarbon analysis. Applicants must have a Ph.D. in coastal or marine sciences, geomicrobiology, biogeochemistry or similar field. The hire will be encouraged to participate in the planning and execution of oceanographic research onboard USM’s research vessel Point Sur for periods of up to two weeks at sea, and contribute to student mentoring. Excellent written and oral communication skills are needed, as well as a commitment to developing peer-reviewed manuscripts. Pending funding, the position will support the hire for 3 years, starting as early as June 2017.
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