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C-DEBI Newsletter – April 17, 2017
This newsletter is also accessible via our website.



Message from the Director:

Looking forward to another great Networked Speaker Series talk on 5/11: Dr. Andrew Steen, Assistant Professor at the University of Tennessee, Knoxville presents "What Heterotrophs Want: Using extracellular enzyme assays to probe the lifestyle of heterotrophic microorganisms in subsurface sediments." The intent of these half-hour talks is to connect all of us interested "deeply" or broadly in the deep biosphere. Note, these early career investigators were nominated by members of the community for their exciting research and effective communication!

If you missed this season's previous talk, Dr. Annie Rowe: Eating rocks! Investigating microbial energy conservation with microbes that utilize solid mineral electron donors, you can watch it now online.

Cheers,

Jan Amend
C-DEBI Director
 

 

Publications


PeerJ
Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems NEW!
Sean P. Jungbluth*​, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé
*C-DEBI Contribution 356


It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.


Geobiology
Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations NEW!
M.S. Bray, J. Wu, B.C. Reed, C.B. Kretz, K.M. Belli, R.L. Simister, C. Henny, F.J. Stewart, T.J. DiChristina, J.A. Brandes, D.A. Fowle, S.A. Crowe, J.B. Glass*
*C-DEBI Contribution 365


Reactive Fe(III) minerals can influence methane (CH4) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4-stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.


Environmental Microbiology
Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria NEW!
Nagissa Mahmoudi*, Steven R. Beaupré, Andrew D. Steen, Ann Pearson
*C-DEBI Contribution 366


Aquatic sediments harbor diverse microbial communities that mediate organic matter degradation and influence biogeochemical cycles. The pool of bioavailable carbon continuously changes as a result of abiotic processes and microbial activity. It remains unclear how microbial communities respond to heterogeneous organic matrices and how this ultimately affects heterotrophic respiration. To explore the relationships between the degradation of mixed carbon substrates and microbial activity, we incubated batches of organic-rich sediments in a novel bioreactor (IsoCaRB) that permitted continuous observations of CO2 production rates, as well as sequential sampling of isotopic signatures (δ13C, Δ14C), microbial community structure and diversity, and extracellular enzyme activity. Our results indicated that lower molecular weight (MW), labile, phytoplankton-derived compounds were degraded first, followed by petroleum-derived exogenous pollutants, and finally by higher MW polymeric plant material. This shift in utilization coincided with a community succession and increased extracellular enzyme activities. Thus, sequential utilization of different carbon pools induced changes at both the community and cellular level, shifting community composition, enzyme activity, respiration rates, and residual organic matter reactivity. Our results provide novel insight into the accessibility of sedimentary organic matter and demonstrate how bioavailability of natural organic substrates may affect the function and composition of heterotrophic bacterial populations. This article is protected by copyright. All rights reserved.


Frontiers Research Topic on Environmental Bioenergetics: Call for Manuscripts
Abstract submission deadline: June 30, 2017.



Proposal Calls


IODP: Apply to Sail: Expedition 380 NanTroSEIZE Frontal Thrust LTBMS NEW!
The International Ocean Discovery Program (IODP) is now accepting applications for Expedition 380 NanTroSEIZE Frontal Thrust Long-Term Borehole Monitoring System (LTBMS) aboard the D/V Chikyu. The Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE) Project comprises multiple expeditions over a multi-year period aimed at sampling and instrumenting the up-dip transition into the subduction seismogenic zone. The goal of Expedition 380 is to install an LTBMS in the accretionary toe region near the trough axis at Site C0006, previously drilled during IODP Expeditions 314 and 316. The LTBMS sensors will include: seafloor reference and formation pressure sensors, broadband seismometer, tiltmeters, volumetric strainmeter, geophones, and accelerometers. This will be the third LTBMS installed for the NanTroSEIZE project. The expedition is currently planned for 43 days, beginning on 23 October, sailing on 26 October (after three days of portcall), and finishing on 5 December, 2017. If LTBMS/CORK installation goes ahead of schedule, the ship will return early to port and the expedition will be complete. Additional information about this expedition can be found in the Expedition 380 Call For Participation. Opportunities exist for researchers (including graduate students) to sail on the expedition. Scientific specialties that will likely be required for the shipboard science party include observatory science and downhole logging. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program. The deadline to apply is April 28, 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
Applications are due May 16, 2017.

NAS: Building Capacity for Science Communication Partnership Awards NEW!
With support from the Rita Allen Foundation, the National Academy of Sciences is pleased to offer two awards of $37,500 each to support the formation and development of collaborative science communication researcher-practitioner partnerships. These awards are intended to facilitate the efforts of science communication researchers and practitioners to plan collaborative projects that pursue shared research interests aligned with the recently released consensus report, Communicating Science Effectively: A Research Agenda. Those receiving awards will present details about their collaborations at a special session of the Arthur M. Sackler Colloquium on the Science of Science Communication III to be held on November 16-17, 2017. Additional support for the Colloquium is provided by the Annenberg Public Policy Center of the University of Pennsylvania and the Burroughs Wellcome Fund. To apply for these awards, researchers and practitioners who have agreed to work in partnership should submit a proposal by June 1, 2017.

Simons Foundation: 2017 Postdoctoral Fellowships in Marine Microbial Ecology NEW!
The Simons Foundation invites applications for postdoctoral fellowships to support research on fundamental problems in marine microbial ecology. The foundation is particularly interested in applicants with training in different fields who want to apply their experience to understanding the role of microorganisms in shaping ocean processes and vice versa, as well as applicants with experience in modeling or theory development. While these cross-disciplinary applicants will receive particular attention, applicants already involved in ocean research are also encouraged to apply. The foundation anticipates awarding five fellowships in 2017. Applicants should have received their Ph.D. or equivalent degree within two years of the fellowship’s start date. Preference will be for applicants with no more than one year of postdoctoral experience. Applicants may be citizens of any country. Awards can only be issued to nonprofit research universities or research institutions in the U.S. Application deadline: June 15, 2017.

WGBH: Rita Allen Fellowship for Science Communication NEW!
The Rita Allen Foundation and WGBH Boston are pleased to announce the Rita Allen Fellowship for Science Communication. This new program will provide a year’s support for one fellow to study the field of science media, experiment with successful media formats and work to expand science literacy in the general public. The fellow will embed at WGBH, one of the pre-eminent science media producers in the US and home to the flagship public media science series NOVA. The goal of the Rita Allen Fellowship is to identify ways to expand how and to whom science news and information are communicated. It also aims to discover new information by experimenting with best practices that will provide all science media producers with tools to reach new audiences more effectively. The Fellow will receive a stipend of $82,000 plus benefits, for the year. Applications due June 30, 2017.

NSF: Using JOIDES Resolution to Collect Cores with Advanced Piston Coring (APC) System NEW!
The Division of Ocean Sciences (OCE) of the National Science Foundation (NSF) announces that proposals will now be accepted for U.S. researchers to use the drill ship JOIDES Resolution to collect cores using the Advanced Piston Coring (APC) system up to sub-bottom depths of 100 meters to address research on multiple aspects of the ocean basins. This program, referred to as “JR100,” was outlined in a previous Dear Colleague Letter (NSF 17-018). This new NSF Dear Colleague Letter provides the specific dates and geographic area of operation for the first JR100 cruise and updates information previously provided on proposal preparation requirements. JOIDES Resolution is scheduled to be transiting from Papeete, Tahiti, to Punta Arenas, Chile, from 19 December 2018 to 18 January 2019. Approximately thirteen (13) days during this transit period will be available for cruise operations (including coring and site-to-site transit time) with the remaining seventeen (17) days allocated to the direct transit route between ports. The cruise participants will stay on the ship during the entire thirty days. For a successful proposal, the NSF science program to which the proposal is submitted will provide funding for the types of items normally included in an ARF-based coring proposal including, but not limited to, funding for PI and cruise participant salaries, core shipments, non-standard analytical equipment required at sea, and post-cruise research funding. Funding sources for the ship operations to implement successful proposals will be determined through conversations between cognizant NSF Program Directors.

DCO: Deep Life Cultivation Internship Program

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).

C-DEBI: Rolling call for Research Exchange proposals



Education & Outreach


NSF Advanced Training Program in Antarctica for Early-Career Scientists: Biological Adaptations to Environmental Change
Deadline for receipt of completed applications is TODAY, April 17, 2017.

AAAS: Science & Human Rights Coalition: 2017 Student Essay Competition NEW!
Undergraduate and graduate students are invited to participate in the AAAS Science and Human Rights Coalition Essay Competition. This essay competition was created to inspire students to explore connections between human rights and science, engineering and the health professions. Students may write on any topic at the intersection of science and/or technology with human rights. Submissions should be written in the form of an analytical or critical paper that raises thought-provoking questions. For example, potential essay topics might include: the applications of a scientific approach or a new technology to address specific human rights concerns; an analysis of synergies between human rights obligations and the social responsibilities of scientists, engineers and/or health professionals; or the ways in which full implementation of the right to enjoy the benefits of scientific progress may influence realization of other human rights. These examples are only provided to spark ideas: students are encouraged to write essays that reflect their own ideas, interests, and insights. Essay submission open through April 30, 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


Indian Ocean community workshop, September 11-13, 2017, La Jolla, CA NEW!
2015 marked the 50th anniversary of the International Indian Ocean Expedition and the beginning of a new phase of coordinated international research dubbed the Second International Indian Ocean Expedition (IIOE-2). This 5-year global science initiative is engaging the international science community in collaborative research to improve our understanding of key ocean and climate drivers in the Indian Ocean basin. To harness growing interest among US scientists in Indian Ocean research, the US IIOE-2 Steering Committee is organizing an Indian Ocean community workshop September 11-13, 2017 in La Jolla, CA. Through a combination of plenary sessions and smaller group discussions, participants in this workshop will work across disciplines of biological, chemical, physical, and geological oceanography, as well as climate dynamics and atmospheric science to generate integrated observing and process experiment strategies to address some of the leading, multidisciplinary science questions in the Indian Ocean basin. The workshop will be sponsored by the US Ocean Carbon and Biogeochemistry (OCB) Program, NASA Physical Oceanography, NOAA Ocean Observing and Monitoring Division, and the Scripps Institution of Oceanography (SIO). If you think you might be interested in participating, please pre-register. Please note that pre-registration does not commit you to attend the workshop; rather, this form is intended to gauge community interest in the workshop for planning purposes.

Special Call for Early Career Participants in the Australasian Regional Planning Workshop
Applications due TODAY, April 17, 2017.

AGU 2017 Fall Meeting: Request for Session Proposals 
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.

C-DEBI: Rolling call for Community Workshop support



Employment


SIO: Researcher Positions - BiologySection
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

University of Southern Mississippi: Postdoctoral Research Position in Marine Microbial Ecology

University of Munich: Postdoctoral scholar, microbial transcriptional activity in subseafloor sediment

Rutgers: Assistant Professor - AY (TenureTrack)

Shanghai Ocean University: Faculty Positions in Bioinformatics and Proteomics at HAST






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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