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C-DEBI Newsletter – June 1, 2016
This newsletter is also accessible via our website.

 


I hope you enjoyed our Networked Speaker Series talks this year from Dr. Stephanie Carr, Dr. Olivia Nigro, and Dr. Katrina Twing on integral pieces in our understanding of the deep biosphere - methanogens, viruses, and serpentinites. If you missed any of these talks, you can watch them now online. We will be posting instructions on the website for nominating speakers for the 2016-2017 NSS, so please keep in mind any early career investigators with exciting research and effective communication that you'd like to nominate!

Congratulations also to C-DEBI Graduate Student Fellow Dr. Alex Michaud who is starting a postdoc position at Aarhus University in Denmark in the group of Bo Barker Jørgensen. See his C-DEBI project abstract on investigating microbial carbon cycling beneath the West Antarctic Ice Sheet and stay tuned for his dissertation publications such as his recent C-DEBI Contribution 321.

Cheers,

Jan Amend
C-DEBI Director


 

Publications


Frontiers in Microbiology
Fungal and prokaryotic activities in the marine subsurface biosphere at Peru Margin and Canterbury Basin inferred from RNA-based analyses and microscopy
Maria G. Pachiadaki*, Vanessa Rédou, David Beaudoin, Gaëtan Burgaud and Virginia P. Edgcomb*
*C-DEBI Contribution 323


The deep sedimentary biosphere, extending hundreds of meters below the seafloor harbors unexpected diversity of Bacteria, Archaea and microbial eukaryotes. Far less is known about microbial eukaryotes in subsurface habitats, albeit several studies have indicated that fungi dominate microbial eukaryotic communities and fungal molecular signatures (of both yeasts and filamentous forms) have been detected in samples as deep as 1740mbsf. Here we compare and contrast fungal ribosomal RNA gene signatures and whole community metatranscriptomes present in sediment core samples from 6 and 95mbsf from Peru Margin site 1229A and from samples from 12 and 345 mbsf from Canterbury Basin site U1352. The metatranscriptome analyses reveal higher relative expression of amino acid and peptide transporters in the less nutrient rich Canterbury Basin sediments compared to the nutrient rich Peru Margin, and higher expression of motility genes in the Peru Margin samples. Higher expression of genes associated with metals transporters and antibiotic resistance and production was detected in Canterbury Basin sediments. A poly-A focused metatranscriptome produced for the Canterbury Basin sample from 345 mbsf provides further evidence for active fungal communities in the subsurface in the form of fungal-associated transcripts for metabolic and cellular processes, cell and membrane functions, and catalytic activities. Fungal communities at comparable depths at the two geographically separated locations appear dominated by distinct taxa. Differences in taxonomic composition and expression of genes associated with particular metabolic activities may be a function of sediment organic content as well as oceanic province. Microscopic analysis of Canterbury Basin sediment samples from 4 and 403mbsf produced visualizations of septate fungal filaments, branching fungi, conidiogenesis and spores. These images provide another important line of evidence supporting the occurrence and activity of fungi in the deep subseafloor biosphere.


Current Opinion in Microbiology
The bright side of microbial dark matter: lessons learned from the uncultivated majority
Lindsey Solden, Karen Lloyd, Kelly Wrighton


Microorganisms are the most diverse and abundant life forms on Earth. Yet, in many environments, only 0.1–1% of them have been cultivated greatly hindering our understanding of the microbial world. However, today cultivation is no longer a requirement for gaining access to information from the uncultivated majority. New genomic information from metagenomics and single cell genomics has provided insights into microbial metabolic cooperation and dependence, generating new avenues for cultivation efforts. Here we summarize recent advances from uncultivated phyla and discuss how this knowledge has influenced our understanding of the topology of the tree of life and metabolic diversity.


 

Proposal Calls


IODP: Apply to Sail: Expedition 370, T-Limit of the Deep Biosphere off Muroto: Deciphering factors that constrain the extent of the deep biosphere in a subduction zone
The International Ocean Discovery Program (IODP) Expedition 370 Scientific Prospectus (doi:10.14379/iodp.sp.370.2016) is now published on the IODP website. 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 June 10, 2016. Also, the applicants are encouraged to participate in the T-Limit workshop on the Chikyu on June 25 before the Goldschmidt conference. Registration fee is free. Scientists interested in this workshop can get more information and registration through the Deep Carbon Observatory (DCO) website. Additional information about this expedition can be found on the IODP Expedition 370 website.

DCO: Census of Deep Life Sequencing Opportunities
Since 2011, the Deep Carbon Observatory’s Deep Life Community has sponsored the Census of Deep Life (CoDL) that has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of diversity of subsurface microbial communities at numerous sites worldwide including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt bacterial sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples can also be performed. This call for proposals aims to support sequencing that represents expanded analyses from ongoing Deep Life Community projects or projects that represent sites and investigators new to the DCO’s Deep Life Community. Deadline: July 15, 2016.

CIES: 2017-2018 Fulbright U.S. Scholar Program in Arctic Affairs
The Core Fulbright U.S. Scholar Program competition is now open and accepting applications for 2017-2018 awards in arctic affairs! Opportunities are available for teaching and/or research in nearly every discipline, from engineering to political science, anthropology, sociology, communications and more! Applicants must be U.S. citizens and the deadline for complete applications is August 01, 2016.

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 (next call due Today), related to the International Ocean Discovery Program (IODP).

IODP: Volunteer to serve on the IODP Science Evaluation Panel or the Environmental Protection and Safety Panel
Deadline: July 08, 2016.

DCO: Second Call for Proposals: Deep Energy Community
Deadline July 20, 2016.


 

Meetings & Activities


Goldschmidt/DCO/Jamstec: IODP "T-Limit" Project Workshop - Expedition 370: T-Limit of the Deep Biosphere off Muroto
Please register online by June 21, 2016. Registration may close sooner if the maximum number of participants have registered. Participation is limited to 50 scientists (including guests, operators, etc.).

DCO Symposium in Yokohama: Deep Life, Deep Energy, Reservoirs and Flues, and Extreme Physics and Chemistry, June 26, 2016
Register by June 21, 2016.

Kyoto University: 5th International Workshop on Deep Sea Microbiology, September 10-11, 2016
Abstract submission deadline: July 23, 2016.

 

 
Other Announcements

NSF Division of Ocean Sciences (OCE) Strategy for Supporting Coring for Scientific Research

 


Employment

NASA-JSC: Geomicrobiologist
The Astromaterials Acquisition and Curation Office at the NASA Johnson Space Center seeks a specialist in the field of geomicrobiology or astrobiology. The successful candidate will serve NASA as curator for biological components in astromaterials. Specifically, we seek an individual with expertise in at least one of the following areas: (1) biological cleanliness and quantitative biological contaminant characterization; (2) chemical, mineralogical, or petrological consequences of microbial interaction with astromaterials, astromaterials simulants, and terrestrial analogs of astromaterials; (3) sample collection and handling (including transport, containment, preservation, and curation) of geological materials that contain microbial matter. The successful candidate shall develop an externally funded research program in the area of geomicrobiology and/or astrobiology. Additional duties include development and implementation of curation plans for astromaterials returned from future missions with possible extraterrestrial biological components; conducting advanced curation research to prevent biological contamination of NASA’s past, present, and future astromaterials collections. Furthermore, he or she will be expected to develop methods of monitoring for biological contamination within curation facilities and in NASA’s astromaterials collections. This individual will also provide expertise in the area of contamination knowledge as it relates to biological cleanliness of NASA spacecraft at all stages of a mission. The position will be posted at USAJobs, starting May 24 and closing June 14, 2016.

University of St. Andrews: PhD Studentship available - Oct 2016
A fully-funded 42 month PhD Studentship is available within the Planetary Habitability group at the University of St Andrews, supervised by myself (Dr. Claire Cousins) and Aubrey Zerkle. The project will investigate feasible chemolithotrophic metabolisms on Mars and their resulting stable isotope biosignatures, using unusual ice-fed hydrothermal lakes and ponds in Iceland as a ‘biological analogue’ for past habitats and microbial communities on Mars. Please note this project is open to UK and EU nationals only. Application deadline: June 30, 2016.

St. Johns Hopkins: Faculty Positions in Geosciences and in Environmental Sciences
The Department of Earth and Planetary Sciences at Johns Hopkins University invites applications for multiple tenure-track or tenured faculty positions. The positions can be filled at the Assistant, Associate, or Full Professor level, starting as early as Fall 2016. The successful candidates are expected to develop internationally recognized and externally funded research programs, to help develop and participate in undergraduate and graduate teaching, and to supervise graduate student research. In the case of an appointment with tenure, the candidate must already be internationally recognized and have a demonstrated record of external research funding. A PhD is required in the Earth Sciences or a related natural sciences discipline; post-doctoral experience is desirable. Applicants are sought for two focus areas: Geosciences, including low-temperature geochemistry and studies of the early Earth, cosmochemistry, geophysics and geodynamics, volcanology and igneous petrology. We are particularly interested in candidates whose research has synergies with our recent hires with expertise in sedimentary, metamorphic and tectonic processes, planetary geology, and planetary atmospheres; and Environmental Sciences, including natural resources (including water, metals, soils, and energy), ecology, critical zone science, marine sciences, cryospheric sciences, geomorphology, landscape hydrology, environmental change, air pollution, and biogeochemistry. We are particularly interested in candidates whose research has synergies with our program in Global Environmental Change and Sustainability. Applications received by June 30, 2016, will receive full consideration.

Moore Foundation: Program Fellow, Marine Microbiology Initiative
To complement activities in the Marine Microbiology Initiative (MMI) and other current science program grantmaking, we seek a program fellow to explore opportunities for further foundation impact in the realm of symbiosis. Here, we refer to symbiosis as the interactions between microbes (bacteria, archaea, and protists) and animals, plants, fungi, and other microbes. We also consider the role of viruses in these relationships. We consider symbiosis broadly in terms of habitat (terrestrial and marine), degree of interdependence (transient, obligatory, endosymbiotic, and that which results in organelle evolution), and time (ancient to modern). The fellow will synthesize information regarding the state of symbiosis research and related fields in the U.S. and abroad. The fellow may also work on related topics that link with MMI and other current symbiosis grantmaking at the foundation. The Program Fellow role has a term of 12 months, with the possibility of renewal for up to 12 additional months. Those with a relevant advanced graduate degree—as well as researchers considering a sabbatical—are welcome to apply.

Bigelow: Postdoctoral Research Scientist 
The position is offered for two years. The position has an expected start date of September 2016, but this may be negotiated. Review of applicants will begin immediately and proceed until the position is filled.

Rutgers University Deep Sea Microbiology Lab: Bioinformatics Postdoctoral Position
The position is available immediately and potential candidates should contact group leader Constantino Vetriani directly at vetriani@marine.rutgers.edu.

Montana State University, Thermal Biology Institute: Two Postdoctoral Scholar Positions Open
Applications will be reviewed starting March 21, 2016 and will continue until positions are filled.

IODP at Texas A&M: Assistant Research Scientist
We will begin reviewing applications on May 16, 2016, but will continue to accept applications until candidates are selected for interviews.





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
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

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