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C-DEBI Newsletter – March 15, 2017
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Publications


Limnology and Oceanography: Methods
A new solution 31P NMR sample preparation scheme for marine sediments
 NEW!
Delphine Defforey*, Barbara J. Cade-Menun, Adina Paytan*
*C-DEBI Contribution 353


A new approach for the preparation of marine sediment samples for solution 31P nuclear magnetic resonance spectroscopy (31P NMR) has been developed and tested. This approach addresses important aspects associated with sample pretreatments for marine sediments, including the effects of sample pretreatment on sedimentary P composition. The method increases the signals of low abundance P species in 31P NMR spectra by quantitatively and precisely removing up to 80% of inorganic P (orthophosphate) from sediment samples while causing minimal alteration of the chemical structure of organic P compounds. This method uses a reductive step to solubilize P bound to iron oxyhydroxides, followed by a low pH digestion to extract P from authigenic and biogenic apatite, as well as P bound to calcium carbonate. These P forms combined represent the most abundant inorganic P reservoir in marine sediments. The sample residue is then extracted in an alkaline solvent, 0.25 M NaOH with 0.05 M Na2EDTA, and processed for 31P NMR spectroscopy. The method was tested on natural marine sediment samples from different localities with high inorganic P content (>85% molybdate reactive P), and allowed for the detection of orthophosphate monoesters and pyrophosphate in samples for which only an orthophosphate signal could be resolved with an NaOH-EDTA extraction alone. This new approach will allow the use of 31P NMR on samples for which low organic P concentrations previously hindered the use of this tool, and will help answer longstanding question regarding the fate of organic P in marine sediments.


mBio
Viruses in the Oceanic Basement
 NEW!
Olivia Nigro*, Sean P. Jungbluth, Huei-Ting Lin, Chih-Chiang Hsieh, Jaclyn. A. Miranda, Christopher. R. Schvarcz, Michael S. Rappé, Grieg Steward*
*C-DEBI Contribution 354


Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 105 to 2 × 105 ml−1 (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.


WHOI Theses
Geochemical controls on the distribution and composition of biogenic and sedimentary carbon NEW!
Emily R. Estes*
*C-DEBI Contribution 359


Organic carbon (OC) preserved in marine sediments acts as a reduced carbon sink that balances the global carbon cycle. Understanding the biogeochemical mechanisms underpinning the balance between OC preservation and degradation is thus critical both to quantifying this carbon reservoir and to estimating the extent of life in the deep subsurface biosphere. This work utilizes bulk and spatially-resolved X-ray absorption spectroscopy to characterize the OC content and composition of various environmental systems in order to identify the role of minerals and surrounding geochemistry in organic carbon preservation in sediments. Biogenic manganese (Mn) oxides formed either in pure cultures of Mn-oxidizing microorganisms, in incubations of brackish estuarine waters, or as ferromanganese deposits in karstic cave systems rapidly associate with OC following precipitation. This association is stable despite Mn oxide structural ripening, suggesting that mineral-associated OC could persist during early diagenetic reactions. OC associated with bacteriogenic Mn oxides is primarily proteinaceous, including intact proteins involved in Mn oxidation and likely oxide nucleation and aggregation. Pelagic sediments from 16 sites underlying the South Pacific and North Atlantic gyres and spanning a gradient of sediment age and redox state were analyzed in order to contrast the roles of oxygen exposure, OC recalcitrance, and mineral-based protection of OC as preservation mechanisms. OC and nitrogen concentrations measured at these sites are among the lowest globally (<0.1%) and, to a first order, scale with sediment oxygenation. In the deep subsurface, however, molecular recalcitrance becomes more important than oxygen exposure time in protecting OC against remineralization. Deep OC consists of primarily amide and carboxylic carbon in a scaffolding of aliphatic and O-alkyl moieties, corroborating the extremely low C/N values observed. These findings suggest that microbes in oxic pelagic sediments are carbon-limited and may preferentially remove carbon relative to nitrogen from the organic matter pool. As a whole, this work documents how interactions with mineral surfaces and exposure to oxygen generate a reservoir of OC stabilized in sediments on at least 25-million year time scales.


PeerJ
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation NEW!
Elaina D. Graham*​, John F. Heidelberg*, Benjamin J. Tully*
*C-DEBI Contribution 360


Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.


Frontiers in Earth Science
Microbial and biogeochemical dynamics in glacier forefields are sensitive to century-scale climate and anthropogenic change NEW!
James A. Bradley*,  Alexandre M. Anesio and Sandra Arndt
*C-DEBI Contribution 363


The recent retreat of glaciers and ice sheets as a result of global warming exposes forefield soils that are rapidly colonised by microbes. These ecosystems are dominant in high-latitude carbon and nutrient cycles as microbial activity drives biogeochemical transformations within these newly exposed soils. Despite this, little is known about the response of these emerging ecosystems and associated biogeochemical cycles to projected changes in environmental factors due to human impacts. Here, we applied the model SHIMMER to quantitatively explore the sensitivity of biogeochemical dynamics in the forefield of Midtre Lovénbreen, Svalbard, to future changes in climate and anthropogenic forcings including soil temperature, snow cover, and nutrient and organic substrate deposition. Model results indicated that the rapid warming of the Arctic, as well as an increased deposition of organic carbon and nutrients, may impact primary microbial colonisers in Arctic soils. Warming and increased snow-free conditions resulted in enhanced bacterial production and an accumulation of biomass that was sustained throughout 200 years of soil development. Nitrogen deposition stimulated growth during the first 50 years of soil development following exposure. Increased deposition of organic carbon sustained higher rates of bacterial production and heterotrophic respiration leading to decreases in net ecosystem production and thus net CO2 efflux from soils. Pioneer microbial communities were particularly susceptible to future changes. All future climate simulations encouraged a switch from allochthonously-dominated young soils (<40 years) to microbially-dominated older soils, due to enhanced heterotrophic degradation of organic matter. Critically, this drove remineralisation and increased nutrient availability. Overall, we show that human activity, especially the burning of fossil fuels and the enhanced deposition of nitrogen and organic carbon, has the potential to considerably affect the biogeochemical development of recently exposed Arctic soils in the present day and for centuries into the future. These effects must be acknowledged when attempting to make accurate predictions of the future fate of Arctic soils that are exposed over large expanses of presently ice-covered regions.



Proposal Calls


IODP: Apply to Sail on IODP Expedition 376
The deadline to apply is April 1, 2017.

IODP: Submit an IODP Drilling Proposal
Next Proposal Submission Deadline: April 3, 2017.

DCO: Census of Deep Life Sequencing Opportunities: Request for Proposals NEW!
Since 2011, the Deep Carbon Observatory’s (DCO) 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 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. Proposal deadline: April 30, 2017.

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


RGNO Ocean Discovery Camp - Namibia, April 12-May 12, 2017
Application deadline: March 10, 2017.

IODP-USSSP: U.S. Travel Support for Petrophysics Summer School
The deadline to apply for travel support and for the course is March 17, 2017.

C-DEBI: Community College Research Internship for Scientific Engagement (CC-RISE)
CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Woods Hole Oceanographic Institution in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications are due March 20, 2017 for UCSC and March 24, 2017 for WHOI.

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


6th International Symposium on Chemosynthesis-Based Ecosystems (CBE6), Woods Hole, Massachusetts, USA, August 27 – September 1, 2017
Abstract submission deadline March 17, 2017.

The 4th International Conference of Geobiology — Rocks, life and climate, June 24-26, 2017, Wuhan, China
The deadline for abstract submission is April 1, 2017.

Call for Abstracts: Goldschmidt 2017, Paris, August 13-18 NEW!
Please consider submitting your abstract to Goldschmidt Session 15h: Geobiology of the Modern. Convenors: Fumio Inagaki, Kai-Uwe Hinrichs, Chuanlun Zhang, Brian Hedlund, Fengping Wang, Stefan Sievert, Karen Lloyd, Benedicte Menez. Keynote: Victoria Orphan (Caltech). Abstract: The deep ocean and subseafloor biosphere is vast and diverse, harboring many uncultured clades of microorganisms. Energy and nutrients are supplied primarily by transformations of biologically and/or abiotically produced organic matter and the redox chemistry of water-rock interactions. Recent technological breakthroughs in biogeochemistry, geomicrobiology and molecular biology, as well as in obtaining pristine samples from the hadal zone of the ocean and the deep-subsurface biosphere enable us to address essential questions about microbial community composition, biogeochemical contribution, and limits to microbial ecosystems in the deep ocean and subseafloor biosphere. In this session, we would like to highlight studies broadly focusing on the triangular relationship between microbiology, geochemistry, and geophysics in (but not limited to) diverse oceanic and subseafloor biosphere settings. Given the slow pace of deep life activity and the associated challenges for detecting biosignatures in the most extreme sections of the Earth’s microbial ecosystems, we also encourage submissions addressing the exploration of biomarkers. Please also consider submitting your abstract to Goldschmidt Session 15b: Hydrothermal Biogeochemistry and Geobiology. Convenors: Christopher German, Wolfgang Bach, Costantino Vetriani, Donato Giovannelli. Keynote: Ken Takai (JAMSTEC). Abstract submissions are due April 1, 2017.

Aarhus University: International Workshop on "Marine Geomicrobiology" in Denmark
Deadline for applications is April 1, 2017.

IODP: Workshop Announcement: Australasian Regional Planning Workshop, June 13-16, 2017, Sydney, Australia
Applications due April 3, 2017.

NSF Continental Scientific Drilling Coordination Office: Call for participation: CSDCO Science Planning Workshop 2, May 18-19, 2017, Minneapolis NEW!
The NSF Continental Scientific Drilling Coordination Office (CSDCO) at the University of Minnesota requests participation in the development of a community Long Range Science Plan. If you plan to core or drill on Earth’s continents in the next 10 years, your ideas should be included in the Science Plan. This workshop is for scientific disciplines other than Paleorecords requiring continental drilling and coring: Critical Zone, Deep Biosphere, Tectonics/Magmatism, Fault Zone, Impact Structures, Hydrology, Geothermal, Geochemistry, and others. Travel is supported through CSDCO funding from NSF. The goal of this workshop is to identify and prioritize for each discipline the compelling science drivers, drilling/coring targets, strategic frameworks, and timelines focusing on continental localities in the coming decade. Projects include, but are not limited to, collaborative efforts and co-funding with international partners. Investigators with committed funding from the International Continental Scientific Drilling Program (ICDP), or those who will seek such support, are particularly encouraged to participate. Application deadline: April 14, 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 NEW!
July 10-12, 2017; Narragansett, Rhode Island, USA. Interactions between the land and ocean can provide important feedbacks to climatic evolution and surface processes. The Asian monsoon is an impressive example of these interactions as a major component of Earth’s climate affecting over half of the world population. In the Indian Ocean sector, close interactions between physical and biogeochemical processes with the tectonics of the India-Eurasia collision zone may have controlled both regional and global climate during the Cenozoic. The record of such interactions is best preserved in the ocean and was the target of recent scientific drilling across the region. Land-ocean interactions also play a critical role in modulating climate over Africa where complex interactions between the Indian monsoon and Atlantic occurs. Between 2013 and 2016, a series of IODP expeditions drilled in the Indian Ocean and Western Pacific oceans covering the Asian and Australian monsoon domains and adjacent regions. The goal of this 2.5-day workshop is to review results of the recent regionally-focused scientific drilling expeditions in the Indian Ocean, to propose possible paths for an integrated understanding of the role and response of climate in regulating Indian Ocean hydrology, hydrography, sedimentation, and biogeochemistry, and to synthesize practical lessons for future scheduled and proposed regional IODP drilling campaigns. 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


TAMU / IODP: Research Specialist III / Curator
We will begin reviewing applications on April 1, 2017.

University of Munich: Postdoctoral scholar, microbial transcriptional activity in subseafloor sediment NEW!
The Orsi lab at the University of Munich (Ludwig-Maximilians Universität München) is searching for a postdoctoral scholar within the framework of a newly funded project on microbial transcriptional activity in subseafloor sediment. The position involves the extraction and analysis of DNA and RNA from a high number of samples in order to constrain shared and unique biochemical subsistence strategies of subseafloor life. Desired skills in the ideal candidate are experience working with DNA and RNA from low biomass samples, and experience with bioinformatic analysis of large datasets of next generation sequencing data. The city of Munich is located less than 1 hour from the alps and hosts a vibrant and intellectually stimulating academic environment, that includes major Geoscience centers such as the Munich GeoCenter, Munich GeoBio Center, and Origins of Life Munich initiative. The position includes full benefits and is for two years, with the possibility for extension of an additional year (total of 3 years). The position also comes with the possibility (albeit not a requirement) for lecturing at the Bachelors and Masters level, depending on the candidates interests. Interested candidates should submit informal inquiries to Prof. Dr. William D. Orsi (w.orsi@lrz.uni-muenchen.de).

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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