C-DEBI Newsletter – July 15, 2016
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C-DEBI 2016 Education & Diversity Summer Programs

School's out for summer, but our diligent next generation of deep biosphere researchers are keeping active with seven C-DEBI Education & Diversity programs currently underway or recently completed. Check out some highlights from our summer schedule for STEM explorers of all ages!

NSF REU: Community College Cultivation Cohort (C4)
Lab tour, USC
Eight community college students from across the country are working on an exciting project to cultivate and characterize unknown microbes from the deep. Students are spending their summer living and working on the USC campus and for most, it is their first time doing independent lab work and learning about the research culture. The team is also engaged in a bioinformatics course taught by Dr. Ben Tully. We are delighted to have them as our inaugural REU group!
Community College Research Internship for Scientific Engagement (CC-RISE at UCSC)
Student Edward Hughes examines culture, UCSC
Our eight CC-RISE students this year come from diverse backgrounds and universities, and work with mentors on projects that best suit their scientific interests. The student projects are varied and cover the fields of oceanography, biology, geology, chemistry and public policy, and are allowing the students to learn all steps of the scientific process including field work, laboratory work, method development, data analysis, followed by writing and presenting their findings. The students have two weeks to go and we are excited to see what they will accomplish in the remaining weeks!
Community College Research Internship for Scientific Engagement (CC-RISE at MBL)
Huber lab, MBL
Our four Cape Cod Community College students started their internship at the Marine Biological Laboratory on June 20th. The students are doing research in Dr. Julie Huber’s lab working with microbes from hydrothermal vents under the supervision of Dr. Gretta Serres. As a group, the interns will be growing and characterizing several Epsilonproteobacteria isolated by the Huber lab. Having started the summer taking a microbiology course at Cape Cod Community College, the students are ready to explore the microbial physiology of the ocean floor. It has been a great couple of weeks at the MBL and Woods Hole with a very enthusiastic group!
Genomics & Geobiology Undergraduate Research Experience (GGURE)
Finkel, USC
Led by Dr. Steve Finkel, GGURE was established to provide access to research opportunities for students from STEM-underrepresented backgrounds at USC. This summer, 16 students have identified their host labs and become actively involved in a research group with either an experimental or computational focus, and are performing original research under the direct supervision of a faculty mentor. Additionally, students meet weekly for journal clubs and also receive weekly seminars from USC faculty.
Global Environmental Microbiology (GEM) Course
In the Sierras, USC
Sixteen participants from across the country participated in our immersive field and lab course, taught by Drs. John Heidelberg and Eric Webb in June. The students traveled from the USC campus to the Eastern Sierra Mountains and finished at the Wrigley Marine Science Center on Santa Catalina Island. The course explores DNA, genetics and genomics and their potential function in the environment. Students had a great time experiencing snow in the Sierras and going snorkeling on Catalina Island!
High School Marine Lab Camp
In the lab, USC Sea Grant
USC Sea Grant, in partnership with C-DEBI and the Wrigley Institute for Environmental Studies, hosted 20 high school students from across the country at the USC Wrigley Marine Science Center on Catalina Island. Over the course of the week, students worked with local researchers, conducted their own research projects, learned about careers in marine science, built their own ROVs, snorkeled, kayaked, and explored the marine protected areas around the island. To quote an enthusiastic participant “I would recommend this program to anyone who wishes to gain an amazing experience!”
Seafloor Science ROV Camp
Paul, U Alaska Fairbanks
In six week-long, day camps across the Monterey and San Jose areas, approximately 85 students entering 6th-9th grades will be introduced to seafloor exploration with hands-on STEM-based activities. This summer’s Seafloor Science and Remotely Operated Vehicle (SS-ROV) Camp is led by Dr. Geoff Wheat and two community college student interns from central California (Jorge Valdez and Kevin Wong). As part of their 8-week internships, they completed a week of training and will be developing activities for a more advanced program that we hope to offer next year!


Applied and Environmental Microbiology
Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment
Emily A. Walsh, John B. Kirkpatrick*, Robert Pockalny, Justine Sauvage, Arthur J. Spivack, Richard W. Murray, Mitchell L. Sogin and Steven D'Hondt*
*C-DEBI Contribution 328

Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales
John B. Kirkpatrick*, Emily A. Walsh and Steven D'Hondt*
C-DEBI Contribution 329

DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.

Earth and Planetary Science Letters
Cross-hole tracer experiment reveals rapid fluid flow and low effective porosity in the upper oceanic crust
N.M. Neira, J.F. Clark, A.T. Fisher*, C.G. Wheat*, R.M. Haymon, K. Becker
*C-DEBI Contribution 331

Numerous field, laboratory, and modeling studies have explored the flows of fluid, heat, and solutes during seafloor hydrothermal circulation, but it has been challenging to determine transport rates and flow directions within natural systems. Here we present results from the first cross-hole tracer experiment in the upper oceanic crust, using four subseafloor borehole observatories equipped with autonomous samplers to track the transport of a dissolved tracer (sulfur hexafluoride, SF6) injected into a ridge-flank hydrothermal system. During the first three years after tracer injection, SF6 was transported both north and south through the basaltic aquifer. The observed tracer transport rate of ∼2–3 m/day is orders of magnitude greater than bulk rates of flow inferred from thermal and chemical observations and calculated with coupled fluid-heat flow simulations. Taken together, these results suggest that the effective porosity of the upper volcanic crust through which much tracer was transported is <1%, with fluid flowing rapidly along a few well-connected channels. This is consistent with the heterogeneous (layered, faulted, and/or fractured) nature of the volcanic upper oceanic crust.

IODP-USSSP Workshop Report
Exploring Deep Subsurface Life, Sedimentation and Tectonics in a Young Ocean: Workshop to synthesize site survey cruise data and develop new strategies for a scientific ocean drilling proposal in the Guaymas Basin
Conveners: Ivano Aiello, Andreas Teske and Christina Ravelo

A workshop, supported by the U.S. Science Support Program for IODP, was organized by Andreas Teske, Christina Ravelo and Ivano Aiello at the Bugambilias Sheraton Hotel in Puerto Vallarta, Mexico between the 6th and the 10th of November of 2015 in conjunction with the Annual Meeting of the Union Geofisica Mexicana. A multidisciplinary group of scientists was convened to create momentum in producing a drilling proposal to bring the IODP program to the Guaymas Basin in the Gulf of California (GOC). The GOC represents a singular example of interactions between tectonics, sedimentation and microbial life in a very young ocean formed by translation and oblique rifting. Drilling in the Guaymas Basin would offer a unique opportunity to understand how subsurface microbial populations intercept and process hydrothermally generated and mobilized carbon sources. The workshop achieved two main objectives: 1) Produced an in depth panel review of the biogeochemical, sedimentological, microbiological and multichannel seismic results from two site survey cruises investigating the sedimented ridge flanks of the Guaymas Basin and the Sonoran Margin in the Gulf of California; 2) Created renewed impetus towards the formulation of a drilling proposal to bring the R/V JOIDES Resolution to the Guaymas Basin in the Gulf of California. The panel reformulated and modified the scientific objectives and the drilling priorities and created the conditions for the successful revision of pending proposal N.833.


Meetings, Courses & Activities

IODP-USSSP: Short Course on Shipboard Sedimentology - Data Collection, Interpretation, and Integration November 14-17, 2016, IODP Gulf Coast Repository, College Station, TX
Comprehensive shipboard core description and data integration of sedimentary units in the core description lab during IODP expeditions provide a fundamental framework for the science party as they work toward the expedition objectives. It is primarily during this shipboard time that the cores are systematically described and sampled, and the characteristics of the stratigraphy resolved and integrated with paleontological, paleomagnetic, physical property, geochemical, and seismic reflection data sets. This shipboard work provides the science team with a record of what the cores contain, where there are interesting occurrences and transitions in primary composition, depositional style as evidenced by sedimentary structures and bedding, and diagenetic mineralization. This short course on shipboard sedimentology will emphasize marine sediment description, both macroscopically and microscopically, through determination of lithologic attributes during core description (e.g., color, texture, sedimentary structures, trace and other fossil content), as well as sediment composition through smear slide and coarse fraction petrography. We will also cover lithostratigraphic unit definition, preliminary interpretation, and, to some extent, integration of sedimentology data with other shipboard data sets. Graduate students, post-docs, and professionals that will or are planning to sail on future IODP expeditions are particularly encouraged to apply. The course will be geared toward training sedimentologists, but participants may also include paleontologists, paleomagnetists, geochemists, structural geologists, or physical properties scientists. Some previous experience with optical microscopy would be beneficial. Travel support will be provided for U.S.-affiliated scientists through USSSP. Limited travel support may also be available for international scientists through their IODP program member offices. Space is limited and the deadline to apply is August 31, 2016.

2016 AGU Fall Meeting: Deep Biosphere-related Sessions

Abstract submission deadline: August 03, 2016.

IODP-USSSP: Nominate an Ocean Discovery Lecturer!
Nomination deadline: July 18, 2016

IODP-USSSP: Call for Non-U.S.-Based Scientists: Apply for the JOIDES Resolution Facility Board (JRFB)
Application deadline (non-U.S. citizens only): July 22, 2016.

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


Proposal Calls

IODP-USSSP: Apply to Sail on Expedition 373 (Antarctic Cenozoic Paleoclimate)
The International Ocean Discovery Program (IODP) is now accepting applications for scientific participants to sail on Expedition 373 Antarctic Cenozoic Paleoclimate aboard a Mission Specific Platform (MSP) provided by the ECORD Science Operator. The George V and Adélie Land continental shelf of East Antarctica contains a record of Antarctica’s climate and ice history from the warm and vegetated landscapes of Eocene greenhouse climates to latest Eocene glacial inception and the dynamic ice sheet margins of the Oligocene. Because of the gently dipping strata and glacial erosion, sediments of a wide age range reach close to the sea bed and are accessible through shallow drilling by robotic seafloor drills. The history of this Antarctic margin includes warm-world high-CO2 environments, which will help to understand Antarctic climate and the limits of ice sheet stability under future global warming. Up to now there are extremely few well-recovered Eocene sediment sequences from Antarctica, and we aim to fill this gap in knowledge. The expedition aims to drill, core, and log between eight and eighteen 50-m-deep boreholes on the George V Land and Adélie Land continental shelf of East Antarctica, using the British Geological Survey Rockdrill 2 (RD2), deployed from the RVIB Nathaniel B. Palmer, operated by the Lockheed-Martin Antarctic Support Contract (ASC) for the U.S. National Science Foundation’s United States Antarctic Program (USAP). Opportunities exist for for researchers (including graduate students) in all specialties. While other expertise may be considered, specialists in the following fields are required: paleontology, sedimentology, organic geochemistry, structural geology, paleomagnetics, physical properties, geophysics, and petrophysics/downhole logging. U.S. application deadline: August 31, 2016.

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

CIES: 2017-2018 Fulbright U.S. Scholar Program in Arctic Affairs
Application deadline (U.S. citizens only): August 01, 2016.

IODP: Apply to Sail on IODP Expeditions 371, 369, 374
U.S. application deadline: August 15, 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, related to the International Ocean Discovery Program (IODP).


Bigelow: Postdoctoral Research Scientist – Virus Genomics and Ecology
Application deadline: July 31, 2016.

Kiel University / GEOMAR Helmholtz Centre for Ocean Research Kiel: Professorship (W2) in Geomicrobiology
Application deadline: August 15, 2016.

Second Genome Solutions: Laboratory Scientist, Microbiome Assay Development

Columbia University / LDEO: Postdoctoral Research Scientist

Moore Foundation: Program Fellow, Marine Microbiology Initiative

Bigelow: Postdoctoral Research Scientist 

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!

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

Exploring life beneath the seafloor and making transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.

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