|C-DEBI Newsletter – August 15, 2017
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Frontiers in Microbiology
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank – NEW!
Jessica. M. Labonté, Mark A. Lever, Katrina J. Edwards*, Beth N. Orcutt*
*C-DEBI Contribution 370
Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.
Identification of organic compounds in ocean basement fluids – NEW!
Douglas E. LaRowe*, Boris. P. Koch, Alberto Robador, Matthias Witt, Kerstin Ksionzek, Jan P. Amend*
*C-DEBI Contribution 376
We have analyzed the dissolved organic carbon, OC, in ocean basement fluids using Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry (FT-ICR-MS). The compounds identified at the two sites, near the Juan de Fuca and Mid-Atlantic Ridges (North Pond), differ substantially from each other and from seawater. Compared to Juan de Fuca, North Pond organics had a lower average molecular weight (349 vs. 372 g/mol), 50% more identifiable compounds (2181 vs. 1482), and demonstrably lower average nominal oxidation state of carbon (-0.70 vs. -0.57). The North Pond fluids were also found to have many more N- and S-bearing compounds. Based on our data, the marine subsurface can alter the types of dissolved OC, DOC, compounds in seawater.
Meetings & Activities
ICDP: Training Course on Continental Scientific Drilling
Deadline for application is August 18, 2017.
AGU: 2018 Ocean Sciences Meeting Deep Biosphere-related Sessions
Abstracts due: September 6, 2017.
C-DEBI: Next Networked Speaker Series: September 7, 12:30pm PT – NEW!
Dr. Gustavo Ramírez (University of Rhode Island) will give the next Networked Speaker Series Seminar on “Microbial Neter-Khertet: Life and death post-entombment.” Abstract: Deep ocean sediment is a diffusion-limited environment where microbial inhabitants persist despite extreme temporal, physical and nutritional isolation from the ocean above. Burial time increases with sediment depth and, unsurprisingly, community richness, diversity, cell abundance and metabolic activity drop significantly with sediment age, implying both a steep selection curve and concomitant mass death. The extent to which benthic necromass (fragments of cadaverous cells), specifically extracellular DNA, a molecular fossil, may affect environmental sequencing surveys is a critical question that has received little attention. Reasons for this neglect are i) DNA is generally believed to have a short molecular half-life and ii) extracellular DNA represents dissolved C, N and P which should be readily metabolized by active microbes. The scarcity of methods for assessing microbial viability in complex environmental samples further confounds this issue. I interrogated Arctic and Pacific sediments for the presence of detrital DNA using Propidium Monoazide, a photo-active DNA intercalating dye that cannot penetrate intact prokaryotic membranes. This approach employs membrane integrity, a prerequisite for chemiosmotic potential and ATP production, as a viability metric. I detected statistically significant extracellular 16S rRNA gene loads in shallow sediment horizons, but not deep horizons. Measures of Alpha- and Beta-diversity for intra-and total-16rRNA gene pools are somewhat variable. Diversity trends are generally similar for both DNA pools, but noisier at shallow depths.
C-DEBI: Protocols.io Group Page
To help preserve deep biosphere methods for use in future projects, the Center strongly encourages you to describe your lab and software-based methods using protocols.io, and to link them to our group page at https://www.protocols.io/groups/center-for-dark-energy-biosphere-investigations. The protocols.io website provides an easy-to-use platform to share reproducible, step-by-step scientific methods.
C-DEBI: Rolling call for Community Workshop support
The NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI) invites proposals for $15,000 on average (and up to $20,000) in direct funds for community workshops that will help to advance C-DEBI’s central research agenda: to investigate the subseafloor biosphere deep in marine sediment and oceanic crust, and to conduct multi-disciplinary studies to develop an integrated understanding of subseafloor microbial life at the molecular, cellular, and ecosystem scales. C-DEBI’s research agenda balances exploration-based discovery, hypothesis testing, data integration and synthesis, and systems-based modeling. C-DEBI welcomes proposals from applicants who would enhance diversity in C-DEBI and STEM fields.
Education & Outreach
C-DEBI: Next Professional Development Webinar: August 24, 11am PT
Karen G. Lloyd (University of Tennessee) leads the next C-DEBI Professional Development Webinar on “How to Negotiate in Academia,” covering why negotiation is essential, tips for how to do so successfully and what to expect from post-doc and assistant professorship job negotiations. Missed the last webinar on “Proposal Writing, Management, and Budget Planning”? Watch it on YouTube.
Risk Innovation Lab: 2017 Science Showcase Video Contest!
Submissions close August 31, 2017.
NSF: Improving Undergraduate STEM Education: Pathways into Geoscience (IUSE: GEOPATHS)
Letter of intent due date: August 18, 2017.
NSF: Provision of Marine Seismic Capabilities to the U. S. Research Community
Full proposal deadline: August 21, 2017.
NSF: Research Experiences for Undergraduates (REU) Program Solicitation
Full proposal deadline: August 23, 2017.
IODP: Apply to Sail on IODP Expedition 378
The deadline to apply is September 15, 2017.
NSF: National Oceanographic Partnership Program announcement regarding Ocean Sensors, Cubesats, and GHRSST Data
Letters of Intent are required by October, 16 2017.
NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF)
Full Proposal Deadline: October 25, 2017.
NSF: Innovations in Graduate Education (IGE) Program
Full Proposal Deadline: October 25, 2017.
NSF: Management and Operation of the Ocean Bottom Seismometer Instrument Center (OBSIC)
Full Proposal Deadline: October 25, 2017.
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). Next workshop submission deadline: December 1, 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.
MLML: Faculty Position in Chemical Oceanography
Applications due August 23, 2017.
University of Delaware: Postdoctoral Researcher – NEW!
The Biddle laboratory is looking for a postdoctoral researcher to investigate sediment omics across a time gradient, with combined metagenome, metatranscriptome and methylome analysis. The postdoc would be part of a research group funded by the Keck Foundation to investigate microbial epigenetics. Preference will be given to candidates with experience in bioinformatics and coding. The position is located in Lewes, Delaware and subsidized housing is available a few blocks from the beach. Apply through UD Jobs, Position #104855. The position will be open until filled and applications are being reviewed starting August 28, 2017.
TAMU: Research Associate, International Ocean Discovery Program
We will begin reviewing applications on August 28, 2017, but will continue to accept applications until candidates are selected for interviews.
Florida Atlantic University: Research Faculty Position In Geochemistry – NEW!
FAU’s Harbor Branch, located in Fort Pierce, Florida, and FAU’s Institute for Sensing and Embedded Network Systems Engineering (I-SENSE), located in Boca Raton, Florida, seek candidates for an Assistant, Associate, or Full Research Professor with expertise in geochemistry/geochemical sensing and a research background in one or more of the following areas: marine chemistry, nutrient cycling, carbon transformations, particle fluxes across continental shelves, trace metal distributions, and electrochemical sensing. Candidates will also display a broad interest in marine ecology, biological oceanography, marine microbiology, and in situ sensing technologies. Applications are sought from individuals with excellent research/publication records and demonstrated potential to lead a strong, extramurally funded research program that explores opportunities with state, federal agencies, industry and private foundations. Applicants whose research provides a strong background in geochemical processes at sediment-water interfaces are preferred. Applicants must apply electronically by August 31, 2017.
Bigelow: Postdoctoral Research Scientist – Geomicrobiology / Microbial Ecology
For full consideration, the application should be received by August 31, 2017.
Bigelow: Research Associate in Molecular Biology – NEW!
Bigelow Laboratory for Ocean Sciences is searching for a full-time Research Technician to perform laboratory and data handling tasks related to microbial single cell genomics, with the primary focus on genomic sequencing. The candidate should be willing to work with fastidious techniques that require extreme cleanliness and accuracy, operating robotic systems, handling advanced data management systems, and quickly learning new methods. A Masters degree in biology or related field or a relevant Bachelors degree and at least three years of post-degree experience working in a molecular biology laboratory are required. Prior experience with Illumina DNA sequencing technology is preferred. Excellent communication skills and ability to work harmoniously in a collaborative research environment are crucial. For full consideration, the application should be received by September 1, 2017.
Oklahoma State University: Assistant Professor Position in Paleontology/Sedimentary Geology – NEW!
The Boone Pickens School of Geology at Oklahoma State University seeks to fill a tenure track position in paleontology/sedimentary geology at the rank of assistant professor. The anticipated start date is August 1, 2018. The successful applicant should have a Ph.D. degree in geosciences or related field at the time of appointment. For this position, we are seeking a geoscientist with research and teaching interest in paleontology as well as sedimentary geology and stratigraphy. Desired areas of specialization include but are not limited to invertebrate paleontology, biostratigraphy, palynology, ichnology, and paleoecology. The successful candidate will collaborate as part of a diverse faculty with specialties spanning the geosciences and core strengths in disciplines relating to energy and environment. We are seeking an individual who will develop a vigorous, innovative, externally funded research program, who will contribute to undergraduate and graduate teaching, and who will supervise MS and PhD students. Candidates will be expected to support the learning needs of students from diverse backgrounds and demonstrate a commitment to engaging communities underrepresented in the academy. Screening of candidates will begin on September 15, 2017 and will continue until the position is filled.
Bigelow: Postdoctoral Research Scientist – Viral Control of Microbial Communities in Antarctic Lakes – NEW!
Bigelow Laboratory for Ocean Sciences is seeking a qualified and highly motivated individual for a postdoctoral research scientist position. The hired scientist will work on a project investigating the diversity and dynamics of viruses, as well as the effect of viruses on phytoplankton in marine-derived lakes of the Vestfold Hills in Antarctica (https://www.nsf.gov). These “natural laboratories” allow examination of microbial processes and interactions that would be difficult to characterize elsewhere on earth. This project does not require fieldwork in Antarctica. Instead, it will leverage already collected and archived samples that have concurrent measurements of physicochemical information. This project will also capitalize on approximately 2 terabyte of Next Generation Sequencing, including metagenomes, SSU rRNA amplicons and single virus genomes (this project) generated through an ongoing collaborative effort with other institutions. The project is led by Dr. Joaquín Martínez Martínez, and utilizes cutting-edge molecular technologies, and takes advantage of significant bioinformatics support and computational resources at Bigelow Laboratory. Applicants must have a PhD degree or post-degree experience in relevant fields, such as environmental microbiology/virology, bioinformatics, and oceanography. Additional preferred qualifications include working knowledge in one or more of the following techniques: Flow Cytometry, nucleic acids purification, quantitative PCR, whole-genome amplification, and sequencing. Review of applicants will begin immediately and proceed until the position is filled.
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