|C-DEBI Newsletter – May 1, 2018
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Publications & Press
Microbial decomposition of marine dissolved organic matter in cool oceanic crust - NEW!
Sunita R. Shah Walter, Ulrike Jaekel, Helena Osterholz, Andrew T. Fisher*, Julie A. Huber*, Ann Pearson, Thorsten Dittmar, Peter R. Girguis
*C-DEBI Contribution 413
Marine dissolved organic carbon (DOC) is one of the largest active reservoirs of reduced carbon on Earth. In the deep ocean, DOC has been described as biologically recalcitrant and has a radiocarbon age of 4,000 to 6,000 years, which far exceeds the timescale of ocean overturning. However, abiotic removal mechanisms cannot account for the full magnitude of deep-ocean DOC loss. Deep-ocean water circulates at low temperatures through volcanic crust on ridge flanks, but little is known about the associated biogeochemical processes and carbon cycling. Here we present analyses of DOC in fluids from two borehole observatories installed in crustal rocks west of the Mid-Atlantic Ridge, and show that deep-ocean DOC is removed from these cool circulating fluids. The removal mechanism is isotopically selective and causes a shift in specific features of molecular composition, consistent with microbe-mediated oxidation. We suggest organic molecules with an average radiocarbon age of 3,200 years are bioavailable to crustal microbes, and that this removal mechanism may account for at least 5% of the global loss of DOC in the deep ocean. Cool crustal circulation probably contributes to maintaining the deep ocean as a reservoir of ‘aged’ and refractory DOC by discharging the surviving organic carbon constituents that are molecularly degraded and depleted in 14C and 13C into the deep ocean.
See also the accompanying NSF Press Release: Microbes in underground aquifers beneath deep-sea Mid-Atlantic Ridge 'chow down' on carbon.
Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient - NEW!
Angus Angermeyer, Sarah C. Crosby, Julie A. Huber*
*C-DEBI Contribution 426
Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.
NSF Press Release: Earth Week: Giant group of octopus moms discovered in the deep sea - NEW!
We know more about the surface of the moon than we do about the bottom of the ocean. The seafloor is an alien landscape, with crushing pressures, near-total darkness and fluids wafting from cracks in the Earth’s crust. It’s also home to weird animals that scientists are only just getting to know. Now, two deep-sea expeditions have revealed a giant group of octopuses and their eggs in a place where they shouldn’t be able to survive. Featuring C-DEBI Co-I Geoff Wheat and C-DEBI Contribution 419: Clusters of deep-sea egg-brooding octopods associated with warm fluid discharge: an ill-fated fragment of a larger, discrete population?
Meetings & Activities
NAI: Astrobiology Webinar with Rika Anderson (Carleton College), TODAY, May 1, 2018, 3pm PDT, recording to be posted online - NEW!
Genomic Memories of the Past: Using Microbial Genomics to Examine the Co-Evolution of Earth and Life: Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth, and the environment has molded the evolutionary trajectory of life itself. Microbial genomes retain a “memory” of this evolution. I will present two examples of how we can use genomics to study the co-evolution of Earth and life in the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics to investigate environmental drivers in the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats for life’s early evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context has an important impact on evolutionary trends. However, we can also examine evolutionary trends in Earth’s distant past through comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of nitrogen-metabolizing genes, and have found that genes related to denitrification began to spread across the tree of life after the Great Oxidation Event. In contrast, genes related to nitrogen fixation appear to have spread much earlier, consistent with geochemical evidence. As the sequencing revolution supplies ever more data about the tree of life, studies that couple genomics approaches with environmental context have the potential to reveal important insights into the co-evolution of life and Earth over time.
IODP-USSSP: Host an Ocean Discovery Lecturer
The application period will close on May 18, 2018.
GRC: Apply to attend the 2018 Conference on Deep Carbon Science, June 17-22, Smithfield, RI
Applications for this meeting must be submitted by May 20, 2018. Please apply early, as some meetings become oversubscribed (full) before this deadline.
IODP: Workshop Announcement: Scientific Exploration of the Arctic and North Pacific, September 25-27, 2018, Mt. Hood, OR - NEW!
The workshop on Scientific Exploration of the Arctic and North Pacific (SEA-NorP) will focus on the development of new proposals and reinvigoration of existing proposals for scientific ocean drilling in the Northern Pacific, Bering Sea and Western Arctic Ocean region. JOIDES Resolution is scheduled to operate in the Northern Pacific in 2023, so to ensure that the ship is used to best advantage in this region, now is the time to develop drilling proposals that could be linked through regional drilling strategies. The workshop will include discussion of hypotheses that can be tested by scientific drilling in the region, the technology necessary to achieve those goals, ideal sites for drilling based on existing data, and where additional site survey data is needed. Our goal is that multiple proposals will be initiated at the workshop, both for full cruise legs and for shorter, targeted expeditions around the following themes: ocean gateways, geohazards, volatile cycling, ice histories at transition zones, biosphere and climate. Experience in paleoclimate, paleoceanography, sedimentology, geobiology, geophysics, geochemistry, seismology, volcanology, structure and tectonics is sought. We encourage graduate students, early career scientists and those new to IODP to apply, as well as program officers, government representatives, and private sector scientists. A limited number of travel grants will be available. The workshop is open to U.S. and international participants, and the deadline for U.S.-affilitated scientists to apply is June 17, 2018.
C-DEBI: 2018 Networked Speaker Series - NEW!
Our 2018 Networked Speaker Series speakers have been selected! These early career investigators were nominated by members of the community for their exciting research and effective communication, so mark your calendars! The intent of these half-hour talks is to connect all of us interested “deeply” or broadly in the deep biosphere.
- NSS #18: Dr. Alma Parada, Stanford University
Evaluating the diversity and distribution of novel microbes across physical and geochemical gradients in deep-sea sediments
May 31, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
- NSS #19: Dr. Nagissa Mahmoudi, McGill University starting August 2018
September 20, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
- NSS #20: Dr. Jackie Goordial, Bigelow Laboratory for Ocean Sciences
September 27, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
- NSS #21: Dr. Rosa León Zayas, Willamette University
October 18, 2018, live online, 9:30AM HAST / 12:30PM PDT / 3:30PM EDT
C-DEBI: Rolling call for Community Workshop support
C-DEBI: Protocols.io Group Page
C-DEBI: Subseafloor Cultures Database
Education & Outreach
C-DEBI: Latest Professional Development Webinar Now Online! - NEW!
Missed the most recent C-DEBI Professional Development Webinar on “Sharing Data: The Joys of Open Science” with Ben Tully (C-DEBI Bioinformatic Specialist)? Watch it on YouTube.
MARUM: ECORD 2018 Summer School on Sub-seafloor fluid transport and gas hydrate dynamics
The application deadline is May 4, 2018.
NSF-UNOLS: Early Career Training Cruise to the East Pacific Rise 9° 50’N , December 2018
Applicants should submit their application materials by May 15, 2018.
C-DEBI: Bioinformatics Workshop for Metagenomic and Microbiome Analysis
Detailed insight into the microbiome of a system can shape our understanding of it, but the learning curve for incorporating computationally intensive tools can be very high! Join instructor Dr. Benjamin Tully, C-DEBI Bioinformatic Specialist, for an upcoming bioinformatics workshop at the University of Southern California, June 21-22, 2018. All expenses are covered courtesy of the NSF STCs C-DEBI, EBICS, and BEACON. Topics include: Unix command line; Illumina sequence quality control; Metagenomic experimental design; Sequence Assembly; Metageomic binning; Functional Annotation; and Phylogenetic analysis. Note: participation requires a laptop with 40 GB of hard drive space. To apply: email email@example.com by May 28, 2018 – be sure to include your home institution, your home STC, and what you hope to get out of the workshop. All levels are welcome. There is a 15 participant maximum, so apply soon!
NSF: Graduate Research Fellowship Program (GRFP) - Graduate Research Internship Program (GRIP) - NEW!
The Division of Graduate Education announces the continuation of the Graduate Research Internship Program (GRIP). GRIP provides professional development to NSF Graduate Research Fellowship Program (GRFP) Fellows (referred to as “Fellows”) through internships developed in partnership with federal agencies (see https://www.nsf.gov/grip for a current list of partner agencies). Through GRIP, Fellows participate in mission-related, collaborative research under the guidance of host research mentors at federal facilities and national laboratories. GRIP enhances the Fellows’ professional skills, professional networks, and preparation for a wide array of career options. The sponsor agencies benefit by engaging Fellows in applied projects, helping to develop a highly skilled U.S. workforce in areas of national need. GRIP is open to active Fellows (both “on tenure” and “on reserve”) who have completed at least one year of their graduate program at the time of application and will retain their active status for at least 12 months following the application submission deadline. They must be certified by the GRFP Institution to be making satisfactory progress towards their degrees, and have fulfilled all GRFP reporting requirements. For some agencies, Fellows must be U.S. citizens. GRIP applications are due December 4 and May 6, 2018.
NSF: Dear Colleague Letter: Advancing Long-term Reuse of Scientific Data
The deadline for submission of Conference and EAGER proposals proposal submission date is May 23, 2018.
Simons Postdoctoral Fellowships in Marine Microbial Ecology
Application deadline: June 15, 2018.
DCO: RFP: Census of Deep Life Sequencing Opportunities - NEW!
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 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. The proposal deadline is July 15, 2018.
DCO: Deep Life Cultivation Internship Program
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).
NSF: Arctic Sciences Program Solicitation
Proposals accepted anytime.
NSF: Tribal Colleges and Universities Program (TCUP) Program Solicitation
Preparing for TCUP Implementation proposals accepted anytime.
C-DEBI: Rolling call for Research Exchange proposals
TAMU: IODP-JRSO Assistant Research Scientist Position
We will begin reviewing applications on June 30, 2018, but will continue to accept applications until candidates are selected for interviews.
Two Faculty Positions at Shanghai Ocean University - NEW!
The Shanghai Research Center of Hadal Science and Engineering Technology (HAST) of Shanghai Ocean University invites applications for two faculty positions. 1) Analytical Scientist: seeking an expert in analytical mass spectrometry and preferably, with prior experience in high resolution accurate mass spectrometry. The successful applicant will be responsible for maintenance support and day-to-day operations of an ultrahigh resolution mass spectrometer, the Panorama, which will be delivered to HAST in late 2018. Preference will be given to individuals with a proven track record and a combination of skills in laboratory management, instrument troubleshooting, data handling and method development. Extensive experience in the operation of on-line sample preparation, maintenance of vacuum systems, and diagnosis of instrument mechanical and electronic problems is also desired. 2) Research Scientist: We are seeking a highly motivated, collaborative, research scientist for a lab-based position in clumped isotope science. The scientist’s principal responsibility is the design, development, validation and implementation of analytical procedures utilizing the Panorama. This scientist is expected to have a proven track record in clumped isotope research and high productivity in research and publishing. For both positions, applicants should possess a Ph.D. in isotope science or related fields. Applications will continue to be accepted until all available positions are filled.
BIOS: Postdoctoral Scholarship in Oceanography
Karlsruhe Institute of Technology: Two Ph.D. Positions
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