|C-DEBI Newsletter – August 1, 2016
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Be sure to check out our funded projects page for the newly-posted award abstracts from C-DEBI’s latest round of funded research grants, postdoctoral and graduate student fellowships, and education & diversity grants!
And please help spread the word about our new, full-time Diversity Specialist opening! See below or the PDF flyer for more details.
Frontiers in Microbiology
Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales
Jordan T. Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar and Karen G. Lloyd*
*C-DEBI Contribution 332
The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus (Ca.) Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, we sequenced a single cell amplified genome (SAG), WOR_SCG_SM1, and used it to identify and refine two high-quality genomes from metagenomes, WOR_79 and WOR_86-2, from the same site in a different year. These three genomic reconstructions form a monophyletic group which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, causes the protein to be encoded as two subunits at distant loci. Consistent with the terrestrial spring clades, our estuarine genomes contain a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H)-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identify two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which is more widespread, diverse, and not associated with visible mats. The core Alti-1 genome supports Alti-1 as adapted for the stream environment, with lipopolysaccharide production capacity, extracellular hami structures. The core Alti-2 genome members of this clade are free-living, with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These data suggest that hami structure found in Ca. A. hamiconexum are not present outside of stream-adapted Altiarchaeales. Unlike Ca. A. hamiconexum, these sedimentary organisms have membrane-bound coenzyme A disulfide reductases, which suggest they may use reduced sulfur compounds either as electron donors or defense against oxidative stress. Homologs to a Na+ transporter and membrane bound coenzyme A disulfide reductase that are unique to the brackish sediment Alti-2 genomes, could indicate adaptations to the estuarine, sulfur-rich environment.
Deep Sea Research Part I: Oceanographic Research Papers
Assessing microbial processes in deep-sea hydrothermal systems by incubation at in situ temperature and pressure
Jesse McNichol, Sean P. Sylva, François Thomas, Craig D. Taylor, Stefan M. Sievert, Jeffrey S. Seewald
At deep-sea hydrothermal vents, a large source of potential chemical energy is created when reducing vent fluid and oxidizing seawater mix. In this environment, chemolithoautotrophic microbes catalyze exergonic redox reactions which in turn provide the energy needed to fuel their growth and the fixation of CO2 into biomass. In addition to producing new organic matter, this process also consumes compounds contained both in vent fluid and entrained seawater (e.g. H2, NO3−). Despite their biogeochemical importance, such reactions have remained difficult to quantify due to methodological limitations. To address this knowledge gap, this study reports a novel application of isobaric gas-tight fluid samplers for conducting incubations of hydrothermal vent fluids at in situ temperature and pressure. Eighteen ~24 h incubations were carried out, representing seven distinct conditions that examine amendments consisting of different electron donors and acceptors. Microbial activity was observed in all treatments, and time series chemical measurements showed that activity was limited by electron acceptor supply, confirming predictions based on geochemical data. Also consistent with these predictions, the presence of nitrate increased rates of hydrogen consumption and yielded ammonium as a product of nitrate respiration. The stoichiometry of predicted redox reactions was also determined, revealing that the sulfur and nitrogen cycles are incompletely understood at deep-sea vents, and likely involve unknown intermediate redox species. Finally, the measured rates of redox processes were either equal to or far greater than what has been reported in previous studies where in situ conditions were not maintained. In addition to providing insights into deep-sea hydrothermal vent biogeochemistry, the methods described herein also offer a practical approach for the incubation of any deep-sea pelagic sample under in situ conditions.
Meetings, Courses & Activities
USC Wrigley Institute / C-DEBI: Undergraduate Research Symposium
Friday, August 12, 2016; 1-4pm at RRI (USC’s University Park Campus)
The symposium is a collaboration between the Wrigley Institute and C-DEBI undergraduate research programs, with topics ranging in sub-seafloor microbes, coastal ocean processes, and genomics and geobiology. Click here to RSVP by August 10.
- B001: 4 Billion Years of Serpentinization on Earth and Beyond
- B010: Geomicrobiology of extreme environments: Scarcity is the mother of invention
- B040: Fifteen Years of Geobiology: The Significant Highlights and The Future
- B045: Interdisciplinary linkages to better understand microbial metabolism in the deep subsurface
- B073: Roles for uncultured microbes and novel viruses in biogeochemical cycles
- C014: Exploring ice: direct glacial and subglacial exploration missions on Earth and Beyond
- OS014: Life at the marine sediment-water interface: Microbial ecology, physiology and biogeochemistry in deep sea environments
- OS018: New Advances in Understanding Mid-Ocean Ridge Processes from Ocean Drilling and Ophiolites
- PP006: Authigenic processes in marine sediment: influence on seawater composition and the paleoceanographic record
- PP035: Tracing Oxidative Weathering Across Spatial and Temporal Scales
- PP038: What processes regulate atmospheric carbon dioxide, and stabilize climate, on Earth and other planets
Abstract submission deadline: August 03, 2016.
IODP-USSSP: Short Course on Shipboard Sedimentology – Data Collection, Interpretation, and Integration November 14-17, 2016, IODP Gulf Coast Repository, College Station, TX
Application deadline (limited space): August 31, 2016.
NSF: Improving Undergraduate STEM Education: Pathways into Geoscience (IUSE: GEOPATHS)
The IUSE: GEOPATHS funding opportunity invites creative proposals to broaden and strengthen the pathways that will engage and retain undergraduate students in geoscience education and career pathways, and help prepare them for a variety of careers. The long-term goal of this program is to dramatically increase the number and diversity of students earning undergraduate degrees or enrolling in graduate programs in geoscience fields, as well as ensure that they have the necessary skills and competencies to succeed as next generation professionals in a variety of employment sectors. IUSE: GEOPATHS projects are expected to utilize effective, evidence-based strategies for improving student engagement and retention, and to expose students to meaningful experiences in the geosciences through leveraging of academic and/or non-academic research and instrumentation infrastructure. The underlying “theory of change” for this solicitation is that novel, authentic, career-relevant geoscience experiences for larger student populations not only augment existing curricula but will also increase the students’ desire to pursue degrees and Geo-related careers. The IUSE: GEOPATHS solicitation offers two distinct funding Tracks: (1) Engaging students in the geosciences through extra-curricular experiences and training (GEOPATHS-EXTRA) and (2) Improving pathways into the geosciences through institutional collaborations (GEOPATHS-IMPACT). Regardless of which track is selected, the program expects to offer approximately 20 awards, with the average total award size expected to be in the $300,000 to $350,000 range. The duration of awards for both tracks will be up to 36 months. Estimated program budget, number of awards and average award size/duration are subject to the availability of funds. Letter of Intent due date: August 16, 2016.
- Expedition 371, Tasman Frontier Subduction Initiation & Paleogene Climate, July – September 2017
Application deadline: August 15, 2016
Webinar: July 29, 2016 at 12:00 pm EDT
- Expedition 369, Australia Cretaceous Climate & Tectonics, September – November 2017
Application deadline: August 15, 2016
Webinar: August 3, 2016 at 4:00 pm EDT
- Expedition 374, Ross Sea West Antarctic Ice Sheet History, January – March 2018
Application deadline: August 15, 2016
- Expedition 373, Antarctic Cenozoic Paleoclimate, MSP, Dec 2017-Feb 2018
Application deadline: August 31, 2016
Webinar: August 29, 2016 at 9:00 am EDT
- Expedition 372, Creeping Gas Hydrate Slides and Hikurangi LWD, November 2017 – January 2018
Application deadline: October 1, 2016
- Expedition 375, Hikurangi Subduction Margin, March – May, 2018
Application deadline: October 1, 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).
USC / C-DEBI: Full-time Diversity Specialist
The USC Dornsife College of Letters, Arts and Sciences Center for Dark Energy Biosphere Investigations (C-DEBI) is seeking a full-time Program Specialist (Diversity Specialist) to join its team! C-DEBI is a multi-institutional research and education center funded by the National Science Foundation Science and Technology Center (NSF-STC) program, headquartered at USC. Focused on the science of exploring microbial life beneath the seafloor, the Center also prioritizes the integration of deep sea research with education and diversity efforts to strengthen the STEM pipeline for future generations. The Diversity Specialist will help to create, coordinate, and lead our diversity efforts to serve our students, postdocs, faculty, and other participants at USC and across the nation. The Diversity Specialist will assist the C-DEBI Education, Outreach, and Diversity Managing Director who supervises the development and management of these programs. Review of applications begins: August 19, 2016.
University of New Hampshire: Associate or Full Professor of Estuarine Science
We seek an individual who will bring to UNH a dynamic, internationally recognized, extramurally funded, collaborative research program in the area of Estuarine Science. We are interested in candidates with a strong background in the life sciences as applied to estuaries, with particular interest in the areas of coastal ecology, resilience, adaptation, and risk assessment through high-quality research focused on organisms, community, and/or ecosystem-scale estuarine processes. This position will integrate and build upon the University’s strengths in estuarine, marine, and freshwater biology and ecology, biological and physical oceanography, microbial ecology and genomics, and fisheries, and will offer exceptional opportunities for collaboration and synergy across departments and colleges. The position could include the directorship of the Jackson Estuarine Laboratory, located on the shores of Great Bay Estuary, one of the largest estuaries in northern New England. This facility houses well-equipped infrastructure where scientists conduct experimental and field-based research on biological and physical components of coastal ecosystems. The successful candidate is expected to lead a strong, internationally-recognized research program; contribute to the teaching and service mission of the University; and work collaboratively with diverse communities across the institution. Review of applications: August 15, 2016 until position filled.
Kiel University / GEOMAR Helmholtz Centre for Ocean Research Kiel: Professorship (W2) in Geomicrobiology
Application deadline: August 15, 2016.
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