|C-DEBI Newsletter – July 1, 2016
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Congratulations to C-DEBI Postdoctoral Fellow Roland Hatzenpichler who will be starting his own lab this fall at Montana State University. His group will focus on the diversity, in situ activity, and biogeochemical relevance of uncultured archaea living in geothermal, marine, and freshwater sediments. Interested students or potential postdocs are encouraged to contact him. Visit his website at www.environmental-microbiology.com
Also check out his latest paper on using BONCAT, in combination with FACS, for activity-based cell-sorting of methane-oxidizing microbial consortia (see C-DEBI contribution 330 below, and the JGI press release).
Applied and Environmental Microbiology
Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments
Benjamin J. Tully* and John F. Heidelberg*
*C-DEBI Contribution 325
The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry.
Proceedings of the National Academy of Sciences
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia
Roland Hatzenpichler*, Stephanie A. Connon, Danielle Goudeau, Rex R. Malmstrom, Tanja Woyke, and Victoria J. Orphan*
*C-DEBI Contribution 330
To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.
Meetings & Activities
- B001: 4 Billion Years of Serpentinization on Earth and Beyond
Conveners: Frieder Klein (WHOI), Dieter Braun (Ludwig Maximilians University of Munich), Emily H.G. Cooperdock (U Texas at Austin), William Orsi (Ludwig Maximilians University of Munich)
- B040: Fifteen Years of Geobiology: The Significant Highlights and The Future
Conveners: John R Spear (Colorado School of Mines), Frank A Corsetti (USC)
- B045: Interdisciplinary linkages to better understand microbial metabolism in the deep subsurface
Conveners: Brandi Kiel Reese (TAMU), Scott D Wankel (WHOI), Kiana L Frank (Harvard)
- B073: Roles for uncultured microbes and novel viruses in biogeochemical cycles
Conveners: Karen G Lloyd (U Tennessee, Knoxville), Kelly C Wrighton (Ohio State U), Brett Baker (U Texas at Austin)
- C014: Exploring ice: direct glacial and subglacial exploration missions on Earth and Beyond
Conveners: Jill Mikucki (U Tennessee, Knoxville), Julia Kowalski (RWTH Aachen U)
- OS014: Life at the marine sediment-water interface: Microbial ecology, physiology and biogeochemistry in deep sea environments
Conveners: Sebastian Sudek (MBARI), Julie Robidart (National Oceanographic Centre)
- OS018: New Advances in Understanding Mid-Ocean Ridge Processes from Ocean Drilling and Ophiolites
Conveners: Lyderic France (CRPG), Henry J Dick (WHOI), Beth Orcutt (Bigelow), Michael J Cheadle (U Wyoming)
- PP006: Authigenic processes in marine sediment: influence on seawater composition and the paleoceanographic record
Conveners: Claire Cecelia McKinley (TAMU-CC), Chloe H Anderson (Boston U), Ann G Dunlea (Boston U), Emily R Estes (WHOI)
- PP035: Tracing Oxidative Weathering Across Spatial and Temporal Scales
Conveners: Mark A Torres (CalTech), Mathieu Dellinger (Durham U), Alexandra v Turchyn (U Cambridge)
- PP038: What processes regulate atmospheric carbon dioxide, and stabilize climate, on Earth and other planets
Conveners: Laurence A Coogan (U Victoria), David C Catling (U Washington), John A Higgins (Princeton), A. Joshua West (USC)
NSF/UNOLS: Marine Seismic Survey Request
Since the Sea Change Report was issued in January 2015 with the recommendation to redirect funding from infrastructure support to research programs; the MGG division of NSF has been assessing its relative contributions to infrastructure and research funding within the geophysical community. As part of this effort, UNOLS is undertaking a survey that has been designed to determine how widespread marine seismic data collection and usage is within the geophysical community and its affiliated fields. The results will be used to help to identify the instrumentation and methodology that are critical to answer the current questions in the field and also those that are necessary to meet the requirements of future science directions. The survey takes about 15 minutes to complete. Through your feedback important and well informed decisions can be made and your input is both greatly needed and appreciated. Responses are requested by: TODAY, July 01, 2016
ASM Junior Advisory Group: Request for Session Topics
The Junior Advisory Group of ASM is looking for topics of high interest on which we could build next year’s plenary and afternoon sessions! For orientation: this year, our plenary was on ‘identify and function of microbial dark matter’ and our afternoon session was on ‘bacteriophages.’ We also supported the formation of a ‘growing the tree of life’ afternoon session. Any suggestions are welcome; please add your ideas for topics and speakers into our Google Doc. Feel free to forward to any interested researcher. Contact: Roland Haztzenpichler.
SFMC: 2016 Serpentine Days, September 25-29, 2016, Sète, France
The 4th international ‘Serpentine Days’ workshop, supported by the Société Française de Minéralogie et de Cristallographie (SFMC), will be held in the Lazaret resort (Sète, Southern France); it will bring together 120 scientists with an interest in the geological, physical and (bio-)chemical processes of serpentinization and the life it sustains as well as scientists working on its impact for mineral resources and new energy sources and the environmental and societal impact of their exploration and exploitation. Application and abstract submission due July 07, 2016.
IODP-USSP: Volunteer to serve on the U.S. Advisory Committee for Scientific Ocean Drilling (USAC), Science Evaluation Panel (SEP), or Environmental Protection and Safety Panel (EPSP)
Deadline: July 08, 2016. Interested in learning more about the use of seabed drills used in the ocean drilling program? A recent video from the British Geological Survey highlights new capabilities of the RD2 seabed drill, which was used on the recent IODP Expedition 357 to study the Atlantis Massif deep biosphere.
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)
The U.S. Science Support Program (USSSP), in association with the International Ocean Discovery Program (IODP), is seeking two new, non-U.S.-based representatives to serve on the JOIDES Resolution Facility Board. New members will serve three-year terms beginning in October 2016. Deadline: July 22, 2016.
Kyoto University: 5th International Workshop on Deep Sea Microbiology, September 10-11, 2016
Abstract submission deadline: July 23, 2016.
DCO: Census of Deep Life Sequencing Opportunities
Deadline: July 15, 2016.
DCO: Second Call for Proposals: Deep Energy Community
Deadline July 20, 2016.
CIES: 2017-2018 Fulbright U.S. Scholar Program in Arctic Affairs
Applicants must be U.S. citizens and the deadline for complete applications is August 01, 2016.
IODP: Apply to Sail on Three IODP Expeditions
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
The Bigelow Laboratory for Ocean Sciences is seeking a qualified and highly motivated individual for a postdoctoral research scientist position to develop and employ a standardized high-throughput protocol for culture-independent ‘Single Virus Genomics’. The position will be under the supervision of Dr. Joaquín Martínez Martínez, and is part of a collaborative project with Dr. Manuel Martínez García at the University of Alicante (Spain). Applicants must have a Ph.D in environmental microbiology/virology, marine sciences, oceanography, or similar field. The well-suited candidate will have experience with microbiology and molecular biology, with a strong interest and inclination toward experimental laboratory work and methods development. Preferred qualifications include working knowledge in one or more of the following techniques: cultivation of model microbial host–virus systems, use of Flow Cytometry for detection and enumeration of cells and viruses, nucleic acids purification, whole-genome amplification, and sequencing. Good knowledge of bioinformatics analytical tools is a must. Research will be conducted primarily at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine. The position will be initially a 1.5-year, with the possibility of extension contingent upon performance and funding. The position has an expected start date of October 2016 or earlier, but this may be negotiated. For full consideration, the application should be received by July 31, 2016.
Second Genome Solutions: Laboratory Scientist, Microbiome Assay Development
The Second Genome Solutions team is a group of passionate individuals driven to bringing insightful microbiome science to discovery research. We are seeking a motivated Laboratory Scientist ready to join a fast-paced work environment, with experience in a wide range of analytical and experimental techniques, to investigate microbial community composition and function. The successful candidate shall be prepared to plan and execute initiatives to develop novel microbiome laboratory techniques and assays for advancing microbiome research in human health and disease. The Laboratory Scientist shall also be responsible for: devising new microbiome applications through the stages of concept, feasibility, development, and commercialization to build a competitive advantage; on-going optimization of current assays and protocols to improve Second Genome’s overall microbiome profiling offering in terms of robustness, accuracy and scientific validity; conducting detailed studies to validate new protocols and confirm process changes.
Kiel University / GEOMAR Helmholtz Centre for Ocean Research Kiel: Professorship (W2) in Geomicrobiology
The position is located at the “Marine Geosystems” department of the research division “Marine Biogeochemistry” at GEOMAR Helmholtz Centre for Ocean Research Kiel (www.geomar.de).
We are looking for a scientist with an international reputation who will establish his/her own area of research at GEOMAR in the field of geomicrobiology. The candidate is expected to have interest in benthic biogeochemistry. It is further expected that the candidate would work collaboratively within existing large research projects such as the Future Ocean Excellence Cluster (www.futureocean.org). The teaching commitment is 4 semester hours per week. The Kiel University and the GEOMAR Helmholtz Centre for Ocean Research Kiel are seeking to increase the number of women in faculty positions and encourage applications from qualified women. Female applicants will be given priority if their qualifications and achievements are equal to those of male applicants. Applications from scientists with disabilities will be given priority in case of equal qualifications. We explicitly encourage candidates with a migration background to apply. Application deadline: August 15, 2016.
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