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C-DEBI Newsletter – August 1, 2019
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Publications & Press


Geobiology
Diversity decoupled from sulfur isotope fractionation in a sulfate‐reducing microbial community - NEW!
Jesse Colangelo-Lillis*, Claus Pelikan, Craig W. Herbold, Ianina Altshuler, Alexander Loy, Lyle G. Whyte, Boswell A. Wing
*C-DEBI Contribution 483


The extent of fractionation of sulfur isotopes by sulfate‐reducing microbes is dictated by genomic and environmental factors. A greater understanding of species‐specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur‐metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell‐specific sulfate reduction rates < 0.3 × 10−15 moles cell−1 day−1. Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰–45‰) net isotope fractionation (ε34Ssulfide‐sulfate). Measured ε34S values could be reproduced in a mechanistic fractionation model if 1%–2% of the microbial community (10%–60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate‐reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.


Frontiers in Microbiology
Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment - NEW!
Zak Kerrigan, John B. Kirkpatrick, Steven D’Hondt*
*C-DEBI Contribution 484


To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.


Applied and Environmental Microbiology
Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC - NEW!
Andrew D. Steen*, Richard T. Kevorkian, Jordan T. Bird, Nina Dombrowski, Brett J. Baker, Shane M. Hagen, Katherine H. Mulligan, Jenna M. Schmidt, Austen T. Webber, Taylor Royalty*, Marc J. Alperin
*C-DEBI Contribution 485


Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmaxexpressed on a per cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.
 
 
 
 
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DCO: The Ocean Floor Project Explores Uncharted Territory - NEW!
A new initiative entitled The Ocean Floor – Earth’s Uncharted Interface, is receiving more than $8 million annually for seven years to investigate the interactions among biological, geological, and chemical processes at the ocean floor.
 

 

Meetings & Activities



 

Education & Outreach


DCO: Scientists in the Deep Carbon Observatory Heed the Call to Improve Wikipedia - NEW!
Eight members of the DCO science network volunteered to become Wikipedia Fellows and to improve the content of science material on the free online encyclopedia. Through their efforts, they improved 23 articles and contributed more that 13,000 words to this widely read resource.


 

Proposal Calls


NSF: Opportunities for Promoting Understanding through Synthesis (OPUS)
Full proposal deadline: August 5, 2019.

Moore Foundation: Symbiosis Model Systems
The deadline for submitting a pre-application for the Symbiosis Model Systems funding call is August 8, 2019.

NSF: Biological Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Chemical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Physical Oceanography
Full proposal deadline date: August 15, 2019.

NSF: Research Experiences for Undergraduates (REU)
Full Proposal Deadline: August 28, 2019.

International Research Experiences for Students (IRES)
Full Proposal Deadlines: September 10, 2019 (Track I), September 17, 2019 (Track II) and September 24, 2019 (Track III).

Moore Foundation / Simons Foundation: Origin of the Eukaryotic Cell
The deadline for submitting a proposal is September 30, 2019.

NSF: Accelerating Research through International Network-to-Network Collaborations (AccelNet)
Letter of intent due date: October 30, 2019.

NASA: Postdoctoral Program Opportunities - NEW!
Students and postdocs interested  in the field of “Exobiology: Early Evolution of Life and the Biosphere” are encouraged to check out opportunities for NASA Postdoctoral Program fellowships to work with several different investigators. Amongst the available mentors for this opportunity, C-DEBI Senior Scientist Beth Orcutt welcomes discussion with interested applicants that want to use marine deep biosphere “extreme” environments, particularly in oceanic crust, as analog for studying life on ocean worlds. Please contact Orcutt at borcutt@bigelow.org or on Twitter @DeepMicrobe to discuss your interest in this opportunity. Fellowship applications due Nov 1, 2019.

NSF: Research Traineeship (NRT) Program
Next letter of intent window: November 25, 2019 – December 6, 2019.

Queen Mary U of London: PhD Project: Microbial survival in the energy-limited deep biosphere - NEW!
The deep subsurface biosphere contains a vast proportion of Earth’s microbial life and organic carbon. In deep, energy-limited settings, microorganisms persist over extraordinarily long timescales with very slow metabolisms – constituting an important analogue to the potential for life beyond Earth. However, the subsurface is notoriously difficult to study because of its remoteness and limited access, as well as the low biomass concentrations and energy fluxes associated with microbial activity. Therefore, numerical models are pivotal in addressing how microorganisms endure, proliferate, and assemble in deep subsurface settings, and understanding the selective environmental pressures that determine energetic trade-offs between growth and maintenance activities. This PhD project provides the opportunity to work at the frontier of deep biosphere science by developing a microbially-explicit model for the subsurface. This model will provide quantitative insight into microbial and geochemical coupling in deep marine or terrestrial settings, and insight into the energetic limit of life. The project would suit a computational and numerate student with an interest in life in extreme environments, biogeochemistry, and microbial-biogeochemical modelling. Opportunities for funding include London NERC DTP and QMUL Principal’s Postgraduate Research Studentships. For further information about the project, eligibility and future application deadlines in 2019/20, please contact Dr James Bradley.

Queen Mary U of London: PhD Project: Microbial life and activity on glaciers and in Arctic soils - NEW!
The Arctic plays host to a diverse range of microorganisms, including bacteria, algae, and viruses. The activity (or inactivity) or these microorganisms impacts the carbon and nutrient cycling among glaciers and soils, as well as the fertilization and productivity of Polar fjords and oceans, and the albedo of ice surfaces and thus the rate of sea-level rise. Microorganisms in cryospheric habitats must overcome a multitude of environmental stresses, including the freezing of water, desiccation, nutrient deficiencies, and exposure to UV irradiation. To counteract the potentially damaging effects of their harsh environment, they have evolved a range of adaptations. During extended periods of extremely harsh conditions (such as winter), dormancy is essential to enable life to persist. The PhD project seeks to measure the level of activity and dormancy of microorganisms from of a number of Arctic settings including glaciers and soils. This project will develop novel methods to determine the activity of microbial communities from Arctic habitats in situ and in the lab, and will involve laboratory and computational methods, with a possibility of Arctic fieldwork. The student will collaborate within a multi-disciplinary team across Queen Mary University of London and the Natural History Museum. The project would suit a student with an interest in environmental microbiology and biogeochemistry, and Arctic climate change. Opportunities for funding include London NERC DTP and QMUL Principal’s Postgraduate Research Studentships. For further information about the project, eligibility and future application deadlines in 2019/20, please contact Dr James Bradley.

Rolling Calls:


 

Employment

GFZ Potsdam: Research Associate (PostDoc) in Geomicrobiology of Ore Deposits - NEW!
This position will focus on carrying out multi-disciplinary and cutting edge research on the role of microorganisms in forming low temperature ore deposits in Spain and Ireland. The position is jointly hosted by the ore genesis group of the Inorganic and Isotope Geochemistry Section and the Geomicrobiology Section at GFZ Potsdam. Initially the position will be for two years with the possibility of an extension. Please submit your application online by August 20, 2019.

Tokyo Institute of Technology: Principal Investigator (Professor or Associate Professor), Earth-Life Science Institute
Application deadline: August 30, 2019.

MSU: Postdoctoral Positions in the Department of Microbiology & Immunology - NEW!
The Boyd Lab within the Department of Microbiology & Immunology at Montana State University seeks applications for three postdoctoral positions in the areas of microbial physiology and environmental microbiology. We seek to attract exceptional individuals to carry out cutting edge research on one of three recently funded projects: 1) Probing novel pathways of iron sulfur metabolism in model biocatalytic systems, with a focus on interactions between microorganisms and mackinawite/pyrite; 2) Quantifying physiological activity and biodiversity of endolithic microbes in actively serpentinizing rocks recently cored from the Samail Ophiolite, Oman; 3) Characterizing the role of the gut microbiome in mercury demethylation and methylmercury toxicity in humans. These projects are highly collaborative and by their nature, highly interdisciplinary. We seek candidates that are enthusiastic about learning and developing new techniques that integrate across physiological, genetic, voltammetric, proteomic, transcriptomic, bioinformatic, and biochemical disciplines. Potential candidates can contact Dr. Eric Boyd (eboyd@montana.edu) for more information.

Karlsruhe Institute of Technology: PhD / PostDoc position

MBL: Computational Postdoctoral Scientist

DRI: Postdoctoral Fellow, Microbial Ecology: Genomes to Phenomes

UH Manoa: Assistant Researcher (Theoretical Ecologist)




 
 
 
 
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Best, 
 
Matt
 
-- 
Matthew Janicak
Data Manager
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
janicak@usc.edu
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

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