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Aquatic Microbial Ecology
Substrate specificity of aquatic extracellular peptidases assessed by competitive inhibition assays using synthetic substrates
A.D. Steen*, J.P. Vazin, S.M. Hagen, K.H. Mulligan, S.W. Wilhelm
*C-DEBI Contribution 261
The identities and biochemical properties of extracellular enzymes present in natural environments are poorly constrained. We used a series of competitive inhibition experiments with samples from a freshwater environment (the Tennessee River at Knoxville, TN, USA) and a marine environment (Bogue Sound, NC, USA) to characterize the range of substrate specificities of naturally occurring enzymes that hydrolyze L-leucine 7-amido-4-methylcoumarin (Leu-AMC), L‑proline-AMC (Pro-AMC), and L-arginine-AMC (Arg-AMC)—putative substrates for leucyl-aminopeptidase, prolyl-aminopeptidase, and arginyl-aminopeptidase, respectively. Extracellular peptidases which hydrolyzed Arg-AMC and Leu-AMC demonstrated affinity for up to 8 other amino acids, whereas those hydrolyzing Pro-AMC in the Tennessee River, and Arg-AMC at Bogue Sound, were more specific to proline and arginine, respectively. Patterns of substrate affinity showed that Leu-AMC (at both sampling sites) and Arg-AMC (at Bogue Sound) were primarily hydrolyzed by enzymes other than leucyl-aminopeptidase and arginyl-aminopeptidase, respectively. The set of naturally occurring peptidases in both environments showed greater affinity towards a subset of amino acids. These amino acids were on average larger, yielded more free energy from oxidation to CO2, and tended to be depleted in aged organic matter. These relationships indicate that pathways of amino acid diagenesis are at least partially controlled by the substrate specificities of the peptidases involved in protein degradation.
Environmental Microbiology Reports
Viral activities and life cycles in deep subseafloor sediments
T. Engelhardt, W.D. Orsi*, B.B. Jørgensen
*C-DEBI Contribution 271
Viruses are highly abundant in marine subsurface sediments and can even exceed the number of prokaryotes. However, their activity and quantitative impact on microbial populations are still poorly understood. Here, we use gene expression data from published continental margin subseafloor metatranscriptomes to qualitatively assess viral diversity and activity in sediments up to 159 metres below seafloor (mbsf). Mining of the metatranscriptomic data revealed 4651 representative viral homologues (RVHs), representing 2.2% of all metatranscriptome sequence reads, which have close translated homology (average 77%, range 60–97% amino acid identity) to viral proteins. Archaea-infecting RVHs are exclusively detected in the upper 30 mbsf, whereas RVHs for filamentous inoviruses predominate in the deepest sediment layers. RVHs indicative of lysogenic phage–host interactions and lytic activity, notably cell lysis, are detected at all analysed depths and suggest a dynamic virus–host association in the marine deep biosphere studied here. Ongoing lytic viral activity is further indicated by the expression of clustered, regularly interspaced, short palindromic repeat-associated cascade genes involved in cellular defence against viral attacks. The data indicate the activity of viruses in subsurface sediment of the Peruvian margin and suggest that viruses indeed cause cell mortality and may play an important role in the turnover of subseafloor microbial biomass.
Geochimica et Cosmochimica Acta
Geomorphic regime modulates hydrologic control of chemical weathering in the Andes–Amazon
M.A. Torres*, J. West, K.E. Clark
*C-DEBI Contribution 273
The interplay between the hydrologic processes that supply, store, and route water in catchment systems and the chemical weathering reactions that add and remove solutes acts as an important control on chemical weathering fluxes. In this study, we use paired measurements of solute chemistry and runoff in four nested catchments that span the transition from the Andes Mountains to the Amazonian foreland floodplain in Peru in order to investigate the links between hydrology and weathering processes and to determine how these links change across a geomorphic gradient. All of the sites show variation in elemental concentrations and ratios with runoff consistent with hydrologically driven changes in lithologic sources, the extent of secondary mineral precipitation, and, potentially, fluid flow paths. In the Andean sites, solute concentrations are relatively constant despite large changes in runoff. This is in direct contrast to the foreland floodplain site, where solute concentrations are diluted as runoff increases. In the Andes–Amazon, the concentration–runoff behavior is correlated with the mean catchment slope angle, which suggests that erosional processes, by modulating the timescales over which weathering reactions occur within the critical zone, can be an underlying control on solute production and therefore on chemical weathering. Due to the co-variation between the geomorphic and hydrologic controls on chemical weathering, weathering fluxes in Andean sites are more sensitive to seasonal changes in runoff than in the foreland floodplain site.
Frontiers in Microbiology
Power limits for microbial life
D.E. LaRowe*, J.P. Amend*
*C-DEBI Contribution 274
To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm-3) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10-12 and 10-16 W cm-3. The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm-3 can be well-captured using a maintenance power, 190 zW cell-1, two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50–3500 zW cell-1, with most values under ∼300 zW cell-1. Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell-1.
Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor
F. Inagaki, K.-U. Hinrichs, Y. Kubo, M.W. Bowles, V.B. Heuer, W.-L. Hong, T. Hoshino, A. Ijiri, H. Imachi, M. Ito, M. Kaneko, M.A. Lever, Y.-S. Lin, B.A. Methe, S. Morita, Y. Morono, W. Tanikawa, M. Bihan, S.A. Bowden, M. Elvert, C. Glombitza, D. Gross, G.J. Harrington, T. Hori, K. Li, D. Limmer, C.-H. Liu, M. Murayama, N. Ohkouchi, S. Ono, Y.-S. Park, S C. Phillips, X. Prieto-Mollar, M. Purkey, N. Riedinger, Y. Sanada, J. Sauvage, G. Snyder, R. Susilawati, Y. Takano, E. Tasumi, T. Terada, H. Tomaru, E. Trembath-Reichert, D.T. Wang, Y. Yamada
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~104 cells cm−3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
Science: Perspective: Microbial Ecology
Making methane down deep
The global ocean is Earth’s largest biome, which extends into the sediments and igneous crust below the oceans. The abundance of microbial life beneath the sea floor is at least comparable to that in the oceans (1), but this biome remains poorly understood. The ramifications of a massive buried biosphere are important on a global scale, with sub–sea-floor microbes playing a crucial role in carbon sequestration, element cycles, and Earth’s evolution, and likely encompassing staggering metabolic and genetic diversity. On page 420 of this issue, Inagaki et al. (2) report that even at almost 2.5 km beneath the sea floor, microbial life is not only present and compositionally distinct from that in shallower sediments, but also producing methane.
Education & Outreach
Institute for Broadening Participation (IBP): Minorities Striving and Pursuing Higher Degrees of Success in GEO REU (MS PHD’S–GEO REU) Professional Development Program
The MS PHD’S-GEO REU joins the MS PHD’S family as a two-phase program designed specifically for underrepresented minority (URM) undergraduates who have participated in a recent National Science Foundation Research Experience for Undergraduates (NSF REU) program in one of the following disciplines: Earth Sciences, Ocean Sciences, Polar Sciences, or Atmospheric and Geospace Sciences. Consideration will also be given to applicants who have completed REUs in other STEM fields (e.g. environmental engineering, ecology, computational mathematics, etc.) and who demonstrate strong interest in the geosciences and articulate potential benefits received as participants in this program. Selected participants will attend the December 2015 American Geophysical Union (AGU) Fall Meeting. Financial support to attend the AGU Fall Meeting including air travel, lodging, meeting registration and meals is provided to all students who are accepted to the MS PHD’S-GEO REU program and engage in all MS PHD’S-GEO REU activities. Application deadline: September 14, 2015.
The Rolex Scholarships
Currently there are three Rolex Scholarships: North America, Europe, and Australasia. Each Rolex Scholarship provides a hands-on introduction to underwater and other aquatic-related endeavors for a young person considering a career in an underwater-related discipline. Application deadline: December 15, 2015.
The Data Incubator: Data Science Fellowship Opportunity
The next session will be from 09/08/15 to 10/16/15.
Meetings, Workshops and Activities
AGU Session #7571: B088. Uncultured microorganisms and their geochemical roles in deep-sea environments
Conveners Stephanie Carr (C-DEBI Postdoc Fellow, CO School of Mines), Jessica Labonté (Bigelow), FengPing Wang (Shanghai JiaoTong University) and Mohamed Jebbar (Université de Bretagne Occidentale) would like to encourage you to submit an abstract to their deep biosphere session at this year’s AGU Fall Meeting. Their session, entitled “Uncultured microorganisms and their geochemical roles in deep-sea environments,” will feature presentations from the following scientists: Takuro Nunoura (JAMSTEC – Japan), Jennifer Biddle (C-DEBI researcher, University of Delaware), Roland Hatzenpichler (C-DEBI Postdoc, California Institute of Technology) and Karthik Anantharaman (University of California, Berkeley).
Remember to submit your AGU abstracts by August 5, 2015. Other deep biosphere-related sessions include…
- B027. Connecting single-cell processes to global biogeochemical cycles: a multidisciplinary challenge
- B051. Microbial Growth on Iron: You can’t spell life without Fe
- OS012. Follow the fluids: Integrating multi-disciplinary observations of deep-sea hydrothermal systems
- OS014. Interplay between tectonics, oceanography, hydro-thermal circulation and microbial processes in the Gulf of California
- ED008. Climate Literacy in K-12 Classrooms: Challenges, Solutions, and Change
- PP017. Geochemistry and Microbiology of Oxic and Suboxic Deep Sea Pelagic Sediments
- See also the AGU 2015 Sessions of Interest to the DCO Community
IODP: Apply to Sail on Expedition 363 Western Pacific Warm Pool, Expedition 366 Mariana Convergent Margin and Expedition 365 NanTroSEIZE Shallow Megasplay Long-Term Borehole Monitoring System
The deadline to apply for Expeditions 363 and 366 is August 15, 2015. The Expedition 365 deadline is August 31, 2015.
NSF: Scholarships in Science, Technology, Engineering, and Mathematics (S-STEM)
Full proposal deadline: September 22, 2015.
National Academies: Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes November 01, 2015.
NSF: Earth Sciences Postdoctoral Fellowships (EAR-PF)
Full proposal deadline: January 12, 2016
NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.
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).
Ecole Polytechnique Federale Lausanne (EPFL) / Environmental Microbiology Laboratory (EML): Postdoctoral researcher position to investigate the microbial community in deep sulfidic boreholes in Finland
The project deals with characterizing the microbial community responsible for sulfate reduction in deep boreholes in Finland in order to decipher the electron donor fueling this process. The work will entail sampling, carrying out metagenomic and metaproteomic analyses, and using this information to reconstruct the relevant metabolic pathways. For further information, please contact Professor Rizlan Bernier-Latmani via e-mail: email@example.com. Start date: October 01, 2015.
University of California San Diego / Scripps Institution of Oceanography (SIO): Associate or Full Professor (or Acting) – Earth and Planetary Sciences
We seek outstanding candidates for up to two positions from a broad range of disciplines within the Earth and Planetary Sciences, including geochemistry, tectonic processes, theoretical and computational geophysics, seismology, and marine and terrestrial geodesy. The successful candidate(s) will be expected to teach classes, supervise research at both the graduate and undergraduate level and contribute to leadership on issues of equity and diversity. The position requires a PhD degree in a relevant field and a competitive record of publication, as well as evidence of the ability to conduct and fund an active research program consistent with the opportunity to have done so at this career level. The successful candidate will also demonstrate the highest standards of scholarship and professional activity, or for junior scholars to have the potential thereof. Applicants for tenured positions are expected to have demonstrated excellence in research, teaching, mentoring and service. Review date: September 15, 2015.
University of California San Diego / Scripps Institution of Oceanography (SIO): Associate or Full Professor (or Acting) – Polar Science
We seek outstanding candidates in Polar Science. Relevant research areas could include glaciology, oceanography, climate, biogeochemistry, and microbiology. We are particularly interested in individuals able to establish connections between more than one element of the polar system. Possible foci include land ice, sea ice, biogeochemistry, the carbon cycle, microbial processes, paleoclimate, subglacial processes (including biology), and high-latitude climate processes. Research approaches can include observations (field and remote sensing), modeling, genomics, and dynamics. The successful candidate will be expected to teach classes, supervise research at both the graduate and undergraduate level and contribute to leadership on issues of equity and diversity. The position requires a PhD degree in a relevant field and a competitive record of publication, as well as evidence of the ability to conduct and fund an active research program consistent with the opportunity to have done so at this career level. The successful candidate will also demonstrate the highest standards of scholarship and professional activity, or for junior scholars to have the potential thereof. Applicants for tenured positions are expected to have demonstrated excellence in research, teaching, mentoring and service. Review date: September 15, 2015.
IODP/Texas A&M: Assistant Research Scientist – Expedition Project Manager/Staff Scientist – Borehole Geophysics
We will begin reviewing applications on September 15, 2015, but will continue to accept applications until candidates are selected for interviews.
All required application materials submitted by September 15, 2015 are ensured full consideration.
Rice University: Wiess Post-Doctoral Research Fellowship in Earth and Planetary Science
The application deadline is November 1, 2015.
Montana State University: PhD Position, Astrobiology
The Priscu Research Group is seeking a motivated Ph.D. Student to work on a recently funded NASA Planetary Science and Technology Through Analog Research (PSTAR) grant.
Don’t forget to email me with any items you’d like to share in future newsletters! You are what makes our deep biosphere community!