C-DEBI Newsletter – February 16, 2016

Publications

ISME Journal
Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent
Caroline S. Fortunato and Julie A. Huber*
*C-DEBI Contribution 267

The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched ¹³C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO₂ fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.

ISME Journal
The energetics of anabolism in natural settings
Douglas E. LaRowe* and Jan P. Amend*
*C-DEBI Contribution 284

The environmental conditions that describe an ecosystem define the amount of energy available to the resident organisms and the amount of energy required to build biomass. Here, we quantify the amount of energy required to make biomass as a function of temperature, pressure, redox state, the sources of C, N and S, cell mass and the time that an organism requires to double or replace its biomass. Specifically, these energetics are calculated from 0 to 125 °C, 0.1 to 500 MPa and −0.38 to +0.86 V using CO₂, acetate or CH₄ for C, NO₃⁻ or NH₄⁺ for N and SO₄²⁻ or HS⁻ for S. The amounts of energy associated with synthesizing the biomolecules that make up a cell, which varies over 39 kJ (g cell)⁻¹, are then used to compute energy-based yield coefficients for a vast range of environmental conditions. Taken together, environmental variables and the range of cell sizes leads to a ~4 orders of magnitude difference between the number of microbial cells that can be made from a Joule of Gibbs energy under the most (5.06 × 10¹¹ cells J⁻¹) and least (5.21 × 10⁷ cells J⁻¹) ideal conditions. When doubling/replacement time is taken into account, the range of anabolism energies can expand even further.

ISME Journal
Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt
Sean P. Jungbluth*, Robert M. Bowers, Huei-Ting Lin, James P. Cowen*, and Michael S. Rappé*
*C-DEBI Contribution 289

Although little is known regarding microbial life within our planet’s rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.

Environmental Microbiology Reports
Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California
Luke McKay*, Vincent W. Klokman, Howard P. Mendlovitz, Douglas E. LaRowe*, Daniel R. Hoer, Daniel Albert, Jan P. Amend*, Andreas Teske*
*C-DEBI Contribution 293

Extreme thermal gradients and compressed metabolic zones limit the depth range of microbial colonization in hydrothermally active sediments at Guaymas Basin. We investigated the physicochemical characteristics of this ecosystem and their influence on microbial community structure. Temperature-related trends of δ¹³C values of methane and dissolved inorganic carbon from 36 sediment cores suggest in situ thermal limits for microbial anaerobic methane oxidation and organic carbon re-mineralization near 80°C and 100°C respectively. Temperature logging probes deposited in hydrothermal sediments for 8 days demonstrate substantial thermal fluctuations of up to 25°C. Putative anaerobic methanotroph (ANME) populations dominate the archaeal community, transitioning from ANME-1 archaea in warm surficial sediments towards ANME-1 Guaymas archaea as temperatures increase downcore. Since ANME archaea performing anaerobic oxidation of methane double on longer time scales (months) compared with relatively rapid in situ temperature fluctuations (hours to days), we conclude that ANME archaea possess a high tolerance for short-term shifts in the thermal regime.

Proposal Calls

DCO: Deep Life Cultivation Internship Program
The Deep Life Community (DLC) within the Sloan Foundation supported Deep Carbon Observatory realizes that the majority of deep microbial life has been resistant to cultivation in the laboratory, which complicates the characterization of physiological characteristics of deep community members. However, recent studies using bioreactor-cultivation techniques, under high pressure and/or temperature, have resulted in successful enrichment of previously uncultivable archaeal and bacterial components that mediate biogeochemical carbon cycling in deep subsurface (1-7). In order to maintain and strengthen cultivation strategies in future deep life missions, the DLC will support early-carrier researchers to visit some key laboratories (Inagaki – Kochi, Japan, Bartlett – La Jolla, USA, and others) to learn and practice newly developed cultivation and cultivation-dependent molecular/biogeochemical techniques using samples from the DLC’s field missions. Financial support includes $5,400 per person for travel and lodging costs and host lab research supply reimbursement. Interested applicants should send their cv, a brief one page statement of their cultivation plans, and a letter of support from their intended host to Fumio Inagaki (inagaki@jamstec.go.jp) and Douglas Bartlett (dbartlett@ucsd.edu).

NAS: Gulf Research Program Exploratory Grants
Letter of Intent due February 17, 2016. 

NAS: Gulf Research Program Early-Career Research Fellowships
Application deadline: February 17, 2016.

IODP: Call for Scientific Drilling Proposals
Next proposal submission deadline: April 01, 2016.

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 2016.

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.

Employment

Cardiff University: Senior Lecturer / Reader / Chair in Geomicrobiology, School of Earth and Ocean Sciences
To maintain its international research activity in Geomicrobiology the School of Earth and Ocean Sciences, Cardiff University, intends to appoint a Senior Lecturer, Reader or Professor in Geomicrobiology. We seek exceptional candidates whose research is focused on microbial impacts on the Earth's biosphere, atmosphere, hydrosphere and geosphere, past and present. We are particularly looking for applicants with experience in one or more of the following fields: near surface to deep subsurface biosphere, microbial influences on element cycling, biosphere/geosphere interactions, anaerobic microbiology, biomineralization and microbe/mineral interactions, sedimentary and/or soil biogeochemistry, biogeochemical cycles, anaerobic microbial ecology and applied environmental microbiology. The successful candidate must develop and sustain an internationally recognized, externally funded research programme in geomicrobiology. We particularly seek candidates who complement our current geomicrobiology research programme and can integrate across other research areas in the. This position is a full-time (35 hours per week), open-ended post and is available immediately. For informal enquiries, please contact Professor Ian Hall, Head of School (EarthHos@cardiff.ac.uk). More information on the School of Earth and Ocean Sciences can be found at: http://www.cardiff.ac.uk/earth-ocean-sciences. Closing date: March 31, 2016.

University of Hawaii at Manoa: Post Doctoral and Graduate Student Research
Positions
The Rappé laboratory at the University of Hawaii at Manoa's Hawaii Institute of Marine Biology is seeking a postdoctoral researcher and one to two graduate students (M.S. or Ph.D.) to join a project investigating the population genomics of planktonic marine bacteria. Review of applications will begin immediately; to ensure full consideration, apply by February 25, 2016.

LMU Munich: Postdoctoral Research Fellowship Program
The Orsi lab at the University of Munich is inviting interested graduate students and postdocs to apply for the LMU Postdoctoral Research Fellowship Program, to study the activity, biochemistry, and genomics of bacteria in subseafloor sediment. Informal inquiries should be sent to Bill Orsi (william.orsi@gmail.com). The deadline for applications is February 29, 2016.

IFREMER: Life at the extremes: microbial EcoGenomics of deep-sea extremophiles: Postdoctoral position (starting immediately) 
The Lab for Microbiology of Extreme environments in Brest (France) has an 18-month postdoctoral position available to carry out research in the ecology of bacterial and archaeal communities in deep-sea brine lakes and hydrothermal vent systems. The appointment should start no later than April 1 2016. Please send inquiries and application to Loïs Maignien (lois.maignien@univ-brest.fr) and A.M. Eren (meren@mbl.edu).