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2008 Annual Science Report

Marine Biological Laboratory Reporting  |  JUL 2007 – JUN 2008

Microbial Communities and Activities in the Deep Marine Subsurface

Project Summary

Novel and unexplored microorganisms thrive in deeply buried marine sediments hundreds of meters below the sea bottom. They extend the domain of life into these energy-starved deep sediments and into the underlying ocean crust. These organisms play essential roles in the microbial cycling of carbon in the deep subsurface. We are exploring their biodiversity, their genetic and physiological repertoire, their role in the ocean ecosystem, and their potential as analogs for extraterrestrial life (see Fig. 1)

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

1) Deep subsurface Microbiology

A) In collaboration with MBL, we have completed a V6-tag sequencing analysis of deep subsurface sediment samples, using pyrosequencing of short 16S rRNA gene fragments (V6 tags) to identify the full range of subsurface archaea and bacteria including rare phylotypes (presentations: Biddle et al. 2008; Teske 2008; Biddle and Teske 2008). This high-throughput biodiversity survey exceeded all our previous clone library work by 2-3 orders of magnitude, and yielded a much more detailed picture of microbial biodiversity of the deep subsurface. Overall bacterial to archaeal biodiversity ratios (phylotype ratios) were near 2.6, showing a much greater archaeal contribution to overall diversity than in other marine habitats. We suggest that this relative prominence of archaea, and decline of bacteria, reflects metabolic and biochemical adaptations of archaea to energy-limited subsurface conditions.
B) We have examined the archaeal methane cycle in the deep subsurface of the Juan de Fuca Ridge flanks (sediment column and basement basalt) based on functional genes, 13C isotope signatures of methane, and thermodynamic modeling of methanogenesis, methane oxidation, and sulfate reduction. In the same ridge flank system, we have examined the microbial sources for a key precursor of methanogenesis, acetate, by functional gene studies, 13C signatures of acetate, DIC and methane, and thermodynamic modeling of acetogenesis in comparison to competing pathways. This is the most comprehensive study of its kind, to demonstrate how microbial and biogeochemical cycles in a specific deep subsurface location actually work. A key step was new primer design for the functional key gene of the methane cycle, methane coenzyme M reductase alpha subunit (presentation: Lever et al. 2008).

2) Guaymas Project: Methane cycling

Anaerobic Methane-oxidizing Archaea. We are continuing habitat and microbial community studies of anaerobic methane-oxidizing archaea, due to the importance of these archaea for the early carbon cycle of the Earth and their unique ability to complete the anaerobic carbon cycle in an oxidative direction from methane to CO2. These archaea are candidate organisms for driving carbon cycling in the deep marine subsurface biosphere.
—- My graduate student Karen Lloyd is working microbial communities on methane seeps and brine pools in the Gulf of Mexico, to expand her prior work on biodiversity of methane cycling communities (Lloyd et al. 2006). In collaboration with Samantha Joye (Univ. of Georgia), we are completing a comparison of the microbial communities of a mud volcano and a brine seep, and link the clone library results to geochemical process rates from these habitats; initial results show that the structures of sulfur- and methane-cycling microbial communities are controlled by subsurface fluid flow regimes and seawater inmixing at these sites. The project will be continued with NSF Microbial Observatory funding.
—- A suite of methane seep samples from Guaymas Basin and diverse Gulf of Mexico sites will be submitted for V6 tag sequencing at the MBL, for a comprehensive biodiversity survey of these methane cycling hot spots (funded by the Keck Foundation and by ICOMM)
—- We obtained NSF funding for Alvin cruises to Guaymas Basin in December 2008, and expect considerable synergy of our current NAI- and NSF-funded efforts.


A) The marine subsurface biosphere is to an unexpected degree an archaeal world. Archaeal biodiversity is on a par with bacterial biodiversity, as shown by V6-tag sequencing. Archaea are thriving under the energy-limiting conditions of the deep subsurface, whereas bacteria are declining and show lesser biodiversity and biomass than expected based on other marine habitats.

B) The marine methane cycle is catalyzed by methanogenic and methane-oxidizing archaeal communities that change according to in-situ thermodynamic regime, and extend throughout the deep subsurface sediment column into basement basalt.

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    Andreas Teske Andreas Teske
    Mark Lever
    Doctoral Student

    Karen Lloyd
    Doctoral Student

    Objective 5.1
    Environment-dependent, molecular evolution in microorganisms

    Objective 5.3
    Biochemical adaptation to extreme environments

    Objective 6.1
    Environmental changes and the cycling of elements by the biota, communities, and ecosystems

    Objective 6.2
    Adaptation and evolution of life beyond Earth