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2003 Annual Science Report

University of Rhode Island Reporting  |  JUL 2002 – JUN 2003

Executive Summary

The University of Rhode Island (URI) team of the NASA Astrobiology Institute (NAI) works to gain a fundamental understanding of Earth’s subsurface life. The team’s research is principally, but not exclusively, focused on study of life in deeply buried marine sediments. Earth’s deep biosphere is a critical component of Earth’s biogeochemical cycles and serves as a model for possible life on other planets. Consequently, the team’s objectives are to understand the subsurface microbial ecosystems of marine sediments, their role in Earth’s biogeochemical cycles, and their relevance to the search for life on other planets.

Environments of special interest for our team include: 1) old, deeply buried sediments where life exists despite extremely low concentrations of electron donors and key nutrients, and 2) hot, deeply buried anoxic sediments where life may exist independently of the photosynthesis-based ecosystem at Earth’s surface. The ecosystems of these subsurface habitats are potentially representative of the ecosystems that may exist on other planets.

The team’s investigators are based at the University of Rhode Island, Woods Hole Oceanographic Institution, and the University of North Carolina at Chapel Hill. To effectively accomplish their objectives, URI team researchers collaborate with each other and with scientists at other institutions throughout the world. For example, over the last year, team members have collaborated closely with scientists at the Massachusetts Institute of Technology, the Max Planck Institute for Marine Microbiology (Germany), the NASA Ames Research Center, Pennsylvania State University, the University of Aarhus (Denmark), and the University of Miami. To gain access to subsurface environments, URI team members participate in international expeditions through the Ocean Drilling Program (ODP).

Over the last decade and a half, scientists throughout the world have documented the widespread occurrence of life deep beneath Earth’s surface. However, fundamental questions about Earth’s subsurface life have yet to be answered. The URI team is actively addressing many of these questions: What categories of organisms live beneath Earth’s surface? How are they related to surface organisms? How closely related are subsurface organisms in geographically distant but similar environments? How much living biomass inhabits Earth’s subsurface environments? What do subsurface organisms do for a living? How active is subsurface life? What is its effect on the surface world?

To explore the taxonomic composition of subseafloor ecosystems, URI team members recently finished a 16S ribosomal ribonucleic acid (rRNA) survey of bacteria and archaea in subseafloor sediments of the Nankai Trough (Kormas et al., 2003) and are working on genetic studies of subseafloor sediments from ODP Leg 201 (in the Peru Margin and the eastern equatorial Pacific). Karen Lloyd, Mark Lever and Andreas Teske are working to isolate, polymerase chain reaction (PCR) amplify, clone and sequence diagnostic key genes for methanogens and sulfate reducers from Leg 201 samples. Antje Lauer, Ketil Soerenson and Teske are developing deoxyribonucleic acid (DNA) isolation procedures and documenting bacterial and archaeal 16S rRNA profiles from the Leg 201 samples, using Denaturing Gradient Gel Electrophoresis (DGGE).

Our genetic studies to date have revealed high diversity in subseafloor prokaryotic communities e.g., Kormas et al, 2003). They have also shown that distinct communities occur at different subseafloor depths. Our studies of bacterial nucleic acids demonstrate that several unique bacterial lineages occur repeatedly in deep subseafloor sediments, suggesting that deep subseafloor sediments constitute a unique environment (Kormas et al, 2003). These unique lineages are candidates for sharing physiological characteristics that predispose them to a subsurface mode of life. Our studies have also identified a specific archaeal phylotype (within the genus Thermococcus) with a trans-Pacific distribution pattern (Figure 1) (Kormas et al., 2003). This archaeal distribution and the repeated occurrence of bacterial lineages mentioned above demonstrate the “connectedness” of life across great distances in deep subseafloor sediments.

URI team members have also made significant headway toward documenting biogeochemical signatures of present and past microbial processes. Kai-Uwe Hinrichs, Helen Sturt, Kristin Smith and Roger Summons’ analyses of intact polar lipids from microbial isolates demonstrate great potential to distinguish microbial phylotypes in natural samples on a species level. John Hayes, Hinrichs and Laura Hmelo are actively developing protocols for isotopic analysis of volatile fatty acids in subseafloor pore waters. Hinrichs, Wolfgang Bach, Hmelo and Sturt are undertaking mechanistic studies of biological hydrocarbon formation in the deep subsurface (Hinrichs et al., 2003).

These Year-5 biosignature studies have led to several interesting results. For example, one line of our biosignature study showed that concentrations of intact polar lipids in the deep subsurface are generally orders of magnitude lower than in surface sediments, reflective of significantly lower densities of microbial populations. Another line of study suggests that ethane and propane are biologically created by hydrogenation of small carbon-bearing organic and inorganic molecules in a variety of deep subseafloor sedimentary environments. Finally, a third line of biosignature study demonstrated that adsorption of biologically produced hydrocarbons is an important process in subseafloor environments. By removing these hydrocarbons, this adsorption enhances free energy yields and allows biological production of the hydrocarbons to continue in subseafloor environments (Hinrichs et al., 2003).

URI team members are also advancing understanding of subseafloor microbial activity and its effects on Earth’s biogeochemical cycles. To assess relationships between cell counts and community activity, David C. Smith, Beverly Chen and Andrew Staroscik developed protocols for adenosine triphosphate (ATP) analysis of subseafloor sediments and completed ATP analyses of ODP Site 1230. Scott Rutherford, Steven D’Hondt and Arthur J. Spivack mapped global patterns of subseafloor sulfate reduction (Figure 2) and estimated their effect on the global sulfur cycle (Rutherford et al., 2003). Guizhi Wang, Rutherford, D’Hondt and Spivack are using chemical data and biogeochemical flux models to estimate net rates of several metabolic processes in subseafloor sediments (D’Hondt et al., 2003; Wang et al., 2003).

The early results of our ATP studies suggest that the active subseafloor biomass is substantially smaller than estimates of subseafloor biomass based on cell counts. This finding suggests that the living subsurface biomass may be substantially lower than generally estimated (the dead may greatly outnumber the quick in subseafloor body counts). Despite this low estimate of living biomass, our studies of subseafloor sulfur fluxes indicate that prokaryotes in deeply buried marine sediments play an important role in the global sulfur cycle; our global flux calculations indicate that subseafloor activities permanently remove about 50% of the sulfur that enters the ocean each year (Rutherford et al., 2003).

Graduate, undergraduate and post-doctoral education and research are integral parts of the URI team’s mission. During the Year-5 report interval, our active research team included four post-doctoral scholars (Lauer, Soerenson, Sturt and Rutherford), three graduate students (Lever, Lloyd, and Wang) and five undergraduate students. All of these individuals played vital roles in our ongoing program. To introduce astrobiology to young scientists with particularly strong potential, this year the URI team initiated nationally competed summer research fellowships for upper-class (junior or senior) students to work with URI investigators on projects of astrobiological significance. Two summer fellows (Uri Manor and Beverly Chen) were selected from 16 applicants in this year’s competition. Chen is working on the ATP studies mentioned above. Manor is working with Rutherford, Wang and D’Hondt to develop an inverse-modeling program for estimating net rates of microbial activity from deep subsurface biogeochemical data. Both students are expected to complete their fellowships in the Year-5 report period.

To build a deeper institutional base of astrobiology awareness among undergraduate and graduate scientists and engineers, URI astrobiologists expanded the academic programs of their home institutions by integrating astrobiological themes into existing microbiology courses, as well as by offering a new URI graduate course, “Subsurface Life” (Autumn, 2002), and an upper-class undergraduate URI engineering and science course, “Exploring the Ocean of Europa” (Spring, 2003). To introduce our work and the field of astrobiology to the broader public, URI team investigators gave public presentations and lectures at a variety of universities and other venues. To disseminate our work and its relevance more broadly, in the Year-5 interval the team also completed and now maintains a website on URI astrobiology efforts in research and education (

In short, research, education and outreach by the NAI URI Team and its collaborators are steadily advancing knowledge and awareness of life deep beneath Earth’s surface, its role in Earth’s surface processes, and its relevance to the search for life on other planets.

Figure 1. Archaeal 16S rRNA tree of deep subsurface archaeal populations in Nankai Trough sediments, based on ca. 900 sequence positions (Kormas et al., 2003). The subsurface Thermococcus species in Nankai are related to Thermococcus spp. from vent effluents at the Juan de Fuca vents offshore Washington, indicating a trans-Pacific occurrence of closely related strains.

Figure 2. Map of sulfate flux to subseafloor predicted from regression of porewater data against distance from shore and chlorophyll concentration in surface waters (Rutherford et al., 2003)


D’Hondt, S., Jørgensen, B.B., & the ODP Leg 201 Shipboard Scientific Party. (2002). Respiration in Deeply Buried Marine Sediments (Early Results from ODP Leg 201) [Abstract: NASA Astrobiology Institute General Meeting 2003]. Astrobiology, 2(4): 502.

Hinrichs, K.-U, Spivack,A.J. & ODP Leg 201 Shipboard Scientific Party. (2002). The distribution of volatile fatty acids in the marine subsurface [Abstract: NASA Astrobiology Institute General Meeting 2003]. Astrobiology, 2(4): 633-634.

Kormas, K.A., Smith, D.C., Edgcomb, V.E. & Teske, A. (2003). Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176A). FEMS Microbiology Ecology, 45: 115-125.

Rutherford, S., D’Hondt, S. & Spivack, A.J. (2002). Global Rates of Sulfate Reduction in Deeply Buried Marine Sediments [Abstract: NASA Astrobiology Institute General Meeting 2003]. Astrobiology, 2(4): 550.

Wang, G., Rutherford, S., D’Hondt, S., Spivack, A.J. & ODP Leg 201 Shipboard Scientific Party. (2002). Distribution of Metabolic Activity Within a Deep-Sea Sediment Column [Abstract: NASA Astrobiology Institute General Meeting 2003]. Astrobiology, 2(4): 556.