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2013 Annual Science Report

Carnegie Institution of Washington Reporting  |  SEP 2012 – AUG 2013

Project 5: Geological-Biological Interactions

Project Summary

We continue to study the intersection between geology and biology. We continue to explore how sub-seafloor interactions support deep ocean hydrothermal ecosystems. We study life’s adaption to extremes of pressure, cold, and salinity. We adapt and apply multiple isotopic sulfur geochemistry towards the understanding of microbial metabolism and as a means of detecting ancient metabolisms recorded in the rock record through characteristic sulfur isotopic signatures. We apply state-of-the-art methods to derive chemical and isotopic biosignatures of life in the Earth’s most ancient rocks.

4 Institutions
3 Teams
30 Publications
2 Field Sites
Field Sites

Project Progress

Project 5. Geological-Biogical Intersections

5.1 Exploring the diversity, physiology and evolution of microbial communities in deep-sea hydrothermal vent environments

The focus of CoI Baross’s research is the diversity, physiology and evolution of microbial communities in deep-sea hydrothermal vent and sub-seafloor environments and the possible role these environments played as settings for the origin of life. CoI Baross and students preformed deep-sequencing analyses (tens of thousands of reads) of sub-seafloor vent fluids and found many rare groups of archaeal species (<10 in the sample) some of which are known to be dominant groups in the hot sections of active sulfide structures. These results show the existence of a high diversity of generally unidentified hyperthermophilic archaea in the deep sub-seafloor that has not previously been detected using older molecular methods. Included in our research is also an emphasis on understanding the mechanisms by which bacteria and archaea adapt and survive the extreme conditions in these environments. To address this, we have explored the evolutionary strategies of the microbial and viral communities through comparative analysis of the cellular and viral metagenome collected from these diffuse-flow fluids from these extreme environments. High numbers of viruses were detected in the samples. Furthermore, results from the viral metagenome showed evidence that a high proportion were lysogenic, that is, capable of integrating into the host genome. Overall, we demonstrated a high potential for hydrothermal vent viruses to facilitate horizontal gene transfer and thus affect the host’s physiology and evolutionary history.

5.2 Marilyn Fogel Transitions to University of California, Merced

2013 was a year of change for Fogel, as she moved from the Geophysical Laboratory to the University of California at Merced. Projects at the GL continued and papers were published. Derek Smith, graduate student at Dartmouth College and GL, finished his dissertation in August and accepted a position as an Agouron Fellow at Caltech working with Victoria Orphan. Dr. Roxane Bowden, Lab Manager for the stable isotope astrobiology lab, continues to do research in collaboration with scientists at GL and DTM.

5.3 Tracing biological processes using multiple sulfur isotopes

Research by CoI Farquhar and students during this reporting period focused on continued development of a framework for interpreting isotope signatures produced by microbial sulfur metabolisms in experiments and in nature. This work continues to include analyses of laboratory culture experiments with sulfate reducers and sulfide oxidizers. This work also continues to extend laboratory analyses to studies of biological processes that need to be characterized so that metabolic isotopic signatures can be uniquely identified. Work on the products of laboratory culture experiments was conducted by PhD student Brian Harms and laboratory manager/researcher Joost Hoek who continued to study isotope fractionations produced by thermophiles A. fulgidus and T. indicus. The work on A. fulgidus involves interpretation of data collected for a temperature block experiment with this organism, and construction of an inverse model sulfur metabolism to understand how it responds to different temperature conditions. Harms is in the final stages of modeling these data, and anticipates preparing a manuscript for submission in the next year. Work with T. indicus involves analysis of archived samples collected from experiments conducted by Dr. Hoek that examined the metabolic response of this organism to changing hydrogen activity. Dr. Hoek has already shown that the fractionations increase as hydrogen activity decreases. The focus of the present work will be used with multiple sulfur isotopes to isolate the natureal changes in the flow of metabolites through the dissimilartory sulfate reduction metabolism of this organism to generate these changes in fractionations. Research by PhD student Daniel Eldridge and undergraduate student Noah Bowman focused on developing an apparatus to study the abiotic oxidation of sulfide in natural (seawater) and laboratory (pure water) media. This work was the focus of a senior thesis by Noah Bowman, and has resulted in the development of an apparatus that can be used to collect rate data for the abiotic chain of reactions that is associated with sulfide oxidation. Rate data can be collected for sulfide consumption as well as for the production and consumption of sulfur intermediate oxidation state compounds such as polysulfides, thiosulfate, and sulfite as well as for the accumulation of ultimate product sulfate. The experiments also provide a way to measure the isotopic compositions of these compounds. Work in the previous reporting period identified isotopic signatures that are inconsistent with classical isotope exchange reactions. The rate data as well as ab initio calculations using Gaussian software will be used to identify hypotheses that explain the origin of these isotope effects. A framework that describes the isotope effects is needed for interpretation of metabolic effects in natural systems.

5.3 Evidence of 3.5 billion-year-old bacterial ecosystems found in Australia

Earth’s oldest sedimentary rocks are not only rare, but also almost always altered by hydrothermal and tectonic activity. We have identified the well-preserved remnants of a complex ecosystem in a nearly 3.5 billion-year-old sedimentary rock sequence in Australia. We described the various MISS from the ancient coastal flats preserved in the Dresser Formation. Chemical analyses point towards a biological origin of the material. The Dresser MISS fossils resemble strongly in form and preservation the MISS from several other younger rock samples, such as a 2.9 billion-year-old ecosystem in South Africa. These sedimentary structures, which arose from the interactions of bacterial films with shoreline sediments from the region, are promising targets for Mars rovers.

5.4 Mars Science Laboratory: Mission involvement

During the past reporting period, CoI Steele has been an active participating scientist on the MSL mission. In particular he has focused on the SAM instrument suite and associated experiments. The results of these initial experiments have been published. CoI Steele has continued working with the SAM team as Curiosity continues its journey. He is a co-author on a number of papers in preparation. In concert with his involvement in MSL, CoI Steele has continued his analysis of organics in Martian Meteorites focusing in particular on the Tissint Martian meteorite. CoI Steele has performed micro-RAMAN spectroscopy, secondary ion mass spectrometry (nanoSIMS), pyrolysis Gas Chromatography-Mass Spectrometry, Time of Flight Secondary ion Mass Spectrometry (ToF-SIMS), Transmission Electron Microscopy and C-, N-, and O-micro X-ray Absorption Near Edge Structure (XANES) spectroscopy on these organic inclusions in the Tissint meteorite. These data are aiding in the interpretation of the MSL SAM data.

Macrostructures of the lower supratidal zone, 3.48 Ga Dresser Formation, Pilbara, Western Australia, plus possible modern equivalents. The center images show the Dresser Formation structures; for better visualization, the Dresser structures are outlined in the sketches on the left. The right images show possible modern counterparts of such structures. (A), Fragments deposited along the edge of an erosive margin. One fragment is deposited on top of the elevated, planar surface of the eroded margin; the other fragment is situated close to its original parent site at the edge of the erosive margin. In modern settings, such erosive margins with irregular edges are caused by partial erosion of microbial mat-stabilized surfaces (compare the example shown in the insert of Fig. 1B. The irregular shape of the fossil fragments supports the interpretation as possible mat chip. Note that the microbial mat-covered sediment is elevated (= erosional remnant). In contrast, sediment bare of microbenthos is deeper lying (= erosional pocket; compare with Fig. 10); modern example from Mellum Island, Germany. Scale: 1 cm. (B) Wrinkled upper surface of a rock bed. In modern environments, such wrinkle structures are typical for surfaces of EPS-rich microbial mats; modern example from Mellum Island, Germany. Scale: 1 cm. (C), Sedimentary rock surface arranged into polygons. Many polygons have a hole in their center. In modern settings, such polygons form within microbial mats exposed to seasonal changes of humidity. They are called Polygonal Oscillation Cracks. Each individual polygon is separated from its neighbors by a 3-10 cm wide transition zone (desiccation cracks, often overgrown by a younger generation of microbial mat). The holes in each of the polygons are collapsed gas domes (compare Figs. 1C and 14); modern example from El Bibane, Tunisia. Scale: 10 cm. (D), Honey-comb pattern of ridges and and tufts exposed on a surface of a sedimentary rock bed. In modern settings, such ridges arranged into a honey-comb pattern are typical for microbial mats developing in tidal pools. Meeting points of ridges are marked by tufts; example from Portsmouth Island, USA. Scale: 5 cm. (compare Fig. 1D) (E), Dark-light laminae forming a stack in possibly lagoonal sedimentary rocks. In modern settings, such laminae become visible in vertical section through very mature microbial mats. The laminae represent many layers of succeeding microbial mat generations, or microbial mat-overgrown lagoon sediments. Stacks of mat laminae are called biolaminites. Millimeter-scale mat chips and roll-ups occur within laminae (compare geochemistry in Fig. 17); modern example from El Bibane, Tunisia. Scale: 5 cm.