Extremophiles in the Solar System: the evolution and diversity of halophilic microbial communities in deep time.

National University of Ireland, Galway

Brief of Description of Project

Evaporites have formed throughout geological time. They have the potential to trap microorganisms from the surrounding aqueous environment. The microorganisms become hermetically sealed in micron scale brine pools, called fluid inclusions, during crystal (e.g. halite and gypsum) precipitation. This creates a unique microbial signature from the time the crystal(s) formed. Once trapped within the fluid inclusions, evidence exists indicating that microorganisms can and do persist for at least thousands of years. The question remains however, as to their longevity in deep time i.e. hundreds of millions of years. This project will utilise a combination of microscopic and molecular methodologies to characterise the microbial communities present in a range of evaporite samples spanning the geological timescale. DNA extracted from these samples will provide the molecular template to address questions on microbial evolution and ancient ecosystems. Innovative molecular methodologies have been developed by the Geomicrobiology Group to extract, detect and identify microorganisms trapped in fluid inclusions. Todate, the Group has recovered DNA from fluid inclusion hosted bacteria and archaea in evaporites ranging in age from recent times to ~250 million years.

This project will detect and identify microorganisms present within fluid inclusions, from both modern and ancient evaporites sampled from disparate locations on Earth. Furthermore, it will investigate the viability or otherwise of microorganisms within fluid inclusions and their evolution over geological time. The study of Earth based microorganisms trapped in fluid inclusions will also contribute to the search for life on other planets, such as Mars, where similar evaporite deposits may have resulted in the formation of fluid inclusions that host Martian microbial communities.

Unique selling points of PhD project in NUI Galway:
NUI Galway projects should emphasise features that are not typically available in Brazil – specific equipment, multi-disciplinarity, aspects of structured programme, links with industry, placements, links with other research groups etc.

The disciplines of Earth and Ocean Sciences (EOS) and Microbiology within the School of Natural have a proven track record of joint geomicrobiological research (joint supervision of final year student projects, development of new publishable methodologies for studying microbial communities in geological materials). This is a unique multidisciplinary research opportunity for prospective PhD students from Brazil combining the geological study of fluid inclusions with state of the art molecuar microbiolgical techniques to investigate microbial diversity and evolution in extreme ecosystems over geological time, with obvious links to search for life in the Solar system. All the necessary infrastructure to achieve this is available within the Geomicrobiology Group at NUIG.

The School of Natural Sciences, NUIG offers a four year structured PhD program, encorporating 20 ECTS modules designed to develop a range research, personal development and trasnferable skills please see website for details of modules (www.nuigalway.ie/natural_sciences).


Priority Areas

Principal Investigators

  • Education

    • BSc, National University of Ireland Galway
    • MSc, University College Dublin
    • PhD, National University of Ireland, Galway

    General Research Interests

    • Fluid Inclusion Studies
    • Petroleum & Mineral Deposits
    • Geochemistry
    • Geochronology
    • Gemmology
    • Critical Zone Studies

    Research Projects

    • NUIG Geofluids Research Group
    • Chemical Monitoring Facility
    • Digital Landscapes Group

    Project Specific Research Interests & Roles

    Geofluids Research Group: The GRG investigates the role of fluids in the mineralogical, chemical, and structural evolution of the Earth's crust. Research includes global based studies of: a) groundwater, b) petroleum formation and migration, c) metamorphic, magmatic and mineral deposit fluids and d) gemstone deposits. Current projects include the generation of an orogenic scale temporal and chemical framework for geofluids associated with Mo mineralisation during the Caledonian orogeny.

    Chemical Monitoring Facility: This facility has the capability to analyse a diverse range of materials from the environment (e.g. soils, terrestrial and marine sediments, rocks, waters and biological tissue), to determine elemental abundances (including rare earth elements), elemental speciation and isotopic compositions. Research projects include hydrogeological controls on As abundances in groundwater wells sited in mineralised metamorphic rocks.

    Digital Landscapes Group: This group generates interactive CD-ROMS for second level teaching of Earth Sciences (2 CD produced); Exploring the use of Google Earth/ GIS and Digital Terrain Models for 3 and 4D Simulations of Geological Environments. Current projects include EU NEED project focused on the Burren landscape.


  • Career History:

    2013    Lecturer Above-the-Bar, Marine Microbiology
    2013    Science Foundation Ireland Starting Investigator Research (SIRG) Fellow
    2010    NUI, Galway, University Fellow - Marine Microbiology
    2009    PDRA, Civil and Structural Engineering, University of Sheffield
    2006    Research Co-Investigator, Department of Animal and Plant Sciences, University of Sheffield
    2003    Senior Research Officer, Department of Biology, University of Essex
    2003    Ph.D. Marine Microbiology, UCD.
    1999    B.Sc. (Hons.) Environmental Biology. UCD. 1st Class Honours.

    Position Available:

    SFI funded 3-year Post Doctoral Research position in The Molecular Ecology of Ammonia Oxidation in Coastal Sediments, from January 2014.  Click here for details

    Research Interests:

    My research interests are focused on accessing microbial community structure and function in the environment using molecular approaches. Research themes include:

    • Marine microbial diversity and ecology.
    • Biogeochemical cycling of nitrogen in temperate and tropical coastal zones.
    • Microbial associations with marine fish and in aquaculture.

    • Environmental microbiology of water distribution systems.
    • Geomicrobiology:  MIcrobes trapped in halite fluid inclusions.


    Google Scholar Profile: http://scholar.google.com/citations?user="XMTmeEMAAAAJ&hl="en

    Barrett, M., Jahangir, M.M.R., Lee, C., Smith, C.J., Bhreathnach, N., Collins, G., Richards, K.G., O'Flaherty, V.  Abundance of Denitrification genes under different piezometer depths in four Irish agricultural groundwater sites.  Environmental Science and Pollution Research, 1-12.

    Dong, L.F., Naqasima-Sobey, M., Smith, C.J., Rusmana I., Phillips W, Stott, A., Osborn, A.M. and Nedwell, D.B. Dissimilatory reduction of nitrate to ammonium (DNRA) not denitrification dominates benthic nitrate reduction in tropical estuaries. Limnology and Oceanography 56 (1): 297-291.

    Laverock, B., Smith C. J., Tait, K., Osborn, A. M., Widdicombe, S., Gilbert, J. A. (2010) Changes to the microbial community structure in the burrows of two species of bioturbating shrimp. The ISME Journal, 4: 1531-1544.

    McKew B.A. & C.J. Smith (2010) Real-time PCR approaches for analysis of hydrocarbon-degrading bacterial communities in Hydrocarbons, Oils, Lipids, and Derived Compounds. Ed. K.N. Timmis. Springer. pp.3995 - 4009.

    Smith, C.J. and Osborn A.M. (2009) Advantages and limitations of quantitative PCR (Q-PCR) based approaches in microbial ecology. FEMS Microbiology Ecology 67: 6-20.

    Dong, L.F.,* Smith, C.J.,* Papaspyrou, S., Stott, A., Osborn, A.M. and Nedwell, D.B.  (2009) Profiles of benthic denitrification, anammox and nitrate ammonification; and key functional genes along an estuarine nutrient gradient; the Colne estuary, UK. Applied and Environmental Microbiology 75 (10): 3171–3179.     *Both authors contributed equally.

    Smith, C.J., Danilowicz, B.S. and Meijer, W.G. (2009) Bacteria as biological tags for marine fish. Canadian Journal of Fisheries and Aquatic Science 66 (5): 713–716.

    Haynes, K., Hofmann, T.A., Smith, C.J., Ball, A.S., Underwood, G.J.C. and Osborn, A.M. (2007) Diatom-derived carbohydrates as drivers of bacterial community composition in estuarine sediments. Applied and Environmental Microbiology 73 (19): 6112-6124.

    Smith, C.J., Danilowicz, B.S. and Meijer. W.G. (2007) Characterisation of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus). FEMS Microbiology Ecology 62: 90-97.

    Smith, C.J., Nedwell, D.B., Dong, L.F., and Osborn, A.M. (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology 73 (11): 3612–3622.

    McKew, B.A., Coulon, F., Yakimov, M.M., Denaro, R., Genovese, M., Smith, C.J., Osborn, A.M., Timmis, K.N. and McGenity, T.J. (2007) Efficacy of intervention strategies for bioremediation of crude oil in marine systems and effects on indigenous hydrocarbonoclastic bacteria. Environmental Microbiology 9 (6): 1562–1571.

    Smith, C.J., Nedwell, D.B., Dong, L.F., and Osborn, A.M. (2006) Evaluation of Quantitative Polymerase Chain Reaction (Q-PCR) based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology 8 (5): 804-815.

    Smith, C.J. (2005) Quantitative Real Time PCR in Molecular Microbial Ecology Eds. A.M. Osborn and C.J. Smith. pp. 151 – 168.
    Smith, C.J., Danilowicz, B.S., Clear, A.K., Costello, F., Wilson, B., and Meijer. W.G. (2005) T-Align, a web based tool for comparison of multiple Terminal Restriction Fragment Length Polymorphism Profiles. FEMS Microbiology Ecology 54: 375-380.

    Edited Text:

    Molecular Microbial Ecology (2005) Eds. A.M. Osborn and C.J. Smith.  Taylor and Francis Group, Oxford. pp 381

    Current Funded Projects and Group Members:

    EPA, Biogeochemical cycling of nitrates in Irish estuaries:

    • Ms. Agata Lisik, PhD candidate

    SFI, Molecular ecology of ammonia oxidation in coastal sediments:

    • Dr. Limei Zhang, Postdoctoral Researcher
    • Ms. Aoife Duff, PhD candidate

    SFI, Pathogen detection, survival and persistence in a model water distribution system:

    • Ms. Cathy Abberton, MSc by research candidate

    Co-Supervised Research Projects:

    • Molecular diversity of Geomalacus maculosus
    • Ms. Inga Riche, PhD candidate
    • with Dr. Mike Gormally, Environmental Science, NUIG.


Research Groups

  • Geomicrobiology Research Group
    Investigation of microbial life in deep time: Elucidating the evolution of extremophile life,hermetically sealed, in micron scale brine pools (a.k.a fluid inclusions) in crystals during the formation of evaporite deposits. Already the Geomicrobiology Group at NUIG has recovered DNA from evaporites that range in age from recent times to 250 million years old. This research has links with the search for life in other parts of the Solar System i.e. NASA’s Mars based Curiosity rover projectProf. Feely’s Geofluids Group has supervised to copletion a PhD study (and published) on Brazilian carbonatites and presented results at numerous international conferences, currently publishing (in press) on a fluid inclusion study of the Brazilian emerald deposit at the Piteiras Mine. Interactions with Prof. Lydia M. Lobato, (UFMG Universidade Federal de Minas Gerais, Dept. Geologia-IGC, Campus Pampulha, 31270-901.) ensued during this research and these links will be continued during this project. Prof Lobato’s research centre can be acessed at http://www.cpmtc-igc-ufmg.org/ and her geofluids laboratory at http://www.cpmtc-igc-ufmg.org/laboratorios5.htm. Prof. Lobato will help source a PhD student for this project.