Workshop white paper
| 
29 May 2015
Workshop white paper |
| 29 May 2015
Workshop to develop deep-life continental scientific drilling projects
T. L. Kieft
CORRESPONDING AUTHOR
Department of Biology, New Mexico Tech, Socorro, NM 87801, USA
T. C. Onstott
Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
L. Ahonen
Geological Survey of Finland, P.O. Box 96, 02151 Espoo, Finland
V. Aloisi
Laboratoire d'Océanographie Dynamique et de Climatologie, Université Pierre et Marie Curie, Place Jussieu 4, Case 100, 75252 Paris Cedex 05, France
F. S. Colwell
College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR 97331, USA
B. Engelen
Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
S. Fendrihan
Romanian Bioresources Centre, Sector 6, Bucharest, Romania
E. Gaidos
Dept. of Geology & Geophysics, University of Hawaii at Mānoa, Honolulu, HI 96822, USA
International Scientific Drilling Program, Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Telegrafenberg C-425, 14473 Potsdam, Germany
I. Head
Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE17RU, UK
J. Kallmeyer
Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Telegrafenberg C-425, 14473 Potsdam, Germany
B. Kiel Reese
Department of Life Sciences, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Unit 5800, Corpus Christi, TX 78412-5800, USA
L.-H. Lin
Department of Geosciences National Taiwan University, Taipei 106, Taiwan
P. E. Long
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
D. P. Moser
Division of Earth and Ecosystem Sciences, Desert Research Institute, 755 E. Flamingo Road, Las Vegas, NV 89119, USA
H. Mills
Division of Natural Sciences, School of Science and Computer Engineering, University of Houston Clear Lake, Houston, TX 77058, USA
P. Sar
Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
D. Schulze-Makuch
Technical University Berlin, Berlin, Germany, and Washington State University, Pullman, WA 99164, USA
H. Stan-Lotter
Division of Molecular Biology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
D. Wagner
Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Telegrafenberg C-425, 14473 Potsdam, Germany
P.-L. Wang
Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
F. Westall
Centre de Biophysique Moléculaire, UPR CNRS 4301, rue Charles Sadron, 45071 Orléans Cedex 2, France
M. J. Wilkins
School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
Related authors
No articles found.
Ellen Schnabel, Aurèle Vuillemin, Cédric C. Laczny, Benoit J. Kunath, André R. Soares, Rolando Di Primio, Jens Kallmeyer, and the PROSPECTOMICS Consortium
EGUsphere, https://doi.org/10.5194/egusphere-2024-1603, https://doi.org/10.5194/egusphere-2024-1603, 2024
Short summary
Short summary
This study analyzed marine sediment samples from areas with and without minimal hydrocarbon seepage from reservoirs underneath. Depth profiles of dissolved chemical components in the pore water as well as molecular biological data revealed differences in microbial community composition and activity. These results indicate that even minor hydrocarbon seepage affects sedimentary biogeochemical cycling in marine sediments, potentially providing a new tool for detection of hydrocarbon reservoirs.
Chueh-Chen Tung, Yu-Shih Lin, Jian-Xiang Liao, Tzu-Hsuan Tu, James T. Liu, Li-Hung Lin, Pei-Ling Wang, and Chih-Lin Wei
Biogeosciences, 21, 1729–1756, https://doi.org/10.5194/bg-21-1729-2024, https://doi.org/10.5194/bg-21-1729-2024, 2024
Short summary
Short summary
This study contrasts seabed food webs between a river-fed, high-energy canyon and the nearby slope. We show higher organic carbon (OC) flows through the canyon than the slope. Bacteria dominated the canyon, while seabed fauna contributed more to the slope food web. Due to frequent perturbation, the canyon had a lower faunal stock and OC recycling. Only 4 % of the seabed OC flux enters the canyon food web, suggesting a significant role of the river-fed canyon in transporting OC to the deep sea.
George Westmeijer, Cristina Escudero, Claudia Bergin, Stephanie Turner, Magnus Ståhle, Maliheh Mehrshad, Prune Leroy, Moritz Buck, Pilar López-Hernández, Jens Kallmeyer, Ricardo Amils, Stefan Bertilsson, and Mark Dopson
Biogeosciences, 21, 591–604, https://doi.org/10.5194/bg-21-591-2024, https://doi.org/10.5194/bg-21-591-2024, 2024
Short summary
Short summary
Rock cores down to 2250 m depth, groundwater-bearing fractures, and drilling fluid were sampled for DNA to characterize the subsurface microbial community. In general, microbial biomass was extremely low despite the employment of detection methods widespread in low-biomass environments. The described contamination control measures could support future sampling efforts, and our findings emphasize the use of sequencing extraction controls.
Steffen Kutterolf, Mark Brenner, Robert A. Dull, Armin Freundt, Jens Kallmeyer, Sebastian Krastel, Sergei Katsev, Elodie Lebas, Axel Meyer, Liseth Pérez, Juanita Rausch, Armando Saballos, Antje Schwalb, and Wilfried Strauch
Sci. Dril., 32, 73–84, https://doi.org/10.5194/sd-32-73-2023, https://doi.org/10.5194/sd-32-73-2023, 2023
Short summary
Short summary
The NICA-BRIDGE workshop proposes a milestone-driven three-phase project to ICDP and later ICDP/IODP involving short- and long-core drilling in the Nicaraguan lakes and in the Pacific Sandino Basin to (1) reconstruct tropical climate and environmental changes and their external controlling mechanisms over several million years, (2) assess magnitudes and recurrence times of multiple natural hazards, and (3) provide
baselineenvironmental data for monitoring lake conditions.
Tomáš Fischer, Pavla Hrubcová, Torsten Dahm, Heiko Woith, Tomáš Vylita, Matthias Ohrnberger, Josef Vlček, Josef Horálek, Petr Dědeček, Martin Zimmer, Martin P. Lipus, Simona Pierdominici, Jens Kallmeyer, Frank Krüger, Katrin Hannemann, Michael Korn, Horst Kämpf, Thomas Reinsch, Jakub Klicpera, Daniel Vollmer, and Kyriaki Daskalopoulou
Sci. Dril., 31, 31–49, https://doi.org/10.5194/sd-31-31-2022, https://doi.org/10.5194/sd-31-31-2022, 2022
Short summary
Short summary
The newly established geodynamic laboratory aims to develop modern, comprehensive, multiparameter observations at depth for studying earthquake swarms, crustal fluid flow, mantle-derived fluid degassing and processes of the deep biosphere. It is located in the West Bohemia–Vogtland (western Eger Rift) geodynamic region and comprises a set of five shallow boreholes with high-frequency 3-D seismic arrays as well as continuous real-time fluid monitoring at depth and the study of the deep biosphere.
Gilles Reverdin, Claire Waelbroeck, Catherine Pierre, Camille Akhoudas, Giovanni Aloisi, Marion Benetti, Bernard Bourlès, Magnus Danielsen, Jérôme Demange, Denis Diverrès, Jean-Claude Gascard, Marie-Noëlle Houssais, Hervé Le Goff, Pascale Lherminier, Claire Lo Monaco, Herlé Mercier, Nicolas Metzl, Simon Morisset, Aïcha Naamar, Thierry Reynaud, Jean-Baptiste Sallée, Virginie Thierry, Susan E. Hartman, Edward W. Mawji, Solveig Olafsdottir, Torsten Kanzow, Anton Velo, Antje Voelker, Igor Yashayaev, F. Alexander Haumann, Melanie J. Leng, Carol Arrowsmith, and Michael Meredith
Earth Syst. Sci. Data, 14, 2721–2735, https://doi.org/10.5194/essd-14-2721-2022, https://doi.org/10.5194/essd-14-2721-2022, 2022
Short summary
Short summary
The CISE-LOCEAN seawater stable isotope dataset has close to 8000 data entries. The δ18O and δD isotopic data measured at LOCEAN have uncertainties of at most 0.05 ‰ and 0.25 ‰, respectively. Some data were adjusted to correct for evaporation. The internal consistency indicates that the data can be used to investigate time and space variability to within 0.03 ‰ and 0.15 ‰ in δ18O–δD17; comparisons with data analyzed in other institutions suggest larger differences with other datasets.
Henning Lorenz, Jan-Erik Rosberg, Christopher Juhlin, Iwona Klonowska, Rodolphe Lescoutre, George Westmeijer, Bjarne S. G. Almqvist, Mark Anderson, Stefan Bertilsson, Mark Dopson, Jens Kallmeyer, Jochem Kück, Oliver Lehnert, Luca Menegon, Christophe Pascal, Simon Rejkjær, and Nick N. W. Roberts
Sci. Dril., 30, 43–57, https://doi.org/10.5194/sd-30-43-2022, https://doi.org/10.5194/sd-30-43-2022, 2022
Short summary
Short summary
The Collisional Orogeny in the Scandinavian Caledonides project provides insights into the deep structure and bedrock of a ca. 400 Ma old major orogen to study deformation processes that are hidden at depth from direct access in modern mountain belts. This paper describes the successful operations at the second site. It provides an overview of the retrieved geological section that differs from the expected and summarises the scientific potential of the accomplished data sets and drill core.
Tzu-Hsuan Tu, Li-Ling Chen, Yi-Ping Chiu, Li-Hung Lin, Li-Wei Wu, Francesco Italiano, J. Bruce H. Shyu, Seyed Naser Raisossadat, and Pei-Ling Wang
Biogeosciences, 19, 831–843, https://doi.org/10.5194/bg-19-831-2022, https://doi.org/10.5194/bg-19-831-2022, 2022
Short summary
Short summary
This investigation of microbial biogeography in terrestrial mud volcanoes (MVs) covers study sites over a geographic distance of up to 10 000 km across the Eurasian continent. It compares microbial community compositions' coupling with geochemical data across a 3D space. We demonstrate that stochastic processes operating at continental scales and environmental filtering at local scales drive the formation of patchy habitats and the pattern of diversification for microbes in terrestrial MVs.
Ulrich Harms, Ulli Raschke, Flavio S. Anselmetti, Michael Strasser, Volker Wittig, Martin Wessels, Sebastian Schaller, Stefano C. Fabbri, Richard Niederreiter, and Antje Schwalb
Sci. Dril., 28, 29–41, https://doi.org/10.5194/sd-28-29-2020, https://doi.org/10.5194/sd-28-29-2020, 2020
Short summary
Short summary
Hipercorig is a new modular lake sediment coring instrument based on a barge and a hydraulic corer system driven by a down-the-hole hammer. Hipercorig's performance was tested on the two periglacial lakes, namely Mondsee and Constance, located on the northern edge of the Alpine chain. Up to 63 m of Holocene lake sediments and older meltwater deposits from the last deglaciation were recovered for the first time.
Aurèle Vuillemin, André Friese, Richard Wirth, Jan A. Schuessler, Anja M. Schleicher, Helga Kemnitz, Andreas Lücke, Kohen W. Bauer, Sulung Nomosatryo, Friedhelm von Blanckenburg, Rachel Simister, Luis G. Ordoñez, Daniel Ariztegui, Cynthia Henny, James M. Russell, Satria Bijaksana, Hendrik Vogel, Sean A. Crowe, Jens Kallmeyer, and the Towuti Drilling Project
Science team
Biogeosciences, 17, 1955–1973, https://doi.org/10.5194/bg-17-1955-2020, https://doi.org/10.5194/bg-17-1955-2020, 2020
Short summary
Short summary
Ferruginous lakes experience restricted primary production due to phosphorus trapping by ferric iron oxides under oxic conditions. We report the presence of large crystals of vivianite, a ferrous iron phosphate, in sediments from Lake Towuti, Indonesia. We address processes of P retention linked to diagenesis of iron phases. Vivianite crystals had light Fe2+ isotope signatures and contained mineral inclusions consistent with antecedent processes of microbial sulfate and iron reduction.
Julia Mitzscherling, Fabian Horn, Maria Winterfeld, Linda Mahler, Jens Kallmeyer, Pier P. Overduin, Lutz Schirrmeister, Matthias Winkel, Mikhail N. Grigoriev, Dirk Wagner, and Susanne Liebner
Biogeosciences, 16, 3941–3958, https://doi.org/10.5194/bg-16-3941-2019, https://doi.org/10.5194/bg-16-3941-2019, 2019
Short summary
Short summary
Permafrost temperatures increased substantially at a global scale, potentially altering microbial assemblages involved in carbon mobilization before permafrost thaws. We used Arctic Shelf submarine permafrost as a natural laboratory to investigate the microbial response to long-term permafrost warming. Our work shows that millennia after permafrost warming by > 10 °C, microbial community composition and population size reflect the paleoenvironment rather than a direct effect through warming.
Laura Perrin, Ian Probert, Gerald Langer, and Giovanni Aloisi
Biogeosciences, 13, 5983–6001, https://doi.org/10.5194/bg-13-5983-2016, https://doi.org/10.5194/bg-13-5983-2016, 2016
Short summary
Short summary
Coccolithophores are calcifying marine algae that play an important role in the oceanic carbon cycle. Deep niches of coccolithophores exist in the ocean and are poorly understood. Laboratory cultures with the coccolithophore Emiliania huxleyi were carried out to reproduce the environmental conditions (light–nutrient limitation) of a deep niche in the South Pacific Ocean. Physiological modelling of experimental results allows us to estimate the growth rates of coccolithophores in this niche.
Anh Phuong Tran, Baptiste Dafflon, Susan S. Hubbard, Michael B. Kowalsky, Philip Long, Tetsu K. Tokunaga, and Kenneth H. Williams
Hydrol. Earth Syst. Sci., 20, 3477–3491, https://doi.org/10.5194/hess-20-3477-2016, https://doi.org/10.5194/hess-20-3477-2016, 2016
Short summary
Short summary
Quantifying water and heat fluxes in the shallow subsurface is particularly important due to their strong control on recharge, evaporation and biogeochemical processes. This study developed and tested a new inversion scheme to estimate subsurface hydro-thermal parameters by joint using different hydrological, thermal and geophysical data. It is especially useful for the increasing number of studies that are taking advantage of autonomously collected measurements to explore ecosystem dynamics.
James M. Russell, Satria Bijaksana, Hendrik Vogel, Martin Melles, Jens Kallmeyer, Daniel Ariztegui, Sean Crowe, Silvia Fajar, Abdul Hafidz, Doug Haffner, Ascelina Hasberg, Sarah Ivory, Christopher Kelly, John King, Kartika Kirana, Marina Morlock, Anders Noren, Ryan O'Grady, Luis Ordonez, Janelle Stevenson, Thomas von Rintelen, Aurele Vuillemin, Ian Watkinson, Nigel Wattrus, Satrio Wicaksono, Thomas Wonik, Kohen Bauer, Alan Deino, André Friese, Cynthia Henny, Imran, Ristiyanti Marwoto, La Ode Ngkoimani, Sulung Nomosatryo, La Ode Safiuddin, Rachel Simister, and Gerald Tamuntuan
Sci. Dril., 21, 29–40, https://doi.org/10.5194/sd-21-29-2016, https://doi.org/10.5194/sd-21-29-2016, 2016
Short summary
Short summary
The Towuti Drilling Project seeks to understand the long-term environmental and climatic history of the tropical western Pacific and to discover the unique microbes that live in metal-rich sediments. To accomplish these goals, in 2015 we carried out a scientific drilling project on Lake Towuti, located in central Indonesia. We recovered over 1000 m of core, and our deepest core extended 175 m below the lake floor and gives us a complete record of the lake.
Lotta Purkamo, Malin Bomberg, Riikka Kietäväinen, Heikki Salavirta, Mari Nyyssönen, Maija Nuppunen-Puputti, Lasse Ahonen, Ilmo Kukkonen, and Merja Itävaara
Biogeosciences, 13, 3091–3108, https://doi.org/10.5194/bg-13-3091-2016, https://doi.org/10.5194/bg-13-3091-2016, 2016
Short summary
Short summary
The microbial communities of up to 2.3 km depth of Precambrian crystalline bedrock fractures share features with serpenization-driven microbial communities in alkaline springs and subsurface aquifers. This study suggests that phylotypes belonging to Burkholderiales and Clostridia are possible "keystone microbial species" in Outokumpu deep biosphere. Many of the keystone species belong to the rare biosphere with low abundance but a wide range of carbon substrates and a capacity for H2 oxidation.
H. J. Mills, J. de Leeuw, K.-U. Hinrichs, F. Inagaki, and J. Kallmeyer
Sci. Dril., 20, 59–65, https://doi.org/10.5194/sd-20-59-2015, https://doi.org/10.5194/sd-20-59-2015, 2015
Short summary
Short summary
Proceedings and results are presented from the Seoul 2014 Advancing Subsurface Biosphere and Paleoclimate Research workshop. Participants discussed past and present directions of IODP and ICDP subsurface research, including efforts with DCO and IMPRESS. Discussions led to the formation of a level-based communication system with the goal of improving communication and expectations between all drilling disciplines. The production of a biology-themed handbook to guide surface research is planned.
G. Aloisi
Biogeosciences, 12, 4665–4692, https://doi.org/10.5194/bg-12-4665-2015, https://doi.org/10.5194/bg-12-4665-2015, 2015
Short summary
Short summary
Metabolic rates and cell size in coccolithophore algae covary consistently in a large number of separate culture experiments as temperature, irradiance, nutrient and pCO2 conditions change.
These changes are comparable to the changes in cell size observed in the natural environment, both in the modern ocean and in marine sediments.
Changes in coccolithophore cell size in the field will help in understanding how this key phytoplankton species reacts to climate change.
B. N. Orcutt, D. E. LaRowe, K. G. Lloyd, H. Mills, W. Orsi, B. K. Reese, J. Sauvage, J. A. Huber, and J. Amend
Sci. Dril., 17, 61–66, https://doi.org/10.5194/sd-17-61-2014, https://doi.org/10.5194/sd-17-61-2014, 2014
Related subject area
Location/Setting: Continental | Subject: Microbiology | Geoprocesses: Deep biosphere
Microbial diversity of drilling fluids from 3000 m deep Koyna pilot borehole provides insights into the deep biosphere of continental earth crust
Drilling into an active mofette: pilot-hole study of the impact of CO2-rich mantle-derived fluids on the geo–bio interaction in the western Eger Rift (Czech Republic)
Himadri Bose, Avishek Dutta, Ajoy Roy, Abhishek Gupta, Sourav Mukhopadhyay, Balaram Mohapatra, Jayeeta Sarkar, Sukanta Roy, Sufia K. Kazy, and Pinaki Sar
Sci. Dril., 27, 1–23, https://doi.org/10.5194/sd-27-1-2020, https://doi.org/10.5194/sd-27-1-2020, 2020
Short summary
Short summary
Drilling fluid (DF) used in the drilling of crystalline continental crust is considered a potent contaminant for subsurface rock samples, though it could provide a glimpse into the nature of deep subsurface life. Microbial communities of DF retrieved from Koyna pilot borehole (3000 m) in the Deccan Traps was explored through 16S rRNA and other diagnostic marker genes. Detection of extremophilic and other deep biosphere relevant microorganisms in DF redefined the role of DF in deep life research.
Robert Bussert, Horst Kämpf, Christina Flechsig, Katja Hesse, Tobias Nickschick, Qi Liu, Josefine Umlauft, Tomáš Vylita, Dirk Wagner, Thomas Wonik, Hortencia Estrella Flores, and Mashal Alawi
Sci. Dril., 23, 13–27, https://doi.org/10.5194/sd-23-13-2017, https://doi.org/10.5194/sd-23-13-2017, 2017
Cited articles
Andersen, D. T., Pollard, W. H., and McKay, C. P.: The perennial springs of Axel Heiberg Island as an analogue for groundwater discharge on Mars, in: Ninth international conference on permafrost, edited by: Kane, D. L. and Hinkel, K. M., Fairbanks, Alaska, Institute of Northern Engineering, University of Alaska Fairbanks, 43–48, 2008.
Baker, B. J. and Dick, G. J.: Omic approaches in microbial ecology: charting the unknown, Microbe, 8, 353–360, 2013.
Bastin, E. S., Greer, F. E., Merritt, C. A., and Moulton, G.: The presence of sulphate reducing bacteria in oil field waters, Science, 63, 21–24, 1926.
Borgonie, G., García-Moyano, A., Litthauer, D., Bert, W., Bester, A., van Heerden, E., and Onstott, T. C.: Nematoda from the terrestrial deep subsurface of South Africa, Nature, 474, 79–82, https://doi.org/10.1038/nature09974, 2011.
Cathrine, S. J. and Raghukumar, C.: Anaerobic denitrification in fungi from the coastal marine sediments off Goa, India, Mycol. Res., 113, 100–109, https://doi.org/10.1016/j.mycres.2008.08.009, 2009.
Chapelle, F. H., O'Neill, K., Bradley, P. M., Methe, B. A., Ciufo, S. A., Knobel, L. L., and Lovley, D. R.: A hydrogen-based subsurface microbial community dominated by methanogens, Nature, 415, 312–315, https://doi.org/10.1038/415312a, 2002.
Chivian, D., Brodie, E. L., Alm, E. J., Culley, D. E., Dehal, P. S., DeSantis, T. Z., Gihring, T. M., Lapidus, A., Lin, L.-H., Lowry, S. R., Moser, D. P., Richardson, P. M., Southam, G., Wanger, G., Pratt, L. M, Andersen, G. L., Hazen, T. C., Brockman, F. J., Arkin, A. P., and Onstott, T. C.: Environmental genomics reveals a single species ecosystem deep within the Earth, Science, 322, 275–278, https://doi.org/10.1126/science.1155495, 2008.
Collier, M.: An Introduction to the Geology of Death Valley, Death Valley, California, Death Valley Natural History Association, LCN 90-081612, 1990.
Colwell, F. S. and D'Hondt, S.: Nature and Extene of the Deep Biosphere, in: Carbon in Earth. Mineralogical Society of America and Geochemical Society, Reviews in Mineralogy and Geochemistry, edited by: Hazen, R. H., Jones, A. P., and Baross, J. A., 75, 547–566, https://doi.org/10.2138/rmg.2013.75.17, 2013.
Colwell, F. S., Stormberg, G. J., Phelps, T. J., Birnbaum, S. A., McKinley, J. P., Rawson, S. A., Veverka, C., Goodwin, S., Long, P. E., Russell, B. F., Garland, T., Thompson, D., Skinner, P., and Grover, S.: Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization, J. Microbiol. Meth., 15, 279–292, https://doi.org/10.1016/0167-7012(92)90047-8, 1992.
Dahm, T., Hrubcová, P., Fischer, T., Horálek, J., Korn, M., Buske, S., and Wagner, D.: Eger Rift ICDP: an observatory for study of non-volcanic, mid-crustal earthquake swarms and accompanying phenomena, Sci. Dril., 16, 93–99, https://doi.org/10.5194/sd-16-93-2013, 2013.
Deep Carbon Observatory: https://deepcarbon.net//, last access: 14 April 2015.
Edgecomb, V. P., Beaudoin, D., Gast, R., Biddle, J. F., and Teske, A.: Marine subsurface eukaryotes: the fungal majority, Environ. Microbiol., 13, 172–183, https://doi.org/10.1111/j.1462-2920.2010.02318.x, 2011.
Ekendahl, S., O'Neill, A. H., Thomson, E., and Pedersen, K.: Characterisation of yeasts isolated from deep igneous rock aquifers of the Fennoscandian shield, Microb. Ecol., 46, 416–428, https://doi.org/10.1007/s00248-003-2008-5, 2003.
Engelhardt, T., Kallmeyer, J., Cypionka, H., and Engelen, B.: High virus-to-cell ratios indicate on-going production of viruses in deep subsurface sediments, ISME J., 8, 1503–1509, https://doi.org/10.1038/ismej.2013.245, 2014.
Eydal, H. S. C., Jagevall, S., Hermansson, M., and Pedersen, K.: Bacteriophage lytic to Desulfovibrio aespoeensis isolated from deep groundwater, ISME J., 3, 1139–1147, https://doi.org/10.1038/ismej.2009.66, 2009.
Gaidos, E., Marteinsson, V., Thorsteinsson, T., Jóhannesson, T., Rúnarsson, A. R., Stefansson, A., Glazer, B., Lanoil, B., Skidmore, M., Han, S., Miller, M., Rusch, A., and Foo, W.: An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake, ISME J., 3, 486–497, https://doi.org/10.1038/ismej.2008.124, 2009.
GFZ German Research Centre for Geosciences: http://www.gfz-potsdam.de/en/home/, last access: 14 April 2015.
Ginsburg-Karagitscheva, T. L.: Microbiological research in the sulphurous and salty waters of Apsheron, Azerbajdzanskoe Neftjanoe Khozjajstvo, Nos. 6–7, 1926.
Gubernatorova, T. N. and Dolgonosov, B. M.: Modeling the biodegradation of multicomponent organic matter in an aquatic environment: 3. Analysis of lignin degradation mechanisms, Water Resources, 37, 332–346, https://doi.org/10.1134/S0097807810030085, 2010.
Gupta, H., Nayak, S., Ellsworth, W., Rao, Y. J. B., Rajan, S., Bansal, B. K., Purnachandra Rao, N., Roy, S., Arora, K., Mohan, R., Tiwari, V. M., Satyanarayana, H. V. S., Patro, P. K., Shashidhar, D., and Mallika, K.: Probing reservoir-triggered earthquakes in Koyna, India, through scientific deep drilling, Sci. Dril., 18, 5–9, https://doi.org/10.5194/sd-18-5-2014, 2014.
Head, I. M., Jones, D. M., and Larter, S. R.: Biological activity in the deep subsurface and the origin of heavy oil, Nature, 426, 344–352, https://doi.org/10.1038/nature02134, 2003.
Heim, C.: Terrestrial deep biosphere, in: Encyclopedia of geobiology, edited by: Reitner, J., Thiel, V., and Dordrecht, The Netherlands, Springer Science+Business Media B.V., 871–876, 2011.
Horsfield, B., Kieft, T. L., Amann, H., Franks, S. G., Kallmeyer, J., Mangelsdorf, K., Parkes, R. J., Wagner, D., Wilkes, H., and Zink, K.-G.: The GeoBiosphere, in: Continental scientific drilling: A decade of progress and challenges for the future, edited by: Harms, U., Koeberl, C., and Zoback, M. D., Berlin, Heidelberg, New York, Springer, 163–211, 2007.
Horsfield, B., Knebel, C., Ludden, J., and Hyndman, R. (Eds.): Unraveling the complexities of planet earth: science plan for 2014–2019, Potsdam, Germany, International Continental Scientific Drilling Program, 2014.
International Continental Scientific Drilling Program: http://www.icdp-online.org/, last access: 14 April 2015.
International Ocean Discovery Program: http://www.iodp.org/, last access: 14 April 2015.
Kallmeyer, J. and Kieft, T. L.: The ubiqiutous hidden biosphere, in: unraveling the complexities of planet earth: science plan for 2014–2019, edited by: Horsfield, B., Knebel, C., Ludden, J., and Hyndman, R., Potsdam, Germany, International Continental Scientific Drilling Program, 56–65, 2014.
Kelemen, P., Al Rajhi, A., Godard, M., Ildefonse, B., Köpke, J., MacLeod, C., Manning, C., Michibayashi, K., Nasir, S., Shock, E., Takazawa, E., and Teagle, D.: Scientific drilling and related research in the Samail ophiolite, Sultanate of Oman. Sci. Dril., 15, 64–71, https://doi.org/10.2204/iodp.sd.15.10.2013, 2013.
Kieft, T. L.: Sampling the deep sub-surface using drilling and coring techniques, in: Microbiology of hydrocarbons and lipids, edited by: Timmis, K. N., Berlin, Springer Verlag, 3427–3441, 2010.
Kieft, T. L.: Microbiology of the deep continental biosphere. Ch. 6, in: Advances in environmental microbiology, Volume 1, Their world: a diversity of environments, edited by: Hurst, C. J., New York, Springer, in press, 2015a.
Kieft, T. L.: Sampling the subsurface, in: Hydrocarbons and lipid microbiology, edited by: McGenity, C. J., Timmis, K. M., and Nogales, B., Heidelberg, Springer Protocols Handbooks, Springer-Verlag, in press, 2015b.
Kieft, T. L., Phelps, T. J., and Fredrickson, J. K.: Drilling, coring, and sampling subsurface environments, in: Manual of environmental microbiology, Third Edition, edited by: Hurst, C. J., Washington, D. C., ASM Press, 799–817, 2007.
Krumholz, L. R., McKinley, J. P., Ulrich, G. A., and Suflita, J. M.: Confined subsurface microbial communities in Cretaceous rock, Nature, 386, 64–66, https://doi.org/10.1038/386064a0, 1997.
Kyle, J. E., Eydal, H. S. C., Ferris, F. G., and Pedersen, K.: Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden, ISME J., 2, 571–574, https://doi.org/10.1038/ismej.2008.18, 2008.
Lau, M. C. Y., Cameron, C., Magnabosco, C., Brown, C. T., Schilkey, F., Grim, S., Hendrickson, S., Pullin, M., Sherwood Lollar, B., van Heerden, E., Kieft, T. L., and Onstott, T. C.: Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships, Front. Microbiol., 5, 531, https://doi.org/10.3389/fmicb.2014.00531, 2014.
Lavalleur, H. J. and Colwell, F. S.: Microbial characterization of basalt formation waters targeted for geological carbon sequestration, FEMS Microbiol. Ecol., 85, 62–73, https://doi.org/10.1111/1574-6941.12098, 2013.
Lin, L. H., Wang, P.-L., Rumble, D., Lippmann-Pipke, J., Boice, E., Pratt, L. M., Sherwood Lollar, B., Brodie, E., Hazen, T., Andersen, G., DeSantis, T., Moser, D. P., Kershaw, D., and Onstott, T. C.: Long term biosustainability in a high energy, low diversity crustal biome, Science, 314, 479–482, https://doi.org/10.1126/science.1127376, 2006.
Magnabosco, C., Tekere, M., Lau, M. C. Y., Linage, B., Kuloyo, O., Erasmus, M., Cason, E., van Heerden, E., Borgonie, G., Kieft, T. L., and Onstott, T. L.: Comparisons of the composition and biogeographic distribution of the bacterial communities occupying South African thermal springs with those inhabiting deep subsurface fracture water, Front. Microbiol., 5, 1–17, https://doi.org/10.3389/fmicb.2014.00679, 2014.
McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Murat Eren, A., and Sogin, M. L.: Sewage reflects the distribution of human faecal Lachnospiraceae, Environ. Microbiol., 15, 2213–2227, https://doi.org/10.1111/1462-2920.12092, 2013.
Mormile, M. R., Biesen, M. A., Gutierrez, M. C., Ventosa, A., Pavolich, J. B., Onstott, T. C., and Fredrickson, J. K.: Isolation of Halobacterium salinarum retrieved directly from halite brine inclusions, Environ. Microbiol., 5, 1094–1102, https://doi.org/10.1046/j.1462-2920.2003.00509.x, 2003.
Nagano, Y., Nagahama, T., Hatada, Y., and Nunoura, T.: Fungal diversity in deep-sea sediments – the presence of novel fungal groups, Fungal Ecol., 3, 316–325, https://doi.org/10.1016/j.funeco.2010.01.002, 2010.
National Science Foundation: EarthLab, NSF-sponsored report of underground opportunities in GeoSciences and GeoEngineering, Washington, DC, National Science Foundation, 2003.
Nyyssönen, M., Bomberg, M., Kapanen, A., Nousiainen, A., Pitkänen, P., and Itävaara, M.: Methanogenic and sulphate-reducing microbial communities in deep groundwater of crystalline rock fractures in Olkiluoto, Finland, Geomicrobiol. J., 29, 863–878, https://doi.org/10.1080/01490451.2011.635759, 2012.
Pedersen, K.: Microbial life in deep granitic rock, FEMS Microbiol. Rev., 20, 399–414, 1997.
Pedersen, K., Aringer, J., Eriksson, S., Hallbeck, A., Hallbeck, L., and Johansson, J.: Numbers, biomass and cultivable diversity of microbial populations relate to depth and borehole-specific conditions in groundwater from depths of 4–450 m in Olkiluoto, Finland, ISME J., 2, 760–775, https://doi.org/10.1038/ismej.2008.43, 2008.
Phelps, T. J., Fliermans, C. B., Garland, T. R., Pfiffner, S. M., and White, D. C.: Methods for recovery of deep subsurface sediments for microbiological studies, J. Microbiol. Meth., 9, 267–280, https://doi.org/10.1016/0167-7012(89)90069-9, 1989.
Reitner, J., Schumann, G. A., and Pedersen, K.: Fungi in subterranean environments, in: Fungi in Biogenchemical Cycles, edited by: Gadd, G. J., Cambridge, Cambridge University Press, 788–1002, 2005.
Russell, B. F., Phelps, T. J., Griffin, W. T., and Sargent, K. A.: Procedures for sampling deep subsurface microbial communities in unconsolidated sediments, Ground Water Monitor Rev., 12, 96–104, https://doi.org/10.1111/j.1745-6592.1992.tb00414.x, 1992.
Sahl, J. W., Schmidt, R., Swanner, E. D., Mandernack, K. W., Templeton, A. S., Kieft, T. L., Smith, R. L., Sanford, W. E., Callaghan, R. L., Mitton, J. B., and Spear, J. R.: Subsurface microbial diversity in deep-granitic fracture water in Colorado, Appl. Environ. Microbiol., 74, 143–152, https://doi.org/10.1128/AEM.01133-07, 2008.
Salter, S., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N., and Walker, A. W.: Reagent contamination can critically impact sequence-based microbiome analyses, BioRxiv, 87, 1–12, https://doi.org/10.1101/007187, 2014.
Sinclair, J. L. and Ghiorse, W. C.: Distribution of aerobic bacteria, protozoa, algae, and fungi in deep subsurface sediments, Geomicrobiol. J., 7, 15–31, 1989.
Sleep, N. H., Meibom, A., Fridriksson, T., Coleman, R. G., and Bird, D. K.: H2-rich fluids from serpentinization: geochemical and biotic implications, P. Natl. Acad. Sci. USA, 101, 12818–12823, https://doi.org/10.1073/pnas.0405289101, 2004.
Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A., Staugudigel, H., and Ocean Drilling Program Leg 185 Shipboard Scientific Party: Tracer-based estimates of drilling-induced microbial contamination of deep sea crust, Geomicrobiol. J., 17, 207–219, https://doi.org/10.1080/01490450050121170, 2000a.
Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A., Staugudigel, H., and Ocean Drilling Program Leg 185 Shipboard Scientific Party: Methods for quantifying potential microbial contamination during deep ocean coring, ODP Technical Note 28, 2000b.
Stan-Lotter, H. and Frendihan, S.: Deep biosphere of salt deposits, in: Encyclopedia of geobiology, edited by: Reitner, J. and Thiel, V., Dordrecht, The Netherlands, Springer Science+Business Media B.V., https://doi.org/10.1007/978-1-4020-9212-1, 2011.
Stevens, T. O. and McKinley, J. P.: Lithoautotrophic microbial ecosystems in deep basalt aquifers, Science, 270, 450–454, 1995.
Thomas, J. M., Moser, D. P., Fisher, J. C., Reihle, J., Wheatley, A., Hershey, R. L., Baldino, C., and Weissenfluh, D.: Using water chemistry, isotopes and microbiology to evaluate groundwater sources, flow paths and geochemical reactions in the Death Valley flow system, USA, Procedia Earth and Planetary Science, 7, 842–845, https://doi.org/10.1016/j.proeps.2013.03.033, 2013.
Wang, P.-L., Lin, L.-H., Yu, H.-T., Cheng, T.-W., Song, S.-R., Kuo, L.-W., Yeh, E.-C., Lin, W., and Wang, C.-Y.: Cultivation-based characterization of microbial communities associated with deep sedimentary rocks from Taiwan Chelungpu Drilling Project cores, Terr. Atmos. Ocean. Sci., 18, 395–412, https://doi.org/10.3319/TAO.2007.18.2.395(TCDP), 2007.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J.: Prokaryotes: the unseen majority, P. Natl. Acad. Sci. USA, 95, 6578–6583, 1998.
Wilkins, M. J., Daly, R., Mouser, P. J., Trexler, R., Wrighton, K. C., Sharma, S., Cole, D. R., Biddle, J. F., Denis, E., Fredrickson, J. K., Kieft, T. L., Onstott, T. C., Petersen, L., Pfiffner, S. M., Phelps, T. J., and Schrenk, M. O.: Trends and Future Challenges in Sampling the Deep Terrestrial Biosphere, Frontiers Microbiol., 5, 481, https://doi.org/10.3389/fmicb.2014.00481, 2014.
Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., VerBerkmoes, N. C., Wilkins, M. J., Hettich, R. L., Lipton, M. S., Williams, K. H., Long, P. E., and Banfield, J. F.: Fermentation, hydrogen and sulfur metabolism in multiple uncultivated bacterial phyla, Science, 337, 1661–1665, https://doi.org/10.1126/science.1224041, 2012.
Zoback, M. D. and Emmermann, R. (Eds.): Scientific rationale for the establishment of an international program of continental scientific drilling, Potsdam, International Lithosphere program, Coordinated Committee Continental Drilling (CC4), 150 pp., 1994.
Zobell, C. E.: The role of bacteria in the formation and transformation of petroleum hydrocarbons, Science, 102, 364–369, 1945.
