Articles | Volume 21, issue 2
https://doi.org/10.5194/bg-21-591-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-21-591-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
26 Jan 2024
Research article |
| 26 Jan 2024
| 26 Jan 2024
Continental scientific drilling and microbiology: (extremely) low biomass in bedrock of central Sweden
George Westmeijer
CORRESPONDING AUTHOR
Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39231 Kalmar, Sweden
Cristina Escudero
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid, Cantoblanco, Calle Nicolás Cabrera 1, 28049 Madrid, Spain
Geomicrobiology Group, Center for Applied Geoscience, University of Tübingen, Schnarrenbergstrasse 94–96, 72076 Tübingen, Germany
Claudia Bergin
Microbial Single Cell Genomics Facility, Science for Life Laboratory, P.O. Box 596, 75123 Uppsala, Sweden
Stephanie Turner
Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39231 Kalmar, Sweden
Magnus Ståhle
Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39231 Kalmar, Sweden
Maliheh Mehrshad
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75005 Uppsala, Sweden
Prune Leroy
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75005 Uppsala, Sweden
Moritz Buck
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75005 Uppsala, Sweden
Pilar López-Hernández
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75005 Uppsala, Sweden
Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
Jens Kallmeyer
Section Geomicrobiology, GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
Ricardo Amils
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid, Cantoblanco, Calle Nicolás Cabrera 1, 28049 Madrid, Spain
Stefan Bertilsson
Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, 75005 Uppsala, Sweden
Mark Dopson
Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Stuvaregatan 4, 39231 Kalmar, Sweden
Related authors
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.
Pankan Linsy, Stefan Sommer, Jens Kallmeyer, Simone Bernsee, Florian Scholz, Habeeb Thanveer Kalapurakkal, and Andrew W. Dale
EGUsphere, https://doi.org/10.5194/egusphere-2025-2905, https://doi.org/10.5194/egusphere-2025-2905, 2025
Short summary
Short summary
Bottom trawling is a fishing method that disturbs the seafloor and affects marine ecosystems. This study conducted experimental trawling and monitored biogeochemical changes over three weeks. Results showed reduced nutrient and alkalinity fluxes, decreased benthic carbon respiration, and disrupted biogeochemical processes. While the decline in alkalinity had only a minor effect on atmospheric CO2, the study highlights the lasting ecological impacts of bottom trawling.
Ellen Schnabel, Aurèle Vuillemin, Cédric C. Laczny, Benoit J. Kunath, André R. Soares, Alexander J. Probst, Rolando Di Primio, Jens Kallmeyer, and the PROSPECTOMICS Consortium
Biogeosciences, 22, 767–784, https://doi.org/10.5194/bg-22-767-2025, https://doi.org/10.5194/bg-22-767-2025, 2025
Short summary
Short summary
This study analysed marine sediment samples from areas with and without minimal hydrocarbon seepage from reservoirs underneath. Depth profiles of dissolved chemical components in the pore water and 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 the detection of hydrocarbon reservoirs.
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.
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.
Cited articles
Amann, R. I., Binder, B. J., Olson, R. J., Chisholm, S. W., Devereux, R., and Stahl, D. A.: Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations, Appl. Environ. Microbiol., 56, 1919–1925, https://doi.org/10.1128/aem.56.6.1919-1925.1990, 1990.
Amils, R., Escudero, C., Oggerin, M., Puente Sánchez, F., Arce Rodríguez, A., Fernández Remolar, D., Rodríguez, N., García Villadangos, M., Sanz, J. L., Briones, C., Sánchez-Román, M., Gómez, F., Leandro, T., Moreno-Paz, M., Prieto-Ballesteros, O., Molina, A., Tornos, F., Sánchez-Andrea, I., Timmis, K., Pieper, D. H., and Parro, V.: Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt, Environ. Microbiol., 25, 428–453, https://doi.org/10.1111/1462-2920.16291, 2023.
Becraft, E. D., Lau Vetter, M. C. Y., Bezuidt, O. K. I., Brown, J. M., Labonté, J. M., Kauneckaite-Griguole, K., Salkauskaite, R., Alzbutas, G., Sackett, J. D., Kruger, B. R., Kadnikov, V., van Heerden, E., Moser, D., Ravin, N., Onstott, T., and Stepanauskas, R.: Evolutionary stasis of a deep subsurface microbial lineage, ISME J., 15, 2830–2842, https://doi.org/10.1038/s41396-021-00965-3, 2021.
Bell, E., Lamminmäki, T., Alneberg, J., Andersson, A. F., Qian, C., Xiong, W., Hettich, R. L., Frutschi, M., and Bernier-Latmani, R.: Active sulfur cycling in the terrestrial deep subsurface, ISME J., 14, 1260–1272, https://doi.org/10.1038/s41396-020-0602-x, 2020.
Bell, E., Lamminmäki, T., Alneberg, J., Qian, C., Xiong, W., Hettich, R. L., Frutschi, M., and Bernier-Latmani, R.: Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface, ISME J., 16, 1583–1593, https://doi.org/10.1038/s41396-022-01207-w, 2022.
Beller, H. R., Chain, P. S. G., Letain, T. E., Chakicherla, A., Larimer, F. W., Richardson, P. M., Coleman, M. A., Wood, A. P., and Kelly, D. P.: The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans, J. Bacteriol., 188, 1473–1488, https://doi.org/10.1128/JB.188.4.1473-1488.2006, 2006.
Bomberg, M., Lamminmäki, T., and Itävaara, M.: Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland, Biogeosciences, 13, 6031–6047, https://doi.org/10.5194/bg-13-6031-2016, 2016.
Borgonie, G., Linage-Alvarez, B., Ojo, A. O., Mundle, S. O. C., Freese, L. B., Van Rooyen, C., Kuloyo, O., Albertyn, J., Pohl, C., Cason, E. D., Vermeulen, J., Pienaar, C., Litthauer, D., Van Niekerk, H., Van Eeden, J., Lollar, B. S., Onstott, T. C., and Van Heerden, E.: Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa, Nat. Commun., 6, 8952, https://doi.org/10.1038/ncomms9952, 2015.
Boylan, A. A., Perez-Mon, C., Guillard, L., Burzan, N., Loreggian, L., Maisch, M., Kappler, A., Byrne, J. M., and Bernier-Latmani, R.: H2-fuelled microbial metabolism in Opalinus Clay, Appl. Clay Sci., 174, https://doi.org/10.1016/j.clay.2019.03.020, 2019.
Braslavsky, I., Hebert, B., Kartalov, E., and Quake, S. R.: Sequence information can be obtained from single DNA molecules, P. Natl. Acad. Sci. USA, 100, 3960–3964, https://doi.org/10.1073/pnas.0230489100, 2003.
Casar, C. P., Kruger, B. R., Flynn, T. M., Masterson, A. L., Momper, L. M., and Osburn, M. R.: Mineral-hosted biofilm communities in the continental deep subsurface, Deep Mine Microbial Observatory, SD, USA, Geobiology, 18, 508–522, https://doi.org/10.1111/gbi.12391, 2020.
Chapelle, F. H., O'Neill, K., Bradley, P. M., Methá, B. A., Ciufo, S. A., Knobel, L. R. 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 Earth, Science, 322, 275–278, https://doi.org/10.1126/science.1155495, 2008.
Dai, X., Wang, Y., Luo, L., Pfiffner, S. M., Li, G., Dong, Z., Xu, Z., Dong, H., and Huang, L.: Detection of the deep biosphere in metamorphic rocks from the Chinese continental scientific drilling, Geobiology, 19, 278–291, https://doi.org/10.1111/gbi.12430, 2021.
Daims, H., Brühl, A., Amann, R., Schleifer, K. H., and Wagner, M.: The domain-specific probe EUB338 is insufficient for the detection of all bacteria: Development and evaluation of a more comprehensive probe set, Syst. Appl. Microbiol., 22, 434–444, https://doi.org/10.1016/S0723-2020(99)80053-8, 1999.
Dutta, A., Dutta Gupta, S., Gupta, A., Sarkar, J., Roy, S., Mukherjee, A., and Sar, P.: Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India, Sci. Rep.-UK, 8, 17459, https://doi.org/10.1038/s41598-018-35940-0, 2018.
Engelhardt, T., Kallmeyer, J., Cypionka, H., and Engelen, B.: High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments, ISME J., 8, 1538, https://doi.org/10.1038/ismej.2013.245, 2014.
Escudero, C., Vera, M., Oggerin, M., and Amils, R.: Active microbial biofilms in deep poor porous continental subsurface rocks, Sci. Rep.-UK, 8, 1538, https://doi.org/10.1038/s41598-018-19903-z, 2018.
Escudero, C., del Campo, A., Ares, J. R., Sánchez, C., Martínez, J. M., Gómez, F., and Amils, R.: Visualizing microorganism-mineral interaction in the Iberian Pyrite Belt subsurface: the Acidovorax case, Front. Microbiol., 11, 572104, https://doi.org/10.3389/fmicb.2020.572104, 2020.
Friese, A., Kallmeyer, J., Kitte, J. A., Martínez, I. M., Bijaksana, S., and Wagner, D.: A simple and inexpensive technique for assessing contamination during drilling operations, Limnol. Oceanogr.-Meth., 15, 200–211, https://doi.org/10.1002/lom3.10159, 2017.
geweaa: geweaa/fractures: Biogeosciences, Version v1.0, Zenodo [code], https://doi.org/10.5281/zenodo.10521982, 2024.
Ghosh, W. and Dam, B.: Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea, FEMS Microbiol. Rev., 33, 999–1043, https://doi.org/10.1111/j.1574-6976.2009.00187.x, 2009.
Gold, T.: The deep, hot biosphere, P. Natl. Acad. Sci. USA, 89, 6045–6049, https://doi.org/10.1073/pnas.89.13.6045, 1992.
Golubic, S., Friedmann, I., and Schneider, J.: The lithobiontic ecological niche, with special reference to microorganisms, J. Sediment. Petrol., 51, 475–478, https://doi.org/10.1306/212f7cb6-2b24-11d7-8648000102c1865d, 1981.
Herlemann, D. P. R., Labrenz, M., Jürgens, K., Bertilsson, S., Waniek, J. J., and Andersson, A. F.: Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea, ISME J., 5, 1571–1579, https://doi.org/10.1038/ismej.2011.41, 2011.
Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., de Bruijn, I., Lundin, D., Andersson, A. F., Bertilsson, S., and Dopson, M.: The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles, Communications Biology, 4, 307, https://doi.org/10.1038/s42003-021-01810-1, 2021.
Hoshino, T., Yilmaz, L. S., Noguera, D. R., Daims, H., and Wagner, M.: Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH, Appl. Environ. Microb., 74, 5068-5077, https://doi.org/10.1128/AEM.00208-08, 2008.
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D. A., Finstad, K. M., Amundson, R., Thomas, B. C., and Banfield, J. F.: A new view of the tree of life, Nat. Microbiol., 1, 16048, https://doi.org/10.1038/nmicrobiol.2016.48, 2016.
Ishii, K., Mußmann, M., MacGregor, B. J., and Amann, R.: An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments, FEMS Microbiol. Ecol., 50, 203–213, https://doi.org/10.1016/j.femsec.2004.06.015, 2004.
Kallmeyer, J.: Contamination control for scientific drilling operations, Adv. Appl. Microbiol., 98, 61–91, https://doi.org/10.1016/bs.aambs.2016.09.003, 2017.
Karnachuk, O. V., Frank, Y. A., Lukina, A. P., Kadnikov, V. V., Beletsky, A. V., Mardanov, A. V., and Ravin, N. V.: Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution, ISME J., 13, 1947–1959, https://doi.org/10.1038/s41396-019-0402-3, 2019.
Kieft, T. L.: Their world: a diversity of microbial environments, in: Microbiology of the deep continental biosphere, Springer, 225–249, https://doi.org/10.1007/978-3-319-28071-4_6, 2016.
Lever, M. A., Alperin, M., Engelen, B., Inagaki, F., Nakagawa, S., Steinsbu, B. O., and Teske, A.: Trends in basalt and sediment core contamination during IODP expedition 301, Geomicrobiol. J., 23, 517–530, https://doi.org/10.1080/01490450600897245, 2006.
Lever, M. A., Torti, A., Eickenbusch, P., Michaud, A. B., Šantl-Temkiv, T., and Jørgensen, B. B.: A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types, Front. Microbiol., 6, 476, https://doi.org/10.3389/fmicb.2015.00476, 2015a.
Lever, M. A., Rogers, K. L., Lloyd, K. G., Overmann, J., Schink, B., Thauer, R. K., Hoehler, T. M., and Jørgensen, B. B.: Life under extreme energy limitation: A synthesis of laboratory- and field-based investigations, FEMS Microbiol. Rev., 39, 688–728, https://doi.org/10.1093/femsre/fuv020, 2015b.
Lopez-Fernandez, M., Westmeijer, G., Turner, S., Broman, E., Ståhle, M., Bertilsson, S., and Dopson, M.: Thiobacillus as a key player for biofilm formation in oligotrophic groundwaters of the Fennoscandian Shield, npj Biofilms Microbiomes, 9, 41, https://doi.org/10.1038/s41522-023-00408-1, 2023.
Lorenz, H., Rosberg, J.-E., Juhlin, C., Bjelm, L., Almqvist, B. S. G., Berthet, T., Conze, R., Gee, D. G., Klonowska, I., Pascal, C., Pedersen, K., Roberts, N. M. W., and Tsang, C.-F.: COSC-1 – drilling of a subduction-related allochthon in the Palaeozoic Caledonide orogen of Scandinavia, Sci. Dril., 19, 1–11, https://doi.org/10.5194/sd-19-1-2015, 2015.
Lorenz, H., Juhlin, C., Rosberg, J.-E., Bazargan, M., Klonowska, I., Kück, J., Lescoutre, R., Rejkjær, S., Westmeijer, G., and Ziemniak, G.: COSC-2 operational report – Operational data sets, GFZ Data Services [data set], https://doi.org/10.5880/ICDP.5054.003, 2021.
Lorenz, H., Rosberg, J.-E., Juhlin, C., Klonowska, I., Lescoutre, R., Westmeijer, G., Almqvist, B. S. G., Anderson, M., Bertilsson, S., Dopson, M., Kallmeyer, J., Kück, J., Lehnert, O., Menegon, L., Pascal, C., Rejkjær, S., and Roberts, N. N. W.: COSC-2 – drilling the basal décollement and underlying margin of palaeocontinent Baltica in the Paleozoic Caledonide Orogen of Scandinavia, Sci. Dril., 30, 43–57, https://doi.org/10.5194/sd-30-43-2022, 2022.
Lundin, D. and Andersson, A.: SBDI Sativa curated 16S GTDB database, SciLifeLab [data set], https://doi.org/10.17044/scilifelab.14869077.v4, 2021.
Magnabosco, C., Ryan, K., Lau, M. C. Y., Kuloyo, O., Sherwood Lollar, B., Kieft, T. L., Van HeerDen, E., and Onstott, T. C.: A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust, ISME J., 10, 730–741, https://doi.org/10.1038/ismej.2015.150, 2016.
Magnabosco, C., Lin, L. H., Dong, H., Bomberg, M., Ghiorse, W., Stan-Lotter, H., Pedersen, K., Kieft, T. L., van Heerden, E., and Onstott, T. C.: The biomass and biodiversity of the continental subsurface, Nat. Geosci., 11, 707–717, https://doi.org/10.1038/s41561-018-0221-6, 2018.
Mangelsdorf, K. and Kallmeyer, J.: Integration of Deep Biosphere Research into the International Continental Scientific Drilling Program, Sci. Dril., 10, 46–55, https://doi.org/10.2204/iodp.sd.10.0.2010, 2010.
Morono, Y., Terada, T., Hoshino, T., and Inagaki, F.: Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities, Appl. Environ. Microbiol., 80, 1985–1994, https://doi.org/10.1128/AEM.04150-13, 2014.
Moter, A. and Göbel, U. B.: Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms, J. Microbiol. Meth., 41, 85–112, https://doi.org/10.1016/S0167-7012(00)00152-4, 2000.
Ohkuma, M. and Kudo, T.: Phylogenetic analysis of the symbiotic intestinal microflora of the termite Cryptotermes domesticus, FEMS Microbiol. Lett., 164, 389–395, https://doi.org/10.1016/S0378-1097(98)00244-4, 1998.
Osterholz, H., Turner, S., Alakangas, L. J., Tullborg, E.-L., Dittmar, T., Kalinowski, B. E., and Dopson, M.: Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield, Nat. Commun., 13, 4837, https://doi.org/10.1038/s41467-022-32457-z, 2022.
Pantke, C., Obst, M., Benzerara, K., Morin, G., Ona-Nguema, G., Dippon, U., and Kappler, A.: Green rust formation during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1, Environ. Sci. Technol., 46, 1439–1446, https://doi.org/10.1021/es2016457, 2012.
Paradis, E. and Schliep, K.: ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R, Bioinformatics, 35, 526–528, https://doi.org/10.1093/bioinformatics/bty633, 2019.
Pedersen, K.: Exploration of deep intraterrestrial microbial life: current perspectives, FEMS Microbiol. Lett., 185, 9–16, https://doi.org/10.1111/j.1574-6968.2000.tb09033.x, 2000.
Pernthaler, A., Pernthaler, J., and Amann, R.: Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms, in: Molecular Microbial Ecology Manual, edited by: Kowalchuk, G. A., de Bruijn, F. J., Head, I. M., Akkermans, A. D. L., and van Elsas, J. D., Kluwer Academic Publishers, 711–726, ISBN: 1402021763, 2008.
Puente-Sánchez, F., Moreno-Paz, M., Rivas, L. A., Cruz-Gil, P., García-Villadangos, M., Gómez, M. J., Postigo, M., Garrido, P., González-Toril, E., Briones, C., Fernández-Remolar, D., Stoker, C., Amils, R., and Parro, V.: Deep subsurface sulfate reduction and methanogenesis in the Iberian Pyrite Belt revealed through geochemistry and molecular biomarkers, Geobiology, 12, 34–47, https://doi.org/10.1111/gbi.12065, 2014.
Puente-Sánchez, F., Arce-Rodríguez, A., Oggerin, M., García-Villadangos, M., Moreno-Paz, M., Blanco, Y., Rodríguez, N., Bird, L., Lincoln, S. A., Tornos, F., Prieto-Ballesteros, O., Freeman, K. H., Pieper, D. H., Timmis, K. N., Amils, R., and Parro, V.: Viable cyanobacteria in the deep continental subsurface, P. Natl. Acad. Sci. USA, 115, 10702–10707, https://doi.org/10.1073/pnas.1808176115, 2018.
Purkamo, L., Kietäväinen, R., Nuppunen-Puputti, M., Bomberg, M., and Cousins, C.: Ultradeep microbial communities at 4.4 km within crystalline bedrock: Implications for habitability in a planetary context, Life, 10, 2, https://doi.org/10.3390/life10010002, 2020.
Rahlff, J., Turzynski, V., Esser, S. P., Monsees, I., Bornemann, T. L. V., Figueroa-Gonzalez, P. A., Schulz, F., Woyke, T., Klingl, A., Moraru, C., and Probst, A. J.: Lytic archaeal viruses infect abundant primary producers in Earth's crust, Nat. Commun., 12, 4642, https://doi.org/10.1038/s41467-021-24803-4, 2021.
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., and Walker, A. W.: Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC Biol., 12, 1–12, https://doi.org/10.1186/s12915-014-0087-z, 2014.
Schliep, K. P.: phangorn: phylogenetic analysis in R, Bioinformatics, 27, 592–593, https://doi.org/10.1093/bioinformatics/btq706, 2011.
Sheik, C. S., Reese, B. K., Twing, K. I., Sylvan, J. B., Grim, S. L., Schrenk, M. O., Sogin, M. L., and Colwell, F. S.: Identification and removal of contaminant sequences from ribosomal gene databases: Lessons from the Census of Deep Life, Front. Microbiol., 9, 840, https://doi.org/10.3389/fmicb.2018.00840, 2018.
Smith, D. C., Spivack, A. J., Fisk, M. R., Haveman, S. A., and Staudigel, H.: Tracer-based estimates of drilling-induced microbial contamination of deep sea crust, Geomicrobiol. J., 17, 207–219, https://doi.org/10.1080/01490450050121170, 2000.
Stahl, D. A. and Amann, R.: Development and application of nucleic acid probes in bacterial systematics, in: Nucleic acid techniques in bacterial systematics, edited by: Stackebrandt, E. and Goodfellow, M., John Wiley & Sons, Chichester, England, 205–248, ISBN 9780471929062, 1991.
Starnawski, P., Bataillon, T., Ettema, T. J. G., Jochum, L. M., Schreiber, L., Chen, X., Lever, M. A., Polz, M. F., Jørgensen, B. B., Schramm, A., and Kjeldsen, K. U.: Microbial community assembly and evolution in subseafloor sediment, P. Natl. Acad. Sci. USA, 114, 2940–2945, https://doi.org/10.1073/pnas.1614190114, 2017.
Straub, D., Blackwell, N., Langarica-Fuentes, A., Peltzer, A., Nahnsen, S., and Kleindienst, S.: Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline, Front. Microbiol., 11, 550420, https://doi.org/10.3389/fmicb.2020.550420, 2020.
Suzuki, Y., Konno, U., Fukuda, A., Komatsu, D. D., Hirota, A., Watanabe, K., Togo, Y., Morikawa, N., Hagiwara, H., Aosai, D., Iwatsuki, T., Tsunogai, U., Nagao, S., Ito, K., and Mizuno, T.: Biogeochemical signals from deep microbial life in terrestrial crust, PLoS One, 9, e113063, https://doi.org/10.1371/journal.pone.0113063, 2014.
Teske, A. and Sørensen, K. B.: Uncultured archaea in deep marine subsurface sediments: Have we caught them all?, ISME J., 2, 3–18, https://doi.org/10.1038/ismej.2007.90, 2008.
Teske, A. P.: The deep subsurface biosphere is alive and well, Trends Microbiol., 13, 402–404, https://doi.org/10.1016/j.tim.2005.07.004, 2005.
Wallner, G., Amann, R., and Beisker, W.: Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms, Cytometry, 14, 136–142, https://doi.org/10.1002/cyto.990140205, 1993.
Wu, X., Holmfeldt, K., Hubalek, V., Lundin, D., Åström, M., Bertilsson, S., and Dopson, M.: Microbial metagenomes from three aquifers in the Fennoscandian Shield terrestrial deep biosphere reveal metabolic partitioning among populations, ISME J., 10, 1192–1203, https://doi.org/10.1038/ismej.2015.185, 2016.
Wu, X., Pedersen, K., Edlund, J., Eriksson, L., Åström, M., Andersson, A. F., Bertilsson, S., and Dopson, M.: Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters, Microbiome, 5, 1–13, https://doi.org/10.1186/S40168-017-0253-Y, 2017.
Yu, Y., Lee, C., and Hwang, S.: Analysis of community structures in anaerobic processes using a quantitative real-time PCR method, Water Sci. Technol., 52, 85–91, https://doi.org/10.2166/wst.2005.0502, 2005.
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.
Rock cores down to 2250 m depth, groundwater-bearing fractures, and drilling fluid were sampled...
Altmetrics
Final-revised paper
Preprint