Articles | Volume 22, issue 21
https://doi.org/10.5194/bg-22-6275-2025
© Author(s) 2025. 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-22-6275-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
30 Oct 2025
Research article |
| 30 Oct 2025
| 30 Oct 2025
On-site microbiome study of silica structures in a subterranean Mars analog environment
Martina Cappelletti
CORRESPONDING AUTHOR
Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
La Venta Geographic Exploration Association, Treviso, Italy
Giacomo Broglia
Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
Andrea Firrincieli
Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
Ettore Lopo
Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
Alice Checcucci
Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze, Florence, Italy
Daniele Ghezzi
Department of Pharmacy and Biotechnology (FaBit), University of Bologna, Bologna, Italy
Federico Pisani
Theraphosa Exploring Team, Puerto Ordaz, Venezuela
Freddy Vergara
Theraphosa Exploring Team, Puerto Ordaz, Venezuela
Bruno Casarotto
Department of Geosciences, University of Padova, Padova, Italy
Francesco Sauro
La Venta Geographic Exploration Association, Treviso, Italy
Department of Geosciences, University of Padova, Padova, Italy
Cited articles
Aubrecht, R., Brewer-Carías, C., Šmída, B., Audy, M., and Kováčik, L′.: Anatomy of biologically mediated opal speleothems in the World's largest sandstone cave: Cueva Charles Brewer, Chimantá Plateau, Venezuela, Sediment. Geol., 203, 181–195, https://doi.org/10.1016/J.SEDGEO.2007.10.005, 2008.
Aubrecht, R., Barrio-Amorós, C. L., and Breure, A.: Venezuelan tepuis: their caves and biota, KIP Monogr., 2012.
Auler, A. S. and Sauro, F.: Quartzite and quartz sandstone caves of South America, in: Encycl. of Caves (third edn.), https://doi.org/10.1016/B978-0-12-814124-3.00102-3, 850–860, 2019.
Barton, H. A., Giarrizzo, J. G., Suarez, P., Robertson, C. E., Broering, M. J., Banks, E. D., Vaishampayan, P. A., and Venkateswaran, K.: Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c, Front. Microbiol., 5, https://doi.org/10.3389/fmicb.2014.00615, 2014.
Boston, P. J.: Location, location, location! Lava caves on Mars for habitat, resources, and the search for life, J. Cosmol., 12, 3957–3979, 2010.
Boubekri, K., Soumare, A., Mardad, I., Lyamlouli, K., Hafidi, M., Ouhdouch, Y., and Kouisni, L.: The Screening of Potassium- and Phosphate-Solubilizing Actinobacteria and the Assessment of Their Ability to Promote Wheat Growth Parameters, Microorganisms, 9, 1–16, https://doi.org/10.3390/MICROORGANISMS9030470, 2021.
Burton, A. S., Stahl, S. E., John, K. K., Jain, M., Juul, S., Turner, D. J., Harrington, E. D., Stoddart, D., Paten, B., Akeson, M., and Castro-Wallace, S. L.: Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing, Genes, 11, 76, https://doi.org/10.3390/GENES11010076, 2020.
Bushnell, B.: BBMap short read aligner, and other bioinformatic tools, SourceForge [code], https://sourceforge.net/projects/bbmap/files/BBMap_38.98.tar.gz/download (last access: 27 October 2025), 2022.
Castro-Wallace, S. L., Chiu, C. Y., John, K. K., Stahl, S. E., Rubins, K. H., McIntyre, A. B. R., Dworkin, J. P., Lupisella, M. L., Smith, D. J., Botkin, D. J., Stephenson, T. A., Juul, S., Turner, D. J., Izquierdo, F., Federman, S., Stryke, D., Somasekar, S., Alexander, N., Yu, G., Mason, C. E., and Burton, A. S.: Nanopore DNA Sequencing and Genome Assembly on the International Space Station, Sci. Reports, 7, 1–12, https://doi.org/10.1038/s41598-017-18364-0, 2017.
Chen, Z., Liu, Y., Wei, H., Xu, J., and Guo, W.: Tube coalescence in the jingfudong lava tube and implications for lava flow hazard of tengchong volcanism, Int. J. Speleol., 45, 219–229, https://doi.org/10.5038/1827-806X.45.3.1987, 2016.
Cockell, C. S., Kelly, L. C., and Marteinsson, V.: Actinobacteria-An Ancient Phylum Active in Volcanic Rock Weathering, Geomicrobiol. J., 30, https://doi.org/10.1080/01490451.2012.758196, 2013.
Curry, K. D., Wang, Q., Nute, M. G., Tyshaieva, A., Reeves, E., Soriano, S., Wu, Q., Graeber, E., Finzer, P., Mendling, W., Savidge, T., Villapol, S., Dilthey, A., and Treangen, T. J.: Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads, Nat. Methods, 19, 845, https://doi.org/10.1038/S41592-022-01520-4, 2022.
Daza Brunet, R. and Bustillo Revuelta, M. Á.: Exceptional silica speleothems in a volcanic cave: A unique example of silicification and sub-aquatic opaline stromatolite formation (Terceira, Azores), Sedimentology, 61, 2113–2135, https://doi.org/10.1111/SED.12130, 2014.
De Coster, W., D'Hert, S., Schultz, D. T., Cruts, M., and Van Broeckhoven, C.: NanoPack: visualizing and processing long-read sequencing data, Bioinformatics, 34, https://doi.org/10.1093/bioinformatics/bty149, 2018.
Dhami, N. K., Mukherjee, A., and Watkin, E. L. J.: Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions, Front. Microbiol., 9, 40, https://doi.org/10.3389/FMICB.2018.00040, 2018.
Edwards, A., Soares, A., Rassner, S. M. E., Green, P., Félix, J., and Mitchell, A. C.: Deep Sequencing: Intra-terrestrial metagenomics illustrates the potential of off-grid Nanopore DNA sequencing, bioRxiv, https://doi.org/10.1101/133413, 2017.
Edwards, A., Debbonaire, A. R., Nicholls, S. M., Rassner, S. M. E., Sattler, B., Cook, J. M., Davy, T., Soares, A., Mur, L. A. J., and Hodson, A. J.: In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota, bioRxiv, https://doi.org/10.1101/073965, 2019.
Firrincieli, A.: Cappelletti et al. – On-site microbiome study of stromatolite-like silica structures in a remote cave analog to subterranean Martian environments, figshare [data set], https://doi.org/10.6084/m9.figshare.29514197.v1, 2025.
Ghezzi, D., Sauro, F., Columbu, A., Carbone, C., Hong, P. Y., Vergara, F., De Waele, J., and Cappelletti, M.: Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment, Sci. Rep., 11, 3921, https://doi.org/10.1038/S41598-021-83416-5, 2021.
Ghezzi, D., Foschi, L., Firrincieli, A., Hong, P. Y., Vergara, F., De Waele, J., Sauro, F., and Cappelletti, M.: Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarí Yeutá, Auyan Tepui, Venezuela), Front. Microbiol., 13, 930302, https://doi.org/10.3389/FMICB.2022.930302, 2022.
Ghezzi, D., Jiménez-Morillo, N. T., Foschi, L., Donini, E., Chiarini, V., De Waele, J., Miller, A. Z. and Cappelletti, M.: The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter, Environ Microbiome, 19, 25, https://doi.org/10.1186/s40793-024-00562-9, 2024.
Gunnarsson, I. and Arnórsson, S.: Amorphous silica solubility and the thermodynamic properties of
Insam, H.: A New Set of Substrates Proposed for Community Characterization in Environmental Samples, Microb. Communities, 259–260, https://doi.org/10.1007/978-3-642-60694-6_25, 1997.
Johnson, S. S., Zaikova, E., Goerlitz, D. S., Bai, Y., and Tighe, S. W.: Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer, J. Biomol. Tech., 28, 2–7, https://doi.org/10.7171/JBT.17-2801-009, 2017.
Kalam, S., Basu, A., Ahmad, I., Sayyed, R. Z., El-Enshasy, H. A., Dailin, D. J., and Suriani, N. L.: Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review, Front. Microbiol., 11, https://doi.org/10.3389/FMICB.2020.580024, 2020.
Konhauser, K. O., Jones, B., Phoenix, V. R., Ferris, G., and Renaut, R. W.: The microbial role in hot spring silicification, Ambio, 33, 552–558, https://doi.org/10.1579/0044-7447-33.8.552, 2004.
Latorre-Pérez, A., Gimeno-Valero, H., Tanner, K., Pascual, J., Vilanova, C., and Porcar, M.: A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting, Front. Microbiol., 12, https://doi.org/10.3389/FMICB.2021.768240, 2021.
Lundberg, J., Brewer-Carías, C., and McFarlane, D. A.: On biospeleothems from a Venezuelan tepui cave: U-Th dating, growth rates, and morphology, Int. J. Speleol., 47, 6, https://doi.org/10.5038/1827-806X.47.3.2212, 2018.
Maggiori, C., Stromberg, J., Blanco, Y., Goordial, J., Cloutis, E., García-Villadangos, M., Parro, V., and Whyte, L.: The Limits, Capabilities, and Potential for Life Detection with MinION Sequencing in a Paleochannel Mars Analog, Astrobiology, 20, 375–393, https://doi.org/10.1089/ast.2018.1964, 2020.
Martin-Pozas, T., Gonzalez-Pimentel, J. L., Jurado, V., Laiz, L., Cañaveras, J. C., Fernandez-Cortes, A., Cuezva, S., Sanchez-Moral, S., and Saiz-Jimenez, C.: Crossiella, a Rare Actinomycetota Genus, Abundant in the Environment, Appl. Biosci., 2, 194–210, https://doi.org/10.3390/applbiosci2020014, 2023.
Marijon, P., Chikhi, R., and Varré, J. S.: yacrd and fpa: upstream tools for long-read genome assembly, Bioinformatics, 36, https://doi.org/10.1093/bioinformatics/btaa262, 2020.
Mecchia, M., Sauro, F., Piccini, L., De Waele, J., Sanna, L., Tisato, N., Lira, J., and Vergara, F.: Geochemistry of surface and subsurface waters in quartz-sandstones: Significance for the geomorphic evolution of tepui table mountains (Gran Sabana, Venezuela), J. Hydrol., 511, 117–138, https://doi.org/10.1016/j.jhydrol.2014.01.029, 2014.
Miller, A. Z., Pereira, M. F. C., Calaforra, J. M., Forti, P., Dionísio, A., and Saiz-Jimenez, C.: Siliceous Speleothems and Associated Microbe-Mineral Interactions from Ana Heva Lava Tube in Easter Island (Chile), Geomicrobiol. J., 31, https://doi.org/10.1080/01490451.2013.827762, 2014.
Mojarro, A., Hachey, J., Bailey, R., Brown, M., Doebler, R., Ruvkun, G., Zuber, M. T., and Carr, C. E.: Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection, Astrobiology, 19, 1139–1152, https://doi.org/10.1089/AST.2018.1929, 2019.
Naether, A., Foesel, B. U., Naegele, V., Wüst, P. K., Weinert, J., Bonkowski, M., Alt, F., Oelmann, Y., Polle, A., Lohaus, G., Gockel, S., Hemp, A., Kalko, E. K. V., Linsenmair, K. E., Pfeiffer, S., Renner, S., Schöning, I., Weisser, W. W., Wells, K., Fischer, M., Overmann, J., and Friedrich, M. W.: Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils, Appl. Environ. Microbiol., 78, 7398–7406, https://doi.org/10.1128/AEM.01325-12, 2012.
Nayeli Luis-Vargas, M., Webb, J., White, S., and Bay, S. K.: Linking Surface and Subsurface: The Biogeochemical Basis of Cave Microbial Ecosystem Services, J. Sustain. Agric. Environ., 3, e70031, https://doi.org/10.1002/sae2.70031, 2024.
O'Connor, B. R. W., Fernández-Martínez, M. Á., Léveillé, R. J., and Whyte, L. G.: Taxonomic Characterization and Microbial Activity Determination of Cold-Adapted Microbial Communities in Lava Tube Ice Caves from Lava Beds National Monument, a High-Fidelity Mars Analogue Environment, Astrobiology, 21, 613–627, https://doi.org/10.1089/AST.2020.2327, 2021.
Peresini, P., Boza, V., Brejova, B., and Vinar, T.: Nanopore base calling on the edge, Bioinformatics, 37, 4661, https://doi.org/10.1093/bioinformatics/btab528, 2021.
Perujo, N., Romaní, A. M., and Martín-Fernández, J. A.: Microbial community-level physiological profiles: Considering whole data set and integrating dynamics of colour development, Ecol. Indic., 117, 106628, https://doi.org/10.1016/J.ECOLIND.2020.106628, 2020.
Quintela, I. A., Vasse, T., Lin, C. S., and Wu, V. C. H.: Advances, applications, and limitations of portable and rapid detection technologies for routinely encountered foodborne pathogens, Front. Microbiol., 13, 1054782, https://doi.org/10.3389/FMICB.2022.1054782, 2022.
Ruff, S. W. and Farmer, J. D.: Silica deposits on Mars with features resembling hot spring biosignatures at El Tatio in Chile, Nat. Commun., 7, 13554, https://doi.org/10.1038/ncomms13554, 2016.
Ruff, S. W., Farmer, J. D., Calvin, W. M., Herkenhoff, K. E., Johnson, J. R., Morris, R. V., Rice, M. S., Arvidson, R. E., Bell, J. F., Christensen, P. R., and Squyres, S. W.: Characteristics, distribution, origin, and significance of opaline silica observed by the Spirit rover in Gusev crater, Mars, J. Geophys. Res.-Planets, 116, https://doi.org/10.1029/2010JE003767, 2011.
Sauro, F.: Structural and lithological guidance on speleogenesis in quartz-sandstone: Evidence of the arenisation process, Geomorphology, 226, 106–123, https://doi.org/10.1016/j.geomorph.2014.07.033, 2014.
Sauro, F., Lundberg, J., De Waele, J., Tisato, N., and Galli, E.: Speleogenesis and speleothems of the Guacamaya Cave, Auyán Tepui, Venezuela, in: Proceedings of the 16th International Congress of Speleology (ICS 2013), Brno, Czech Republic, 21–28 July 2013, Czech Speleological Society, 3, 298–304, ISBN 978-80-87857-09-0, 2013.
Sauro, F., Tisato, N., De Waele, J., Bernasconi, S. M., Bontognali, T. R. R., and Galli, E.: Source and genesis of sulphate and phosphate-sulphate minerals in a quartz-sandstone cave environment, Sedimentology, 61, 1433–1451, https://doi.org/10.1111/sed.12103, 2014.
Sauro, F., Cappelletti, M., Ghezzi, D., Columbu, A., Hong, P. Y., Zowawi, H. M., Carbone, C., Piccini, L., Vergara, F., Zannoni, D., and De Waele, J.: Microbial diversity and biosignatures of amorphous silica deposits in orthoquartzite caves, Sci. Rep., 8, 1–14, https://doi.org/10.1038/s41598-018-35532-y, 2018.
Sauro, F., Mecchia, M., Piccini, L., De Waele, J., Carbone, C., Columbu, A., Pisani, L., and Vergara, F.: Genesis of giant sinkholes and caves in the quartz sandstone of Sarisariñama tepui, Venezuela, Geomorphology, 342, 223–238, https://doi.org/10.1016/j.geomorph.2019.06.017, 2019.
Smith, M. R., Bandfield, J. L., Cloutis, E. A., and Rice, M. S.: Hydrated silica on Mars: Combined analysis with near-infrared and thermal-infrared spectroscopy, Icarus, 223, 633–648, https://doi.org/10.1016/J.ICARUS.2013.01.024, 2013.
Theodorescu, M., Bucur, R., Bulzu, P. A., Faur, L., Levei, E. A., Mirea, I. C., Cadar, O., Ferreira, R. L., Souza-Silva, M., and Moldovan, O. T.: Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves, Microb. Ecol., 86, 2847–2857, https://doi.org/10.1007/S00248-023-02286-8, 2023.
Wick, R.: Porechop, GitHub [code], https://github.com/rrwick/Porechop/releases/tag/v0.2.4 (last access: 27 October 2025), 2018.
Wray, R. A. L. and Sauro, F.: An updated global review of solutional weathering processes and forms in quartz sandstones and quartzites, Earth-Science Rev., 171, 520–557, https://doi.org/10.1016/J.EARSCIREV.2017.06.008, 2017.
Xu, Z., Mai, Y., Liu, D., He, W., Lin, X., Xu, C., Zhang, L., Meng, X., Mafofo, J., Zaher, W. A., Koshy, A., Li, Y., and Qiao, N.: Fast-bonito: A faster deep learning based basecaller for nanopore sequencing, Artif. Intell. Life Sci., 1, 100011, https://doi.org/10.1016/J.AILSCI.2021.100011, 2021.
Short summary
In this work, we developed, applied and validated on-site microbiological procedures to study the unique silica stromatolite-like structures present in orthoquartzite caves on venezuelan tepuis. The results prove them as promising terrestrial astrobiological analogues, validate the feasibility of real-time microbial analyses in remote caves and provide novel understanding on the microbiological aspects involved in the formation of silica stromatolites in non-thermal and aphotic environments.
In this work, we developed, applied and validated on-site microbiological procedures to study...
Altmetrics
Final-revised paper
Preprint