{"entity": "researcher", "timestamp": "2026-08-25T13:35:52.984Z", "family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "affiliations": ["Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden margarita.lopezfernandez@lnu.se."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/305bfdd98d4043f1a282ed3e8fccb0c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/305bfdd98d4043f1a282ed3e8fccb0c3"}}, "publications": [{"entity": "publication", "iuid": "a2963f84545246eeb086a95cf3705e29", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a2963f84545246eeb086a95cf3705e29.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a2963f84545246eeb086a95cf3705e29"}}, "title": "Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/305bfdd98d4043f1a282ed3e8fccb0c3.json"}}, {"family": "Broman", "given": "Elias", "initials": "E", "orcid": "0000-0001-9005-5168", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/20be199369da4ed094d9730ad1774019.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D", "orcid": "0000-0003-2858-9809", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9f4221d9a214a55a578186d1f9abba1.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fd9423637a54230892379a5b50cf47f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a72a10e2053e458482a99bcc8ac1d405.json"}}], "type": "journal article", "published": "2019-08-13", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "10", "issue": "4", "issn-l": null}, "abstract": "Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two \"modern marine\" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic \"thoroughly mixed\" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or \"geogases.\"IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.", "doi": "10.1128/mBio.01470-19", "pmid": "31409677", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6692508"}, {"db": "pii", "key": "mBio.01470-19"}], "notes": [], "created": "2026-08-20T12:00:30.710Z", "modified": "2026-08-21T09:30:23.096Z"}, {"entity": "publication", "iuid": "676bbddb239b435bb7cf248d41e934cb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/676bbddb239b435bb7cf248d41e934cb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/676bbddb239b435bb7cf248d41e934cb"}}, "title": "Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere.", "authors": [{"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M", "orcid": "0000-0003-3588-6676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/305bfdd98d4043f1a282ed3e8fccb0c3.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Nilsson", "given": "Emelie", "initials": "E"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fd9423637a54230892379a5b50cf47f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a72a10e2053e458482a99bcc8ac1d405.json"}}], "type": "journal article", "published": "2018-11-20", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "9", "issue": "6", "issn-l": null}, "abstract": "The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as \"modern marine,\" and an \"old saline\" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available.IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the \u00c4sp\u00f6 Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.", "doi": "10.1128/mBio.01792-18", "pmid": "30459191", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6247080"}, {"db": "pii", "key": "mBio.01792-18"}], "notes": [], "created": "2026-08-21T12:24:32.096Z", "modified": "2026-08-21T12:24:32.195Z"}]}