{"entity": "researcher", "timestamp": "2026-10-01T23:07:26.965Z", "family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "affiliations": ["Bioinformatics Infrastructure for Life Sciences (BILS), Stockholm 171 65, Sweden.", "KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm 171 65, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba404f9f9f414b9d94c4ef5634effa90.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba404f9f9f414b9d94c4ef5634effa90"}}, "publications": [{"entity": "publication", "iuid": "76fd8f4798c7498e9465465394b0ccd2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76fd8f4798c7498e9465465394b0ccd2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76fd8f4798c7498e9465465394b0ccd2"}}, "title": "The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.", "authors": [{"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/91cc3035b9b946509a68a0da5c717054.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c8518859ab4481d94809411940e8ada.json"}}, {"family": "Simone", "given": "Domenico", "initials": "D"}, {"family": "Lopez-Fernandez", "given": "Margarita", "initials": "M"}, {"family": "Wu", "given": "Xiaofen", "initials": "X"}, {"family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba404f9f9f414b9d94c4ef5634effa90.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/290a3bc9eb554620906b93d7f1d57184.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.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": "2021-03-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "307", "issn-l": "2399-3642"}, "abstract": "The deep biosphere contains members from all three domains of life along with viruses. Here we investigate the deep terrestrial virosphere by sequencing community nucleic acids from three groundwaters of contrasting chemistries, origins, and ages. These viromes constitute a highly unique community compared to other environmental viromes and sequenced viral isolates. Viral host prediction suggests that many of the viruses are associated with Firmicutes and Patescibacteria, a superphylum lacking previously described active viruses. RNA transcript-based activity implies viral predation in the shallower marine water-fed groundwater, while the deeper and more oligotrophic waters appear to be in 'metabolic standby'. Viral encoded antibiotic production and resistance systems suggest competition and antagonistic interactions. The data demonstrate a viral community with a wide range of predicted hosts that mediates nutrient recycling to support a higher microbial turnover than previously anticipated. This suggests the presence of 'kill-the-winner' oscillations creating slow motion 'boom and burst' cycles.", "doi": "10.1038/s42003-021-01810-1", "pmid": "33686191", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7940616"}, {"db": "pii", "key": "10.1038/s42003-021-01810-1"}], "notes": [], "created": "2026-09-23T09:58:02.593Z", "modified": "2026-09-23T10:34:38.655Z"}, {"entity": "publication", "iuid": "3318de8105694b468e842027d916a9e5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3318de8105694b468e842027d916a9e5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3318de8105694b468e842027d916a9e5"}}, "title": "Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.", "authors": [{"family": "Bagnoud", "given": "Alexandre", "initials": "A"}, {"family": "Chourey", "given": "Karuna", "initials": "K"}, {"family": "Hettich", "given": "Robert L", "initials": "RL"}, {"family": "de Bruijn", "given": "Ino", "initials": "I", "orcid": "0000-0001-5427-4750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba404f9f9f414b9d94c4ef5634effa90.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc9be99ec6ca47ed8a805ebb4db7c168.json"}}, {"family": "Leupin", "given": "Olivier X", "initials": "OX"}, {"family": "Schwyn", "given": "Bernhard", "initials": "B"}, {"family": "Bernier-Latmani", "given": "Rizlan", "initials": "R"}], "type": "journal article", "published": "2016-10-14", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "7", "issue": null, "pages": "12770", "issn-l": "2041-1723"}, "abstract": "The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.", "doi": "10.1038/ncomms12770", "pmid": "27739431", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5067608"}, {"db": "pii", "key": "ncomms12770"}], "notes": [], "created": "2018-12-05T11:05:47.880Z", "modified": "2026-09-23T07:37:11.143Z"}]}