{"entity": "researcher", "timestamp": "2026-09-05T13:59:50.936Z", "family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "affiliations": ["Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176"}}, "publications": [{"entity": "publication", "iuid": "78586428e6d44db2a96ef24198fe1489", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78586428e6d44db2a96ef24198fe1489"}}, "title": "Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.", "authors": [{"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2025-10-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9495", "issn-l": "2041-1723"}, "abstract": "Diverse microorganisms can execute one or more steps in denitrification, during which nitrate or nitrite is successively reduced into nitric oxide, nitrous oxide, and ultimately dinitrogen. Many of the best-characterized denitrifiers are complete denitrifiers capable of executing all steps in the pathway, but their dominance in natural communities and what metabolic traits and environmental factors drive the global distribution of complete vs. partial denitrifiers are unclear. To address this, we conducted a comparative analysis of denitrification genes in 61,293 genomes, 3991 metagenomes, and 413 terrestrial and aquatic metatranscriptomes. We show that partial denitrifiers outnumber complete denitrifiers and the potential to initiate denitrification is more common than the potential to terminate it, particularly in nutrient rich environments. Our results further indicate that complete denitrifiers tend to be fast-growing organisms, favoring organic acid over sugar metabolism, and encoding the ability to oxidize and reduce a broader range of organic and inorganic compounds compared to partial denitrifiers. This suggests complete denitrifiers are metabolically flexible opportunists. Together, our results indicate an environmental footprint on the presence of denitrification genes which favors the genomic potential for partial over complete denitrification in most biomes and highlight that completion of the denitrification pathway is a community effort.", "doi": "10.1038/s41467-025-65319-5", "pmid": "41152293", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12569097"}, {"db": "pii", "key": "10.1038/s41467-025-65319-5"}], "notes": [], "created": "2025-11-28T10:46:06.036Z", "modified": "2025-11-28T10:46:06.107Z"}, {"entity": "publication", "iuid": "e679aca133c2422599ac1891a96c1a05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e679aca133c2422599ac1891a96c1a05"}}, "title": "Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil", "authors": [{"family": "M\u00fcller", "given": "Laura J", "initials": "LJ", "orcid": "0009-0009-5747-2432", "researcher": {"href": "https://publications.scilifelab.se/researcher/11dad561c7e24e68b9ed71a015aa2263.json"}}, {"family": "Alicke", "given": "Mara", "initials": "M", "orcid": "0009-0000-0244-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5d4c9a20fc04322a8babeaded66302f.json"}}, {"family": "Romdhane", "given": "Sana", "initials": "S", "orcid": "0000-0003-0295-2278", "researcher": {"href": "https://publications.scilifelab.se/researcher/494ad3e37974440988db1f7b377bae76.json"}}, {"family": "Pold", "given": "Grace", "initials": "G", "orcid": "0000-0002-7536-3944", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a78bb0a7f6043119b6be5e226983d04.json"}}, {"family": "Jones", "given": "Christopher M", "initials": "CM", "orcid": "0000-0002-2723-6019", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c04ad1e78da45ee8b383fb09fc5d44a.json"}}, {"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal-article", "published": "2025-09-00", "journal": {"title": "Soil Biology and Biochemistry", "issn": "0038-0717", "volume": "208", "pages": "109846", "issn-l": null}, "abstract": null, "doi": "10.1016/j.soilbio.2025.109846", "pmid": null, "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T07:13:11.714Z", "modified": "2025-09-08T07:13:12.028Z"}, {"entity": "publication", "iuid": "f3a2e9a2ed934057bcdb6be6711ac846", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3a2e9a2ed934057bcdb6be6711ac846"}}, "title": "Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.", "authors": [{"family": "Sagha\u00ef", "given": "Aur\u00e9lien", "initials": "A", "orcid": "0000-0002-7069-2159", "researcher": {"href": "https://publications.scilifelab.se/researcher/0341d780c3ad44e3bce819fbc38c0176.json"}}, {"family": "Pold", "given": "Grace", "initials": "G"}, {"family": "Jones", "given": "Christopher M", "initials": "CM"}, {"family": "Hallin", "given": "Sara", "initials": "S", "orcid": "0000-0002-9069-9024", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e3491aec8fe4fbf827e2448c898356e.json"}}], "type": "journal article", "published": "2023-12-12", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "8249", "issn-l": "2041-1723"}, "abstract": "Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.", "doi": "10.1038/s41467-023-44022-3", "pmid": "38086813", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10716430"}, {"db": "pii", "key": "10.1038/s41467-023-44022-3"}], "notes": [], "created": "2024-11-25T10:16:12.005Z", "modified": "2024-11-25T10:16:12.056Z"}]}