{"entity": "researcher", "timestamp": "2026-08-13T18:38:56.089Z", "family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "affiliations": ["Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Sciences, Linnaeus University, SE-39231 Kalmar, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8"}}, "publications": [{"entity": "publication", "iuid": "fd07d95de9ab4362b25137d754c76efa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fd07d95de9ab4362b25137d754c76efa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fd07d95de9ab4362b25137d754c76efa"}}, "title": "Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.", "authors": [{"family": "Rahlff", "given": "Janina", "initials": "J", "orcid": "0000-0002-2132-2709", "researcher": {"href": "https://publications.scilifelab.se/researcher/e809f7c550ab411cbb5f861dbb104a81.json"}}, {"family": "Wietz", "given": "Matthias", "initials": "M"}, {"family": "Giebel", "given": "Helge-Ansgar", "initials": "HA", "orcid": "0000-0002-9452-0810", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e5f611e48b4488b8cb33f393f83d1ac.json"}}, {"family": "Bayfield", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1421-7780", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb071bf951644667b670a0c00f869e46.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K"}, {"family": "Kieft", "given": "Kristopher", "initials": "K"}, {"family": "Anantharaman", "given": "Karthik", "initials": "K", "orcid": "0000-0002-9584-2491", "researcher": {"href": "https://publications.scilifelab.se/researcher/607abfd9013345a7965b5ade8d16c317.json"}}, {"family": "Ribas-Ribas", "given": "Mariana", "initials": "M", "orcid": "0000-0003-3318-5462", "researcher": {"href": "https://publications.scilifelab.se/researcher/40d063dbf04843998bba87236c5a4e77.json"}}, {"family": "Schweitzer", "given": "Hannah D", "initials": "HD"}, {"family": "Wurl", "given": "Oliver", "initials": "O"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Antson", "given": "Alfred", "initials": "A"}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2023-09-18", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "3", "issue": "1", "pages": "97", "issn-l": null}, "abstract": "Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.", "doi": "10.1038/s43705-023-00307-8", "pmid": "37723220", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10507051"}, {"db": "pii", "key": "10.1038/s43705-023-00307-8"}], "notes": [], "created": "2023-10-19T13:56:47.904Z", "modified": "2024-01-16T13:48:32.239Z"}, {"entity": "publication", "iuid": "3d2c0be8738f4321b47129d5ca7625b1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d2c0be8738f4321b47129d5ca7625b1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d2c0be8738f4321b47129d5ca7625b1"}}, "title": "Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.", "authors": [{"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Li", "given": "Ke", "initials": "K"}, {"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "issn-l": "1462-2912", "volume": "24", "issue": "5", "pages": "2270-2281"}, "abstract": "Phages modulate bacterial metabolism during infection by regulating gene expression, which influences aquatic nutrient cycling. However, the effects of shifting nutrient regimes are less understood. Here, we analyzed transcriptomes of an ecologically relevant Gammaproteobacterium and its lytic phage in high (HNM) and low (LNM) nutrient medium. Despite different infection characteristics, including reduced burst size and longer latent period in LNM, the phage had a fixed expression profile. Bacterial transcription was instead different depending on nutrient regime, with HNM bacteria focusing on growth while LNM bacteria focused on motility and membrane transport. Additionally, phage infection had a larger effect on bacterial gene expression in LNM compared to HNM, e.g. suppressing increased iron uptake and altering expression of phosphorus uptake genes. Overall, phage infection influenced host metabolism more in LNM, which was more similar to natural conditions, emphasizing the importance of considering natural conditions to understand phage and host ecology.", "doi": "10.1111/1462-2920.15904", "pmid": "35049095", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9305737"}], "notes": [], "created": "2022-03-29T13:48:07.622Z", "modified": "2024-01-16T13:48:36.787Z"}, {"entity": "publication", "iuid": "e61a5dfc16b449178d8a242d4f877960", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e61a5dfc16b449178d8a242d4f877960.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e61a5dfc16b449178d8a242d4f877960"}}, "title": "Dynamics of Baltic Sea phages driven by environmental changes.", "authors": [{"family": "Hoetzinger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-1932-6479", "researcher": {"href": "https://publications.scilifelab.se/researcher/6324668ed1db48a787d75bd996d5358c.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.json"}}, {"family": "Arabi", "given": "Rahaf", "initials": "R"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Pontiller", "given": "Benjamin", "initials": "B"}, {"family": "Hutinet", "given": "Geoffrey", "initials": "G"}, {"family": "Bayfield", "given": "Oliver W", "initials": "OW"}, {"family": "Traving", "given": "Sachia", "initials": "S"}, {"family": "Kisand", "given": "Veljo", "initials": "V"}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Middelboe", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9587-9171", "researcher": {"href": "https://publications.scilifelab.se/researcher/319059b849c144d8883950f014279c59.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}], "type": "journal article", "published": "2021-08-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "23", "issue": "8", "pages": "4576-4594", "issn-l": "1462-2912"}, "abstract": "Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.", "doi": "10.1111/1462-2920.15651", "pmid": "34190387", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:01:12.767Z", "modified": "2024-01-16T13:48:39.004Z"}, {"entity": "publication", "iuid": "d4fea5c68ca349b3b177908157d63c66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4fea5c68ca349b3b177908157d63c66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4fea5c68ca349b3b177908157d63c66"}}, "title": "Phage Biocontrol of Pseudomonas aeruginosa in Water.", "authors": [{"family": "Kauppinen", "given": "Ari", "initials": "A", "orcid": "0000-0001-7354-5595", "researcher": {"href": "https://publications.scilifelab.se/researcher/a964ecc2db484ad6939da041c8abdad9.json"}}, {"family": "Siponen", "given": "Sallamaari", "initials": "S", "orcid": "0000-0002-9206-7979", "researcher": {"href": "https://publications.scilifelab.se/researcher/59731d8093794f81ad530ffbd87c2a7a.json"}}, {"family": "Pitk\u00e4nen", "given": "Tarja", "initials": "T", "orcid": "0000-0002-7591-9148", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7145dda3b464397bd84dfd21f1523f8.json"}}, {"family": "Holmfeldt", "given": "Karin", "initials": "K", "orcid": "0000-0002-6887-6661", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Pursiainen", "given": "Anna", "initials": "A"}, {"family": "Torvinen", "given": "Eila", "initials": "E"}, {"family": "Miettinen", "given": "Ilkka T", "initials": "IT", "orcid": "0000-0002-6729-5507", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff6de31f6b6343d68bbc7e37b43d139f.json"}}], "type": "journal article", "published": "2021-05-17", "journal": {"title": "Viruses", "issn": "1999-4915", "volume": "13", "issue": "5", "pages": "928", "issn-l": "1999-4915"}, "abstract": "Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50-55 min) and burst size (124-134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log10 reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log10) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments.", "doi": "10.3390/v13050928", "pmid": "34067885", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "v13050928"}, {"db": "pmc", "key": "PMC8156286"}], "notes": [], "created": "2021-10-01T09:01:07.571Z", "modified": "2024-01-16T13:48:39.742Z"}, {"entity": "publication", "iuid": "598bd6b5445f44679e26ebb6cb896fe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/598bd6b5445f44679e26ebb6cb896fe5"}}, "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.scilifelab.se/researcher/cd83087872c248fb9e1ed9e0d8e140f8.json"}}, {"family": "Nilsson", "given": "Emelie", "initials": "E", "orcid": "0000-0001-5103-214X", "researcher": {"href": "https://publications.scilifelab.se/researcher/996d4cbfd1f84e5b9f5847e47223c22d.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.scilifelab.se/researcher/7c71c59a5f064f4c84150c7b5cd366ac.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.json"}}, {"family": "Dopson", "given": "Mark", "initials": "M", "orcid": "0000-0002-9622-3318", "researcher": {"href": "https://publications.scilifelab.se/researcher/1dc9cc6dadf6483e88d855dc78709a59.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": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-021-01810-1"}, {"db": "pmc", "key": "PMC7940616"}], "notes": [], "created": "2021-06-09T12:14:33.814Z", "modified": "2024-01-16T13:48:40.474Z"}]}