{"entity": "researcher", "timestamp": "2026-07-15T16:55:03.792Z", "family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17"}}, "publications": [{"entity": "publication", "iuid": "36ac6e2c75c94614be34596a62cdedbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/36ac6e2c75c94614be34596a62cdedbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/36ac6e2c75c94614be34596a62cdedbf"}}, "title": "Phylogeny-aware comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity.", "authors": [{"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Riedinger", "given": "David J", "initials": "DJ", "orcid": "0009-0002-0221-6772", "researcher": {"href": "https://publications.scilifelab.se/researcher/44aad5ff755241a7b9f8e2c29fa19b8a.json"}}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V", "orcid": "0000-0002-8090-5154", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29935a6fb20407c803cbb6b555573b6.json"}}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR", "orcid": "0000-0002-8100-4649", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a0dc17e46354d5f99250e559b82befe.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M", "orcid": "0000-0001-7751-3187", "researcher": {"href": "https://publications.scilifelab.se/researcher/b652cb5aacc348e0a9a8bb16cfbf83fd.json"}}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Hulterstr\u00f6m", "given": "Jens", "initials": "J", "orcid": "0009-0006-1146-2827", "researcher": {"href": "https://publications.scilifelab.se/researcher/1744cf0e964d4971acc5896e9b218071.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M", "orcid": "0000-0002-7943-8851", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5f532d3f38142478ad0166578ca662b.json"}}, {"family": "Piwosz", "given": "Kasia", "initials": "K", "orcid": "0000-0002-3248-3364", "researcher": {"href": "https://publications.scilifelab.se/researcher/69c75bc4dc65411b9afe81b06a9398fa.json"}}, {"family": "Wo\u017aniczka", "given": "Adam", "initials": "A"}, {"family": "Benterbusch-Brockm\u00f6ller", "given": "Heike", "initials": "H"}, {"family": "Sperlea", "given": "Theodor", "initials": "T", "orcid": "0000-0003-4307-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e0963de222d42eb915c9d5b47c7a1f7.json"}}, {"family": "Dupke", "given": "Susann", "initials": "S", "orcid": "0009-0001-0639-208X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f6184e84afc44098c8d0dc2c84b9443.json"}}, {"family": "Scholz", "given": "Holger C", "initials": "HC", "orcid": "0000-0001-7224-0458", "researcher": {"href": "https://publications.scilifelab.se/researcher/c274e57dfe2a40968e3d9b046e708d26.json"}}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2026-07-08", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "17", "issue": "7", "pages": "e0020526", "issn-l": null}, "abstract": "Vibrio vulnificus, a coastal marine bacterium and opportunistic pathogen, poses increasing health risks due to rising sea water temperatures. While it harbors diverse virulence factors, its disease mechanisms remain poorly understood. To address this, we sequenced 82 environmental isolates from the Baltic Sea and combined them with 325 published genomes (clinical and environmental) for comparative analysis. Phylogenetic reconstruction revealed four major lineages, with Baltic strains restricted to L2 and L4. Clinical and environmental strains were found across all lineages, suggesting phylogeny reflects environmental adaptation more than pathogenicity. Using our newly developed PhyloBOTL pipeline, we identified 128 orthologs enriched in clinical isolates, grouped into 36 co-localization clusters. These include both known and novel virulence candidates, such as chaperone-usher pili, type VI secretion effectors, and spermidine synthases. Some clusters showed convergent loss across clades, implying niche-specific evolution. We also designed PCR primers targeting these genes to aid in the surveillance of pathogenic V. vulnificus strains.IMPORTANCEVibrio vulnificus is a naturally occurring marine bacterium that can cause life-threatening infections, with incidence increasing as coastal waters warm due to climate change. Determining which environmental strains pose the greatest risk remains a major challenge for public health surveillance. By analyzing hundreds of genomes from globally distributed strains, including extensive sampling from the rapidly warming Baltic Sea, this study shows that pathogenic potential is not restricted to specific evolutionary lineages but is instead associated with distinct sets of genes enriched in clinical strains. To support pathogen detection, we developed PCR primers targeting a subset of these clinically associated genes. Together, these findings provide new insight into the molecular basis of V. vulnificus infections and offer practical tools for improved detection, monitoring, and risk assessment of harmful strains in coastal waters and seafood under ongoing climate change.", "doi": "10.1128/mbio.00205-26", "pmid": "42307252", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13348674"}], "notes": [], "created": "2026-07-14T17:40:48.791Z", "modified": "2026-07-14T17:40:49.290Z"}, {"entity": "publication", "iuid": "16a8d45180854dfdb468144fa9775e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16a8d45180854dfdb468144fa9775e34"}}, "title": "Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient", "authors": [{"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fen\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Bengtsson", "given": "Mia M", "initials": "MM"}, {"family": "Gyraite", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Katarzyte", "given": "Marija", "initials": "M"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Martin", "given": "Georg", "initials": "G", "orcid": "0000-0002-5289-6131", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fa7c61072034af188ed3685ce83ca3c.json"}}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2026-04-04", "journal": {"title": "Environ Microbiome", "issn": "2524-6372", "volume": "21", "issue": "1", "issn-l": null}, "abstract": "Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.\n\nAs hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.\n\nOur results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.", "doi": "10.1186/s40793-026-00881-z", "pmid": "41935342", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13067490"}, {"db": "pii", "key": "10.1186/s40793-026-00881-z"}], "notes": [], "created": "2026-04-10T12:05:26.160Z", "modified": "2026-04-16T09:42:39.411Z"}, {"entity": "publication", "iuid": "7ce72a774ad944e293841aa4dca43010", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7ce72a774ad944e293841aa4dca43010.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7ce72a774ad944e293841aa4dca43010"}}, "title": "Temperature, sediment resuspension, and salinity drive the prevalence of Vibrio vulnificus in the coastal Baltic Sea.", "authors": [{"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "V\u00edctor", "initials": "V", "orcid": "0000-0002-8090-5154", "researcher": {"href": "https://publications.scilifelab.se/researcher/a29935a6fb20407c803cbb6b555573b6.json"}}, {"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Gusmao", "given": "Joao Bosco", "initials": "JB"}, {"family": "Delgado-Zambrano", "given": "Luis Fernando", "initials": "LF"}, {"family": "Coll-Garc\u00eda", "given": "Guillem", "initials": "G", "orcid": "0000-0003-2123-4108", "researcher": {"href": "https://publications.scilifelab.se/researcher/5960bdad0e9d4fe2b5b45610cd047c62.json"}}, {"family": "Papazachariou", "given": "Vasiliki", "initials": "V"}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Pansch", "given": "Christian", "initials": "C", "orcid": "0000-0001-8442-4502", "researcher": {"href": "https://publications.scilifelab.se/researcher/50129df0120e441081efa1a9649ffbd5.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-10-16", "journal": {"title": "MBio", "issn": "2150-7511", "volume": "15", "issue": "10", "pages": "e0156924", "issn-l": null}, "abstract": "The number of Vibrio-related infections in humans, e.g., by Vibrio vulnificus, has increased along the coasts of the Baltic Sea. Due to climate change, vibriosis risk is expected to increase. It is, therefore, pertinent to design a strategy for mitigation of the vibriosis threat in the Baltic Sea area, but a prerequisite is to identify the environmental conditions promoting the occurrence of pathogenic Vibrio spp., like V. vulnificus. To address this, we sampled three coastal Baltic sites in Finland, Germany, and Denmark with salinities between 6 and 21 from May to October 2022. The absolute and relative abundances of Vibrio spp. and V. vulnificus in water were compared to environmental conditions, including the presence of the eelgrass Zostera marina, which has been suggested to reduce pathogenic Vibrio species abundance. In the water column, V. vulnificus only occurred at the German station between July and August at salinity 8.1-11.2. Temperature and phosphate (PO43-) were identified as the most influencing factors for Vibrio spp. and V. vulnificus. The accumulation of Vibrio spp. in the sediment and the co-occurrence with sediment bacteria in the water column indicate that sediment resuspension contributed to V. vulnificus abundance. Interestingly, V. vulnificus co-occurred with specific cyanobacteria taxa, as well as specific bacteria associated with cyanobacteria. Although we found no reduction in Vibrio spp. or V. vulnificus associated with eelgrass beds, our study underscores the importance of extended heatwaves and sediment resuspension, which may elevate the availability of PO43-, for Vibrio species levels at intermediate salinities in the Baltic Sea.\n\nElevated sea surface temperatures are increasing the prevalence of pathogenic Vibrio at higher latitudes. The recent increase in Vibrio-related wound infections and deaths along the Baltic coasts is, therefore, of serious health concern. We used culture-independent data generated from three Baltic coastal sites in Denmark, Germany, and Finland from May to October (2022), with a special focus on Vibrio vulnificus, and combined it with environmental data. Our temporal model shows that temperature, combined with sediment resuspension, drives the prevalence of V. vulnificus at intermediate salinities in the coastal Baltic Sea.", "doi": "10.1128/mbio.01569-24", "pmid": "39297655", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11481517"}], "notes": [], "created": "2024-11-25T10:28:33.004Z", "modified": "2025-02-28T14:21:03.290Z"}, {"entity": "publication", "iuid": "81ad9ffc2ee842da9ab47f23725f0cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81ad9ffc2ee842da9ab47f23725f0cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81ad9ffc2ee842da9ab47f23725f0cd9"}}, "title": "Control of Vibrio vulnificus proliferation in the Baltic Sea through eutrophication and algal bloom management", "authors": [{"family": "Riedinger", "given": "David J", "initials": "DJ"}, {"family": "Fern\u00e1ndez-Ju\u00e1rez", "given": "Victor", "initials": "V"}, {"family": "Delgado", "given": "Luis F", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Sperlea", "given": "Theodor", "initials": "T", "orcid": "0000-0003-4307-2963", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e0963de222d42eb915c9d5b47c7a1f7.json"}}, {"family": "Hassenr\u00fcck", "given": "Christiane", "initials": "C", "orcid": "0000-0003-1909-1726", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d2e4404c3844df588509a3efa92a7fa.json"}}, {"family": "Herlemann", "given": "Daniel P R", "initials": "DPR"}, {"family": "Pansch", "given": "Christian", "initials": "C"}, {"family": "Katar\u017eyt\u0117", "given": "Marija", "initials": "M"}, {"family": "Bruck", "given": "Florian", "initials": "F"}, {"family": "Ahrens", "given": "Alwin", "initials": "A"}, {"family": "Rakowski", "given": "Marcin", "initials": "M"}, {"family": "Piwosz", "given": "Kasia", "initials": "K", "orcid": "0000-0002-3248-3364", "researcher": {"href": "https://publications.scilifelab.se/researcher/69c75bc4dc65411b9afe81b06a9398fa.json"}}, {"family": "Stevenson", "given": "Angela", "initials": "A", "orcid": "0000-0001-9487-0047", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4b1330bf98345e8b8f1e63f643929d1.json"}}, {"family": "Reusch", "given": "Thorsten B H", "initials": "TBH", "orcid": "0000-0002-8961-4337", "researcher": {"href": "https://publications.scilifelab.se/researcher/39b27965acd74a7a95e97b77abee769d.json"}}, {"family": "Gyrait\u0117", "given": "Greta", "initials": "G", "orcid": "0000-0002-7079-7997", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9fa8139fbc64e7e990587ca8e5f6d52.json"}}, {"family": "Schulz-Bull", "given": "Detlef", "initials": "D"}, {"family": "Benterbusch-Brockm\u00f6ller", "given": "Heike", "initials": "H"}, {"family": "Kube", "given": "Sandra", "initials": "S"}, {"family": "Dupke", "given": "Susann", "initials": "S"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Labrenz", "given": "Matthias", "initials": "M", "orcid": "0000-0003-3452-8631", "researcher": {"href": "https://publications.scilifelab.se/researcher/38c42f1aada5411281b2bdc4d2f8e934.json"}}], "type": "journal-article", "published": "2024-05-09", "journal": {"title": "Commun Earth Environ", "issn": "2662-4435", "volume": "5", "issue": "1", "issn-l": null}, "abstract": null, "doi": "10.1038/s43247-024-01410-x", "pmid": null, "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-28T14:16:21.117Z", "modified": "2025-12-04T19:40:44.806Z"}, {"entity": "publication", "iuid": "c7dc193c604c4e5fa865e49344129528", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7dc193c604c4e5fa865e49344129528"}}, "title": "New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.", "authors": [{"family": "Bittner", "given": "Meriel J", "initials": "MJ", "orcid": "0000-0002-3798-6315", "researcher": {"href": "https://publications.scilifelab.se/researcher/5abcc332fec3408f996fff6e2470f304.json"}}, {"family": "Bannon", "given": "Catherine C", "initials": "CC", "orcid": "0000-0002-8581-1069", "researcher": {"href": "https://publications.scilifelab.se/researcher/176684868401463e8e36980a8f297ab8.json"}}, {"family": "Rowland", "given": "Elden", "initials": "E", "orcid": "0000-0003-4756-9125", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c1d771d5585492681b9c2a296a78914.json"}}, {"family": "Sundh", "given": "John", "initials": "J", "orcid": "0000-0003-3053-9392", "researcher": {"href": "https://publications.scilifelab.se/researcher/655b68ac26af42ad9fb4dfe0869e15ea.json"}}, {"family": "Bertrand", "given": "Erin M", "initials": "EM", "orcid": "0000-0002-5950-6810", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc79515185fc4304bb690324be48adf2.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Paerl", "given": "Ryan W", "initials": "RW", "orcid": "0000-0003-3980-8181", "researcher": {"href": "https://publications.scilifelab.se/researcher/1267dafcedd84e77aa550169e4340998.json"}}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "issn-l": null, "volume": "4", "issue": "1", "pages": "ycad016"}, "abstract": "Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.", "doi": "10.1093/ismeco/ycad016", "pmid": "38390520", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10881298"}, {"db": "pii", "key": "ycad016"}, {"db": "figshare", "key": "10.6084/m9.figshare.23634429"}], "notes": [], "created": "2024-03-14T11:11:47.095Z", "modified": "2025-02-28T14:18:29.377Z"}, {"entity": "publication", "iuid": "b666d402dd5343929e0fbb695aca0efe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b666d402dd5343929e0fbb695aca0efe"}}, "title": "Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.", "authors": [{"family": "Alneberg", "given": "Johannes", "initials": "J", "orcid": "0000-0002-2467-008X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d517d4f20046c08405f8aeecf4ad2a.json"}}, {"family": "Bennke", "given": "Christin", "initials": "C"}, {"family": "Beier", "given": "Sara", "initials": "S", "orcid": "0000-0003-3707-4487", "researcher": {"href": "https://publications.scilifelab.se/researcher/5358a1e162474073a69b08c32e7c5420.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Quince", "given": "Christopher", "initials": "C"}, {"family": "Ininbergs", "given": "Karolina", "initials": "K"}, {"family": "Riemann", "given": "Lasse", "initials": "L", "orcid": "0000-0001-9207-2543", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fc561d1d5694c4c9fbc9a05dd741e17.json"}}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "J\u00fcrgens", "given": "Klaus", "initials": "K"}, {"family": "Labrenz", "given": "Matthias", "initials": "M"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}], "type": "journal article", "published": "2020-03-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "3", "issue": "1", "pages": "119", "issn-l": "2399-3642"}, "abstract": "The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.", "doi": "10.1038/s42003-020-0856-x", "pmid": "32170201", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-020-0856-x"}, {"db": "pmc", "key": "PMC7070063"}], "notes": [], "created": "2020-07-08T13:04:08.349Z", "modified": "2024-01-16T13:48:42.773Z"}]}