{"entity": "researcher", "timestamp": "2026-07-13T10:13:33.020Z", "family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "affiliations": ["Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60"}}, "publications": [{"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": "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": "b4a18704cfbc4ac4a6d0e4d56abbcea3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b4a18704cfbc4ac4a6d0e4d56abbcea3"}}, "title": "Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.", "authors": [{"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Mehrshad", "given": "Maliheh", "initials": "M", "orcid": "0000-0002-1108-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/d3eca2f7212a4c67bd7b251fa93848e1.json"}}, {"family": "Delgado", "given": "Luis Fernando", "initials": "LF", "orcid": "0000-0001-7850-5285", "researcher": {"href": "https://publications.scilifelab.se/researcher/c90912060686401482b1079bd8251e60.json"}}, {"family": "Deng", "given": "Ziling", "initials": "Z", "orcid": "0000-0002-6970-6453", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0e06ceb2acf478598cc7080e732cd2b.json"}}, {"family": "Bertilsson", "given": "Stefan", "initials": "S", "orcid": "0000-0002-4265-1835", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c17765c2a9f4383b5383138d11ae93f.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": "2023-05-26", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "21", "pages": "eadg2059", "issn-l": "2375-2548"}, "abstract": "The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.", "doi": "10.1126/sciadv.adg2059", "pmid": "37235649", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10219603"}], "notes": [], "created": "2023-11-27T21:57:15.016Z", "modified": "2024-01-16T13:48:33.355Z"}, {"entity": "publication", "iuid": "551c288a5ec247cc99cca4008efbf761", "links": {"self": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761.json"}, "display": {"href": "https://publications.scilifelab.se/publication/551c288a5ec247cc99cca4008efbf761"}}, "title": "Evaluating metagenomic assembly approaches for biome-specific gene catalogues.", "authors": [{"family": "Delgado", "given": "Luis Fernando", "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"}}], "type": "journal article", "published": "2022-05-06", "journal": {"title": "Microbiome", "issn": "2049-2618", "issn-l": "2049-2618", "volume": "10", "issue": "1", "pages": "72"}, "abstract": "For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly.\n\nThe mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated. The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research.\n\nThe mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples. Video abstract.", "doi": "10.1186/s40168-022-01259-2", "pmid": "35524337", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9074274"}, {"db": "pii", "key": "10.1186/s40168-022-01259-2"}], "notes": [], "created": "2022-08-19T08:37:40.525Z", "modified": "2024-01-16T13:48:36.706Z"}]}