{"entity": "researcher", "timestamp": "2026-07-14T03:48:32.463Z", "family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "affiliations": ["Department of Ecology and Environmental Sciences, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879"}}, "publications": [{"entity": "publication", "iuid": "9bafa70241894ebcab4e2bf9d0640d40", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9bafa70241894ebcab4e2bf9d0640d40"}}, "title": "Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak", "authors": [{"family": "Torstensson", "given": "Anders", "initials": "A", "orcid": "0000-0002-8283-656X", "researcher": {"href": "https://publications.scilifelab.se/researcher/352fd53b3b584caa95ee5ff4405498cf.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Hedblom", "given": "Mikael", "initials": "M"}, {"family": "Jurdzinski", "given": "Krzysztof T", "initials": "KT", "orcid": "0000-0001-9544-5755", "researcher": {"href": "https://publications.scilifelab.se/researcher/896a2f678e3143a2b855c1afa8e93499.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Lindh", "given": "Markus", "initials": "M"}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "Andersson", "given": "Agneta", "initials": "A"}], "type": "journal-article", "published": "2026-05-19", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "16", "issue": "1", "issn-l": "2045-2322"}, "abstract": "Marine phytoplankton monitoring has long relied on microscopy, but DNA metabarcoding has recently emerged as a complementary approach. This study assessed the applicability of DNA metabarcoding of the 18S ribosomal RNA gene in marine monitoring and compared its results with conventional microscopy. We analyzed data from 232 surface water samples from 17 monitoring stations in the Baltic Sea, Kattegat, and Skagerrak. Metabarcoding detected more orders, genera, and species than microscopy, with a 43% overlap in the most common genera identified by both methods. Despite attempts to normalize sequence reads to spike-in DNA or DNA concentrations, the correlations between abundances derived from the two methods were weak, though varied considerably between taxonomic groups and geographical areas. Correlations were consistently stronger when using carbon and biovolume concentrations than cell abundances. Our results highlight the potential of metabarcoding to expand biodiversity assessments and advance our understanding of microbial biodiversity in marine ecosystems. As a complement to microscopy, it can enhance existing monitoring efforts. Future improvements in reference database completeness, adoption of long-read sequencing technologies, and better characterization of gene copy number variability per cell are needed to further extend the applicability of metabarcoding for quantitative analyses.", "doi": "10.1038/s41598-026-48838-z", "pmid": "42156811", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13190673"}, {"db": "pii", "key": "10.1038/s41598-026-48838-z"}], "notes": [], "created": "2026-06-08T17:17:40.513Z", "modified": "2026-07-04T18:59:51.656Z"}, {"entity": "publication", "iuid": "6cf92d6cc0394d27ada92112aeec7a98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6cf92d6cc0394d27ada92112aeec7a98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6cf92d6cc0394d27ada92112aeec7a98"}}, "title": "Retention of essential fatty acids in fish differs by species, habitat use and nutritional quality of prey.", "authors": [{"family": "Bandara", "given": "Tharindu", "initials": "T", "orcid": "0000-0002-7211-6374", "researcher": {"href": "https://publications.scilifelab.se/researcher/75c8f752dfe249199064b480bcfeebcc.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.json"}}, {"family": "Lau", "given": "Danny Chun Pong", "initials": "DCP", "orcid": "0000-0002-3246-7508", "researcher": {"href": "https://publications.scilifelab.se/researcher/28aa8ed05fc64662b9a72cf4bde0e59b.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "13", "issue": "6", "pages": "e10158", "issn-l": "2045-7758"}, "abstract": "Algae-produced long-chain polyunsaturated fatty acids (LC-PUFA; with \u226520 carbon atoms) are key biomolecules for consumer production and animal health. They are transferred to higher trophic levels and accumulated in food chains. However, LC-PUFA accumulation in consumers and their trophic transfer vary with the diet quality and the physiological demand for LC-PUFA of consumers. The goal of this study was to investigate spatial and taxonomic differences in LC-PUFA retention of coastal fish predators that potentially differ in their habitat use (benthic versus pelagic) and prey quality. We analyzed the fatty acid (FA) composition of common fish species, namely roach and European perch, as well as their potential prey from benthic and pelagic habitats in three bays of the northern Baltic Sea. We then assessed whether the fish LC-PUFA retention differed between species and among the study bays with different diet quality, that is, LC-PUFA availability. Our data indicated taxon-specific differences in the retention of LC-PUFA and their precursor FA in fish (i.e., short-chain PUFA with <20 carbon atoms). Perch did not show any spatial variation in the retention of all these FA, while roach showed spatial differences in the retention of docosahexaenoic acid (DHA) and their precursor FA, but not eicosapentaenoic acid (EPA). Data suggest that diet quality and trophic reliance on benthic prey underlay the DHA retention differences in roach. Although the PUFA supply might differ among sites, the low spatial variation in LC-PUFA content of perch and roach indicates that both fishes were able to selectively retain dietary LC-PUFA. Climate change together with other existing human-caused environmental stressors are expected to alter the algal assemblages and lower their LC-PUFA supply for aquatic food webs. Our findings imply that these stressors will pose heterogeneous impacts on different fish predators. We advocate further investigations on how environmental changes would affect the nutritional quality of the basal trophic level, and their subsequent impacts on LC-PUFA retention, trophic ecology, and performance of individual fish species.", "doi": "10.1002/ece3.10158", "pmid": "37274152", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10234757"}, {"db": "pii", "key": "ECE310158"}], "notes": [], "created": "2023-08-30T07:04:25.673Z", "modified": "2025-10-17T13:03:13.901Z"}, {"entity": "publication", "iuid": "c3b67c44bad84085803c8a248a084eca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3b67c44bad84085803c8a248a084eca"}}, "title": "Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.", "authors": [{"family": "Latz", "given": "Meike A C", "initials": "MAC", "orcid": "0000-0002-6583-9291", "researcher": {"href": "https://publications.scilifelab.se/researcher/664c30300eab4888a2e5562e077aab01.json"}}, {"family": "Grujcic", "given": "Vesna", "initials": "V", "orcid": "0000-0002-3322-599X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cd1ed7a2d7e477d8f8c5a340152b36c.json"}}, {"family": "Brugel", "given": "Sonia", "initials": "S", "orcid": "0000-0002-1298-3839", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4ed1cef414e4dec9929e64991b49879.json"}}, {"family": "Lycken", "given": "Jenny", "initials": "J"}, {"family": "John", "given": "Uwe", "initials": "U", "orcid": "0000-0002-1297-4086", "researcher": {"href": "https://publications.scilifelab.se/researcher/76918fd58a374cdcacfe02298e7d29a3.json"}}, {"family": "Karlson", "given": "Bengt", "initials": "B", "orcid": "0000-0002-7524-3504", "researcher": {"href": "https://publications.scilifelab.se/researcher/44722b5ece5b420bb59fdb749833f443.json"}}, {"family": "Andersson", "given": "Agneta", "initials": "A", "orcid": "0000-0001-7819-9038", "researcher": {"href": "https://publications.scilifelab.se/researcher/812b8d6654af4482a308367f052f64c7.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": "2022-08-00", "journal": {"title": "Mol Ecol Resour", "issn": "1755-0998", "issn-l": "1755-098X", "volume": "22", "issue": "6", "pages": "2304-2318"}, "abstract": "High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.", "doi": "10.1111/1755-0998.13623", "pmid": "35437888", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2022-08-19T08:37:10.426Z", "modified": "2024-01-16T13:48:35.514Z"}]}