{"entity": "researcher", "timestamp": "2026-08-14T13:18:55.072Z", "family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "affiliations": ["Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371"}}, "publications": [{"entity": "publication", "iuid": "ee01bdbaa4114eec92a4d6c0407a11d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ee01bdbaa4114eec92a4d6c0407a11d8"}}, "title": "Linking prokaryotic genome size variation to metabolic potential and environment.", "authors": [{"family": "Rodr\u00edguez-Gij\u00f3n", "given": "Alejandro", "initials": "A", "orcid": "0000-0002-1649-6894", "researcher": {"href": "https://publications.scilifelab.se/researcher/d25dfecc53e94af0b79799621f131631.json"}}, {"family": "Buck", "given": "Moritz", "initials": "M", "orcid": "0000-0001-6632-5324", "researcher": {"href": "https://publications.scilifelab.se/researcher/ba68bf651630488dab4d146b11cf612a.json"}}, {"family": "Andersson", "given": "Anders F", "initials": "AF", "orcid": "0000-0002-3627-6899", "researcher": {"href": "https://publications.scilifelab.se/researcher/caa76ee4438d4b4aad386ba8a90448c2.json"}}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}, {"family": "Garcia", "given": "Sarahi L", "initials": "SL", "orcid": "0000-0002-8622-0308", "researcher": {"href": "https://publications.scilifelab.se/researcher/8aabc8c17d5b4ad7872c7380301d4562.json"}}], "type": "journal article", "published": "2023-03-27", "journal": {"title": "ISME COMMUN.", "issn": "2730-6151", "volume": "3", "issue": "1", "pages": "25", "issn-l": null}, "abstract": "While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.", "doi": "10.1038/s43705-023-00231-x", "pmid": "36973336", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10042847"}, {"db": "pii", "key": "10.1038/s43705-023-00231-x"}], "notes": [], "created": "2023-10-04T12:20:23.424Z", "modified": "2024-01-16T13:48:33.810Z"}, {"entity": "publication", "iuid": "29eae759f51142a0816fa030d59f00b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29eae759f51142a0816fa030d59f00b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29eae759f51142a0816fa030d59f00b9"}}, "title": "Effects of Recreational Boating on Microbial and Meiofauna Diversity in Coastal Shallow Ecosystems of the Baltic Sea.", "authors": [{"family": "Iburg", "given": "Sven", "initials": "S", "orcid": "0000-0001-6817-5083", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d0e1b1c752643d89db0cc85f5f668f4.json"}}, {"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Austin", "given": "\u00c5sa N", "initials": "\u00c5N", "orcid": "0000-0002-3560-3245", "researcher": {"href": "https://publications.scilifelab.se/researcher/c949c4312b974aed888ff9693b76cde5.json"}}, {"family": "Hansen", "given": "Joakim P", "initials": "JP", "orcid": "0000-0001-9179-4499", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdf20fc9e0e14e8fb6d45bb5a85d2596.json"}}, {"family": "Ekl\u00f6f", "given": "Johan S", "initials": "JS", "orcid": "0000-0001-6936-0926", "researcher": {"href": "https://publications.scilifelab.se/researcher/74833a1558e142028c95c2feb15bc57b.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2021-10-27", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "6", "issue": "5", "pages": "e0012721", "issn-l": "2379-5042"}, "abstract": "Recreational boating can impact benthic ecosystems in coastal waters. Reduced height and cover of aquatic vegetation in shallow Baltic Sea inlets with high boat traffic have raised concerns about cascading effects on benthic communities in these ecosystems. Here, we characterized the diversity and composition of sediment-associated microbial and meiofaunal communities across five bays subjected to low and high degrees of boating activity and examined the community-environment relationships and association with bay morphometry. We found that recreational boating activity altered meiofauna alpha diversity and the composition of both micro- and meiobenthic communities, and there were strong correlations between community structure and morphometric variables like topographic openness, wave exposure, water surface area, and total phosphorous concentrations. Inlets with high boat traffic showed an increase of bacterial taxa like Hydrogenophilaceae and Burkholderiaceae. Several meiofauna taxa previously reported to respond positively to high levels of suspended organic matter were found in higher relative abundances in the bays with high boat traffic. Overall, our results show that morphometric characteristics of inlets are the strongest drivers of benthic diversity in shallow coastal environments. However, while the effects were small, we found significant effects of recreational boating on benthic community structure that should be considered when evaluating the new mooring projects. IMPORTANCE With the increase of recreational boating activity and development of boating infrastructure in shallow, wave-protected areas, there is growing concern for their impact on coastal ecosystems. In order to properly assess the effects and consider the potential for recovery, it is important to investigate microbial and meiofaunal communities that underpin the functioning of these ecosystems. Here, we present the first study that uses DNA metabarcoding to assess how benthic biodiversity in shallow coastal areas is impacted by recreational boating. Our study shows a relatively small, but significant, effect of recreational boating both on meiofauna alpha diversity and meiofauna and bacterial community composition. However, both meiofauna and bacterial community composition in shallow benthic habitats is mediated to a higher degree by abiotic variables, such as topographic openness, area or size of the inlets, and wave exposure. Despite the fact that the effects were small, such impacts on benthic biodiversity should be considered in the management of coastal shallow habitats.", "doi": "10.1128/mSphere.00127-21", "pmid": "34468165", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8550262"}], "notes": [], "created": "2022-11-09T15:50:58.867Z", "modified": "2024-01-16T13:48:38.177Z"}, {"entity": "publication", "iuid": "bf7e976078d04040bcd472b4d8d7c795", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf7e976078d04040bcd472b4d8d7c795.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf7e976078d04040bcd472b4d8d7c795"}}, "title": "Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.", "authors": [{"family": "Izabel-Shen", "given": "Dandan", "initials": "D", "orcid": "0000-0002-3280-1166", "researcher": {"href": "https://publications.scilifelab.se/researcher/21fcbf89ed644524852f2e12217f5371.json"}}, {"family": "Albert", "given": "S\u00e9r\u00e9na", "initials": "S", "orcid": "0000-0002-7299-7263", "researcher": {"href": "https://publications.scilifelab.se/researcher/32b48bc190fa4bd189e0b9a2f2bad8ef.json"}}, {"family": "Winder", "given": "Monika", "initials": "M", "orcid": "0000-0001-9467-3035", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b09dfb6b68445249b8a93c655433189.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJA", "orcid": "0000-0003-3722-1360", "researcher": {"href": "https://publications.scilifelab.se/researcher/5c2cfb0d7a614432b9dfdfcfa3fc4644.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "14", "pages": "3515-3529", "issn-l": "0962-1083"}, "abstract": "Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial \u03b1-diversity was not affected by POM addition, while bacterial \u03b2-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.", "doi": "10.1111/mec.15984", "pmid": "33993575", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:01:06.266Z", "modified": "2024-01-16T13:48:39.232Z"}]}