{"entity": "researcher", "timestamp": "2026-07-17T08:18:30.989Z", "family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "affiliations": ["Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83"}}, "publications": [{"entity": "publication", "iuid": "db4d0488321c44809973ce6d788f31cf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db4d0488321c44809973ce6d788f31cf"}}, "title": "Seasonal dynamics and nutrient controls of biogenic silica in Baltic Sea surface microplankton and picoplankton communities.", "authors": [{"family": "Churakova", "given": "Yelena", "initials": "Y", "orcid": "0000-0002-8017-2122", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e4b7f5ea6e243b6b08008cdfa88c07f.json"}}, {"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Charalampous", "given": "Evangelia", "initials": "E", "orcid": "0000-0002-7724-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c7828275bf44408584d66ceeefa6b6.json"}}, {"family": "Conley", "given": "Daniel J", "initials": "DJ", "orcid": "0000-0001-9668-9284", "researcher": {"href": "https://publications.scilifelab.se/researcher/d95efcbb3ce8420494cbc2260d2b1aa1.json"}}, {"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": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}], "type": "journal article", "published": "2025-05-21", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "91", "issue": "5", "pages": "e0067625", "issn-l": "0099-2240"}, "abstract": "In recent years, new contributors to the marine silica cycle have emerged, including pico-sized phytoplankton (<2-3 \u00b5m in size) such as Synechococcus and picoeukaryotes. Their contribution and relevance to silica cycling are still under investigation. Field studies reporting the biogenic silica (bSi) standing stock in the pico-sized fraction are limited to silica-poor oligotrophic environments, and the mechanism of bSi accumulation in picoplankton remains unknown. We investigated the variability of bSi standing stocks in two size fractions (picoplankton, 0.22-3 \u00b5m and microplankton, >3 \u00b5m) in the dissolved silica-replete Baltic Sea via biweekly time series samplings spanning 2 years. Time series data showed that the large changes in bSi standing stock in the Baltic Proper were primarily related to microplankton biomass and community composition. Meanwhile, picoplankton were, at times, surprisingly high contributors to total bSi year-round (up to 21.6%). Simultaneously, we performed microcosm incubation experiments with natural phytoplankton communities in each season to examine how nutrient additions affected bSi concentrations. In these experiments, increases in microplankton bSi were directly correlated to increases in diatom biomass, highlighting their influential role in the Baltic Sea silica cycle. Meanwhile, phosphorus additions triggered an increase in picoplankton bSi accumulation in all experiments. This uncovers a potential control of bSi accumulation in picoplankton, which can help identify the cellular mechanisms behind this process and uncover their role in silica cycling. The results link phytoplankton community composition and silica cycling, which is important for understanding the consequences of organism shifts due to climate change.IMPORTANCEThe marine carbon and silica cycles are tightly intertwined and largely controlled by diatoms. Nevertheless, recent studies, mostly in oligotrophic waters, have proposed new contributors to the marine silica cycle: picoplankton. Here, we report the first study of seasonal dynamics of biogenic silica (bSi) standing stock in microplankton and picoplankton in the silica-replete Baltic Sea. Microplankton bSi dynamics were correlated with changes in composition and biomass. Picoplankton were consistent contributors to bSi, and for the first time in diverse natural communities, we found a direct correlation between phosphorus and bSi accumulation. The results are important for understanding how climate change-predicted phytoplankton composition shifts will affect carbon and silica cycling and provide a direction for future research on nutrient controls of silica accumulation in picoplankton.", "doi": "10.1128/aem.00676-25", "pmid": "40293244", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12094022"}], "notes": [], "created": "2025-11-26T08:38:35.731Z", "modified": "2025-11-26T08:38:36.366Z"}, {"entity": "publication", "iuid": "bf30bef38e144822aa0db8832eae0142", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bf30bef38e144822aa0db8832eae0142"}}, "title": "The evaluation of biogenic silica in brackish and freshwater strains reveals links between phylogeny and silica accumulation in picocyanobacteria.", "authors": [{"family": "Aguilera", "given": "Anabella", "initials": "A", "orcid": "0000-0001-6743-3001", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6e88f127e7d49d09f593a57aa4a794e.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Charalampous", "given": "Evangelia", "initials": "E"}, {"family": "Churakova", "given": "Yelena", "initials": "Y"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "\u015aliwi\u0144ska-Wilczewska", "given": "Sylwia", "initials": "S"}, {"family": "Conley", "given": "Daniel J", "initials": "DJ"}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2025-04-23", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "issn-l": "0099-2240", "volume": "91", "issue": "4", "pages": "e0252724"}, "abstract": "Through biosilicification, organisms incorporate dissolved silica (dSi) and deposit it as biogenic silica (bSi), driving the silicon (Si) cycle in aquatic systems. While Si accumulation in marine picocyanobacteria has been recently observed, its mechanisms and ecological implications remain unclear. This study investigates biosilicification in marine and brackish picocyanobacteria of the Synechococcus clade and two model freshwater coccoid cyanobacteria. Brackish strains showed significantly higher Si quotas when supplemented with external dSi (100 \u00b5M) compared to controls (up to 60.0 \u00b1 7.3 amol Si.cell-1 versus 9.2 to 16.3 \u00b1 2.9 amol Si.cell-1). Conversely, freshwater strains displayed no significant differences in Si quotas between dSi-enriched treatments and controls, emphasizing that not all phytoplanktons without an obligate Si requirement accumulate this element. The Si-accumulating marine and brackish picocyanobacteria clustered within the Synechococcus clade, whereas their freshwater counterparts formed a distinct sister group, suggesting a link between phylogeny and silicification. Rapid culture growth caused increased pH and led to dSi precipitation, influencing apparent dSi uptake; this was mitigated by pH control through bubbling. This phenomenon has significant implications for natural systems affected by phytoplankton blooms. In such environments, pH-induced silicon precipitation may reduce dSi availability impacting Si-dependent populations like diatoms. Our findings suggest brackish picocyanobacteria could significantly influence the Si cycle through at least two mechanisms: cellular Si accumulation and biologically induced changes in dSi concentrations.IMPORTANCEThis work provides the first evidence of biogenic silica accumulation in brackish picocyanobacteria and uncovers a link between phylogeny and biosilicification patterns. Our findings demonstrate that picocyanobacterial growth induces pH-dependent silica precipitation, which could lead to overestimations of cellular Si quotas by up to 85%. This process may drive substantial silica precipitation in highly productive freshwater and coastal marine systems, with potential effects on silica cycling and the population dynamics of Si-dependent phytoplankton. The extent of biosilicification in modern picocyanobacteria offers insights into the rock record, shedding light on the evolutionary and ecological dynamics that influence sedimentary processes and the preservation of biosilicification signatures in geological formations. Overall, this research adds to the significant impact that microorganisms lacking an obligate silica requirement may have on silica dynamics.", "doi": "10.1128/aem.02527-24", "pmid": "40145754", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Short read": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12016540"}], "notes": [], "created": "2025-08-19T13:32:14.905Z", "modified": "2025-11-28T10:52:04.161Z"}, {"entity": "publication", "iuid": "f3fd67a8a7874db59d6f198e8d3ed45b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f3fd67a8a7874db59d6f198e8d3ed45b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f3fd67a8a7874db59d6f198e8d3ed45b"}}, "title": "Seasonal nitrogen removal in an outdoor microalgal polyculture at Nordic conditions.", "authors": [{"family": "Mattsson", "given": "Lina", "initials": "L"}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Hirwa", "given": "Maurice", "initials": "M"}, {"family": "Olofsson", "given": "Martin", "initials": "M"}, {"family": "Svensson", "given": "Fredrik", "initials": "F"}, {"family": "Legrand", "given": "Catherine", "initials": "C", "orcid": "0000-0001-7155-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2287e0a4ced4bb49ca18a67867a8815.json"}}, {"family": "Lindehoff", "given": "Elin", "initials": "E", "orcid": "0000-0002-1149-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca95ca733ed448d3894e83739d758419.json"}}], "type": "journal article", "published": "2024-10-00", "journal": {"title": "Water Environ Res", "issn": "1554-7531", "volume": "96", "issue": "10", "pages": "e11142", "issn-l": null}, "abstract": "Microalgal solutions to clean waste streams and produce biomass were evaluated in Nordic conditions during winter, spring, and autumn in Southeast Sweden. The study investigated nitrogen (N) removal, biomass quality, and safety by treating industrial leachate water with a polyculture of local microalgae and bacteria in open raceway ponds, supplied with industrial CO2 effluent. Total N (TN) removal was higher in spring (1.5 g-2d-1), due to beneficial light conditions compared to winter and autumn (0.1 and 0.09 g-2d-1). Light, TN, and N species influenced the microalgal community (dominated by Chlorophyta), while the bacterial community remained stable throughout seasons with a large proportion of cyanobacteria. Winter conditions promoted biomass protein (19.6-26.7%) whereas lipids and carbohydrates were highest during spring (11.4-18.4 and 15.4-19.8%). Biomass toxin and metal content were below safety levels for fodder, but due to the potential presence of toxic strains, biofuels or fertilizer could be suitable applications for the algal biomass. PRACTITIONER POINTS: Microalgal removal of nitrogen from leachate water was evaluated in Nordic conditions during winter, spring, and autumn. Total nitrogen removal was highest in spring (1.5 g-2d-1), due to beneficial light conditions for autotrophic growth. Use of local polyculture made the cultivation more stable on a seasonal (light) and short-term (N-species changes) scale. Toxic elements in produced algal biomass were below legal thresholds for upcycling.", "doi": "10.1002/wer.11142", "pmid": "39415406", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-28T14:10:43.102Z", "modified": "2025-02-28T14:10:43.155Z"}, {"entity": "publication", "iuid": "30a1386e02c149b68921f0515981458f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/30a1386e02c149b68921f0515981458f"}}, "title": "Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.", "authors": [{"family": "Fridolfsson", "given": "Emil", "initials": "E", "orcid": "0000-0003-4871-7441", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f9f3d44ed8b46729bf6c3d9984bfbe6.json"}}, {"family": "Bunse", "given": "Carina", "initials": "C", "orcid": "0000-0002-0683-7755", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb255e90d0584d3e8128c5288a715c97.json"}}, {"family": "Lindehoff", "given": "Elin", "initials": "E", "orcid": "0000-0002-1149-6852", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca95ca733ed448d3894e83739d758419.json"}}, {"family": "Farnelid", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3083-7437", "researcher": {"href": "https://publications.scilifelab.se/researcher/d180092da06e4c5aa50d93ae941f1c83.json"}}, {"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "Bergstr\u00f6m", "given": "Kristofer", "initials": "K", "orcid": "0000-0002-6570-5525", "researcher": {"href": "https://publications.scilifelab.se/researcher/8bcd7d3b7b47405185ba0d0062111a13.json"}}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}, {"family": "Legrand", "given": "Catherine", "initials": "C", "orcid": "0000-0001-7155-3604", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2287e0a4ced4bb49ca18a67867a8815.json"}}, {"family": "Hylander", "given": "Samuel", "initials": "S", "orcid": "0000-0002-3740-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/47f71565ec50426e9d4893a5335e5fa3.json"}}], "type": "journal article", "published": "2023-07-22", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "13", "issue": "1", "pages": "11865", "issn-l": "2045-2322"}, "abstract": "The planktonic realm from bacteria to zooplankton provides the baseline for pelagic aquatic food webs. However, multiple trophic levels are seldomly included in time series studies, hampering a holistic understanding of the influence of seasonal dynamics and species interactions on food web structure and biogeochemical cycles. Here, we investigated plankton community composition, focusing on bacterio-, phyto- and large mesozooplankton, and how biotic and abiotic factors correlate at the Linnaeus Microbial Observatory (LMO) station in the Baltic Sea from 2011 to 2018. Plankton communities structures showed pronounced dynamic shifts with recurring patterns. Summarizing the parts of the planktonic microbial food web studied here to total carbon, a picture emerges with phytoplankton consistently contributing > 39% while bacterio- and large mesozooplankton contributed ~ 30% and ~ 7%, respectively, during summer. Cyanophyceae, Actinobacteria, Bacteroidetes, and Proteobacteria were important groups among the prokaryotes. Importantly, Dinophyceae, and not Bacillariophyceae, dominated the autotrophic spring bloom whereas Litostomatea (ciliates) and Appendicularia contributed significantly to the consumer entities together with the more traditionally observed mesozooplankton, Copepoda and Cladocera. Our findings of seasonality in both plankton composition and carbon stocks emphasize the importance of time series analyses of food web structure for characterizing the regulation of biogeochemical cycles and appropriately constraining ecosystem models.", "doi": "10.1038/s41598-023-38816-0", "pmid": "37481661", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10363133"}, {"db": "pii", "key": "10.1038/s41598-023-38816-0"}], "notes": [], "created": "2023-10-04T13:23:17.104Z", "modified": "2023-10-19T12:25:13.624Z"}, {"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"}]}