{"entity": "researcher", "timestamp": "2026-07-20T13:32:17.329Z", "family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "affiliations": ["Centre for Ecology and Evolution in Microbial Model Systems-EEMiS, Linnaeus Universitygrid.8148.5, Kalmar, Sweden.", "GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e"}}, "publications": [{"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": "a88f4582c71849449a5371c7385f78ca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a88f4582c71849449a5371c7385f78ca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a88f4582c71849449a5371c7385f78ca"}}, "title": "Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system.", "authors": [{"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "Mart\u00ednez-Garc\u00eda", "given": "Sandra", "initials": "S", "orcid": "0000-0002-5476-7499", "researcher": {"href": "https://publications.scilifelab.se/researcher/fc1a03d6cd414b748807788a0c8e11fb.json"}}, {"family": "Joglar", "given": "Vanessa", "initials": "V"}, {"family": "Amnebrink", "given": "Dennis", "initials": "D", "orcid": "0000-0002-2747-6346", "researcher": {"href": "https://publications.scilifelab.se/researcher/dcd3d739280a4ce281be628a3b4b217e.json"}}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C", "orcid": "0000-0001-8302-5710", "researcher": {"href": "https://publications.scilifelab.se/researcher/28271fe98d59405b92dc026d1740dd9a.json"}}, {"family": "Gonz\u00e1lez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-9926-3323", "researcher": {"href": "https://publications.scilifelab.se/researcher/985211e3b6354b6e9fe4be56a9c2b5b2.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D", "orcid": "0000-0002-8779-6464", "researcher": {"href": "https://publications.scilifelab.se/researcher/227cc90e084348a193fee05eb23a6bf3.json"}}, {"family": "Fern\u00e1ndez", "given": "Emilio", "initials": "E", "orcid": "0000-0001-7985-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/748dd6833e474966b5c7b79ef52dd1c7.json"}}, {"family": "Teira", "given": "Eva", "initials": "E", "orcid": "0000-0002-4333-0101", "researcher": {"href": "https://publications.scilifelab.se/researcher/5ed7047ae09241a182466fee66736dbd.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": "2022-10-00", "journal": {"title": "ISME J", "issn": "1751-7370", "issn-l": "1751-7362", "volume": "16", "issue": "10", "pages": "2360-2372"}, "abstract": "Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.", "doi": "10.1038/s41396-022-01273-0", "pmid": "35804052", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9478159"}, {"db": "pii", "key": "10.1038/s41396-022-01273-0"}], "notes": [], "created": "2022-08-19T08:38:12.799Z", "modified": "2024-01-16T13:48:34.858Z"}, {"entity": "publication", "iuid": "fc66b426f2b0449c89a990b030c97298", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fc66b426f2b0449c89a990b030c97298.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fc66b426f2b0449c89a990b030c97298"}}, "title": "Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord.", "authors": [{"family": "Pontiller", "given": "Benjamin", "initials": "B", "orcid": "0000-0003-4787-7021", "researcher": {"href": "https://publications.scilifelab.se/researcher/b82bf32f7660447abc8dd6ae14fd598e.json"}}, {"family": "P\u00e9rez-Mart\u00ednez", "given": "Clara", "initials": "C"}, {"family": "Bunse", "given": "Carina", "initials": "C"}, {"family": "Osbeck", "given": "Christofer M G", "initials": "CMG"}, {"family": "Gonz\u00e1lez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-9926-3323", "researcher": {"href": "https://publications.scilifelab.se/researcher/985211e3b6354b6e9fe4be56a9c2b5b2.json"}}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Pinhassi", "given": "Jarone", "initials": "J", "orcid": "0000-0002-6405-1347", "researcher": {"href": "https://publications.scilifelab.se/researcher/b352d814c2534b06a79992fda3bbb075.json"}}], "type": "journal article", "published": "2021-12-21", "journal": {"title": "mSystems", "issn": "2379-5077", "volume": "6", "issue": "6", "pages": "e0057521", "issn-l": "2379-5077"}, "abstract": "A considerable fraction of organic matter derived from photosynthesis in the euphotic zone settles into the ocean's interior and, as it progresses, is degraded by diverse microbial consortia that utilize a suite of extracellular enzymes and membrane transporters. Still, the molecular details that regulate carbon cycling across depths remain little explored. As stratification in fjords has made them attractive models to explore patterns in biological oceanography, we here analyzed bacterial and archaeal transcription in samples from five depth layers in the Gullmar Fjord, Sweden. Transcriptional variation over depth correlated with gradients in chlorophyll a and nutrient concentrations. Differences in transcription between sampling dates (summer and early autumn) were strongly correlated with ammonium concentrations, which potentially was linked with a stronger influence of (micro-)zooplankton grazing in summer. Transcriptional investment in carbohydrate-active enzymes (CAZymes) decreased with depth and shifted toward peptidases, partly a result of elevated CAZyme transcription by Flavobacteriales, Cellvibrionales, and Synechococcales at 2 to 25 m and a dominance of peptidase transcription by Alteromonadales and Rhodobacterales from 50 m down. In particular, CAZymes for chitin, laminarin, and glycogen were important. High levels of transcription of ammonium transporter genes by Thaumarchaeota at depth (up to 18% of total transcription), along with the genes for ammonia oxidation and CO2 fixation, indicated that chemolithoautotrophy contributed to the carbon flux in the fjord. The taxon-specific expression of functional genes for processing of the marine pool of dissolved organic matter and inorganic nutrients across depths emphasizes the importance of different microbial foraging mechanisms over spatiotemporal scales for shaping biogeochemical cycles. IMPORTANCE It is generally recognized that stratification in the ocean strongly influences both the community composition and the distribution of ecological functions of microbial communities, which in turn are expected to shape the biogeochemical cycling of essential elements over depth. Here, we used metatranscriptomics analysis to infer molecular detail on the distribution of gene systems central to the utilization of organic matter in a stratified marine system. We thereby uncovered that pronounced shifts in the transcription of genes encoding CAZymes, peptidases, and membrane transporters occurred over depth among key prokaryotic orders. This implies that sequential utilization and transformation of organic matter through the water column is a key feature that ultimately influences the efficiency of the biological carbon pump.", "doi": "10.1128/mSystems.00575-21", "pmid": "34904860", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8670421"}], "notes": [], "created": "2022-03-29T13:47:25.000Z", "modified": "2022-03-29T13:47:25.112Z"}]}