Daniel Lundin
Forskare
Institutionen för biologi och miljö
Fakulteten för hälso- och livsvetenskap
Jag jobbar med datorbaserade analyser inom mikrobiell ekologi. Mina studier bygger för det mesta på DNA-sekvensering (metagenom, metatranskriptom och amplikon) av prover tagna i naturen eller genom experiment, i syfte att bättre beskriva mikrobers roll i naturen.
Mina forskargrupper
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Linnaeus Mikrobiella Observatorium (LMO) Linnaeus Mikrobiella Observatorium (LMO) är en provtagningsstation i Egentliga Östersjön, och kärnan i en rad forskningsprojekt inom mikrobiell oceanografi vid…
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Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS) EEMiS är en spetsforskningsmiljö som studerar ekologiska och evolutionära interaktioner från land till hav.
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Marin mikrobiologi Inom forskargruppen Marin mikrobiologi studerar vi marina bakteriers biologiska mångfald, ekologi, fysiologi och genomik.
Mina pågående forskningsprojekt
Publikationer
Artikel i tidskrift (Refereegranskat)
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Aguilera, A., Alegria Zufia, J., Bas Conn, L., Gurlit, L., Śliwińska‐wilczewska, S., et al. (2023). Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria. Environmental Microbiology. 25 (9). 1674-1695.
Status: Publicerad -
Prager, M., Lundin, D., Ronquist, F., Andersson, A.F. (2023). ASV portal : an interface to DNA-based biodiversity data in the Living Atlas. BMC Bioinformatics. 24 (1).
Status: Publicerad -
Martinez-Varela, A., Casas, G., Berrojalbiz, N., Lundin, D., Pina, B., et al. (2023). Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica. Environmental Science and Pollution Research.
Status: Epub för tryck -
Bensch, H., Tolf, C., Waldenström, J., Lundin, D., Zöttl, M. (2023). Bacteroidetes to Firmicutes : captivity changes the gut microbiota composition and diversity in a social subterranean rodent. Animal Microbiome. 5 (1).
Status: Publicerad -
Churakova, Y., Aguilera, A., Charalampous, E., Conley, D.J., Lundin, D., et al. (2023). Biogenic silica accumulation in picoeukaryotes : Novel players in the marine silica cycle. Environmental Microbiology Reports. 15 (4). 282-290.
Status: Publicerad -
Vila-Costa, M., Lundin, D., Fernandez-Pinos, M., Iriarte, J., Irigoien, X., et al. (2023). Responses to organic pollutants in the tropical Pacific and subtropical Atlantic Oceans by pelagic marine bacteria. Frontiers in Environmental Science. 11.
Status: Publicerad -
Bensch, H., Lundin, D., Tolf, C., Waldenström, J., Zöttl, M. (2023). Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal. Journal of Evolutionary Biology.
Status: Epub för tryck -
Berggren, H., Tibblin, P., Yildirim, Y., Broman, E., Larsson, P., et al. (2022). Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals. Frontiers in Microbiology. 12.
Status: Publicerad -
Pinhassi, J., Farnelid, H., Garcia, S.M., Teira, E., Galand, P.E., et al. (2022). Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters. Frontiers in Microbiology. 13.
Status: Publicerad -
Hogfors-Ronnholm, E., Lundin, D., Brambilla, D., Christel, S., Lopez-Fernandez, M., et al. (2022). Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils. Communications Earth & Environment. 3 (1).
Status: Publicerad -
Capo, E., Broman, E., Bonaglia, S., Bravo, A.G., Bertilsson, S., et al. (2022). Oxygen-deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments. Limnology and Oceanography. 67 (1). 135-146.
Status: Publicerad -
Martínez-García, S., Bunse, C., Pontiller, B., Baltar, F., Israelsson, S., et al. (2022). Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent. Frontiers in Microbiology. 13.
Status: Publicerad -
Osbeck, C.M.G., Lundin, D., Karlsson, C., Teikari, J.E., Moran, M.A., et al. (2022). Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter. PLOS ONE. 17 (11).
Status: Publicerad -
Nilsson, R.H., Andersson, A.F., Bissett, A., Finstad, A.G., Fossøy, F., et al. (2022). Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms. Metabarcoding and Metagenomics. 6. 239-244.
Status: Publicerad -
Bensch, H., Tolf, C., Waldenström, J., Lundin, D., Zöttl, M. (2022). Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples. PeerJ. 10.
Status: Publicerad -
Vila-Costa, M., Lundin, D., Casamayor, E.O., Meijer, S.N., Fernandez, P., et al. (2022). Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake. Environmental Pollution. 308.
Status: Publicerad -
Pontiller, B., Martínez-García, S., Joglar, V., Amnebrink, D., Pérez Martínez, C., et al. (2022). Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system. The ISME Journal. 16. 2360-2372.
Status: Publicerad -
Laber, C.P., Pontiller, B., Bunse, C., Osbeck, C.M.G., Pérez Martínez, C., et al. (2022). Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak. Frontiers in Microbiology. 13.
Status: Publicerad -
Joglar, V., Pontiller, B., Martinez-Garcia, S., Fuentes-Lema, A., Perez-Lorenzo, M., et al. (2021). Microbial Plankton Community Structure and Function Responses to Vitamin B-12 and B-1 Amendments in an Upwelling System. Applied and Environmental Microbiology. 87 (22).
Status: Publicerad -
Cerro-Galvez, E., Dachs, J., Lundin, D., Fernandez-Pinos, M., Sebastian, M., et al. (2021). Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon. Environmental Science and Technology. 55 (14). 9609-9621.
Status: Publicerad -
Pontiller, B., Pérez Martínez, C., Bunse, C., Osbeck, C.M.G., González, J.M., et al. (2021). Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord. mSystems. 6 (6).
Status: Publicerad -
Joglar, V., Alvarez-Salgado, X.A., Gago-Martinez, A., Leao, J.M., Pérez Martínez, C., et al. (2021). Cobalamin and microbial plankton dynamics along a coastal to offshore transect in the Eastern North Atlantic Ocean. Environmental Microbiology. 23 (3). 1559-1583.
Status: Publicerad -
Hötzinger, M., Nilsson, E., Arabi, R., Osbeck, C.M.G., Pontiller, B., et al. (2021). Dynamics of Baltic Sea phages driven by environmental changes. Environmental Microbiology. 23 (8). 4576-4594.
Status: Publicerad -
Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., et al. (2021). The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles. Communications Biology. 4 (1).
Status: Publicerad -
Nilsson, E., Bayfield, O.W., Lundin, D., Antson, A.A., Holmfeldt, K. (2020). Diversity and host interactions among virulent and temperate Baltic Sea Flavobacterium phages. Viruses. 12 (2). 1-21.
Status: Publicerad -
Pontiller, B., Martinez-Garcia, S., Lundin, D., Pinhassi, J. (2020). Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription. Frontiers in Microbiology. 11. 1-19.
Status: Publicerad -
Gonzalez-Gaya, B., Martinez-Varela, A., Vila-Costa, M., Casal, P., Cerro-Galvez, E., et al. (2019). Biodegradation as an important sink of aromatic hydrocarbons in the oceans. Nature Geoscience. 12 (2). 119-125+2.
Status: Publicerad -
Karlsson, C.M.G., Cerro-Galvez, E., Lundin, D., Karlsson, C., Vila-Costa, M., et al. (2019). Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341. Microbial Biotechnology. 12 (5). 892-906.
Status: Publicerad -
Vila-Costa, M., Sebastian, M., Pizarro, M., Cerro-Galvez, E., Lundin, D., et al. (2019). Microbial consumption of organophosphate esters in seawater under phosphorus limited conditions. Scientific Reports. 9.
Status: Publicerad -
Loderer, C., Holmfeldt, K., Lundin, D. (2019). Non-host class II ribonucleotide reductase in Thermus viruses : sequence adaptation and host interaction. PeerJ. 7. 1-17.
Status: Publicerad -
Nilsson, E., Li, K., Fridlund, J., Šulčius, S., Bunse, C., et al. (2019). Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341. Applied and Environmental Microbiology. 85 (18). 1-19.
Status: Publicerad -
Högfors-Rönnholm, E., Lopez-Fernandez, M., Christel, S., Brambilla, D., Huntemann, M., et al. (2019). Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Scientific Data. 6. 1-6.
Status: Publicerad -
Cerro-Galvez, E., Casal, P., Lundin, D., Pina, B., Pinhassi, J., et al. (2019). Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environmental Microbiology. 21 (4). 1466-1481.
Status: Publicerad -
Alneberg, J., Sundh, J., Bennke, C., Beier, S., Lundin, D., et al. (2018). BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea. Scientific Data. 5.
Status: Publicerad -
Srinivas, V., Lebrette, H., Lundin, D., Kutin, Y., Sahlin, M., et al. (2018). Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens. Nature. 563 (7731). 416-420.
Status: Publicerad -
Salgado, M.G., Van Velzen, R., Nguyen, T.V., Battenberg, K., Berry, A.M., et al. (2018). Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerate (Datiscaceae, Cucurbitales). Frontiers in Plant Science. 9.
Status: Publicerad -
Ni, G., Canizales, S., Broman, E., Simone, D., Palwai, V.R., et al. (2018). Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Frontiers in Microbiology. 9.
Status: Publicerad -
Grinberg, I.R., Lundin, D., Hasan, M., Crona, M., Jonna, V.R., et al. (2018). Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. eLIFE. 7.
Status: Publicerad -
Grinberg, I.R., Lundin, D., Sahlin, M., Crona, M., Berggren, G., et al. (2018). A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant. Journal of Biological Chemistry. 293 (41). 15889-15900.
Status: Publicerad -
Loderer, C., Jonna, V.R., Crona, M., Grinberg, I.R., Sahlin, M., et al. (2017). A unique cysteine-rich zinc finger domain present in a majority of class II ribonucleotide reductases mediates catalytic turnover. Journal of Biological Chemistry. 292 (46). 19044-19054.
Status: Publicerad -
Zhang, S., Masuyer, G., Zhang, J., Shen, Y., Lundin, D., et al. (2017). Identification and characterization of a novel botulinum neurotoxin. Nature Communications. 8.
Status: Publicerad -
Lindh, M.V., Sjöstedt, J., Ekstam, B., Casini, M., Lundin, D., et al. (2017). Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology. 19 (3). 1222-1236.
Status: Publicerad -
Baltar, F., Lundin, D., Palovaara, J., Lekunberri, I., Reinthaler, T., et al. (2016). Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Frontiers in Microbiology. 7.
Status: Publicerad -
Bunse, C., Lundin, D., Karlsson, C.M.G., Akram, N., Vila-Costa, M., et al. (2016). Response of marine bacterioplankton pH homeostasis gene expression to elevated CO2. Nature Climate Change. 6 (5). 483-487.
Status: Publicerad -
Herlemann, D.P.R., Lundin, D., Andersson, A.F., Labrenz, M., Juergens, K. (2016). Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea. Frontiers in Microbiology. 7.
Status: Publicerad -
Dantoft, W., Lundin, D., Esfahani, S.S., Engström, Y. (2016). The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila. Journal of Innate Immunity. 8 (4). 412-426.
Status: Publicerad -
Thureborn, P., Franzetti, A., Lundin, D., Sjöling, S. (2016). Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments. PeerJ. 4.
Status: Publicerad -
Wu, X., Holmfeldt, K., Hubalek, V., Lundin, D., Åström, M.E., et al. (2016). Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations. The ISME Journal. 10 (5). 1192-1203.
Status: Publicerad -
Johansson, R., Jonna, V.R., Kumar, R., Nayeri, N., Lundin, D., et al. (2016). Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones. Structure. 24 (6). 906-917.
Status: Publicerad -
Jonna, V.R., Crona, M., Rofougaran, R., Lundin, D., Johansson, S., et al. (2015). Diversity in Overall Activity Regulation of Ribonucleotide Reductase. Journal of Biological Chemistry. 1-24.
Status: Publicerad -
Lindh, M.V., Lefebure, R., Degerman, R., Lundin, D., Andersson, A., et al. (2015). Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment. Ambio. 44 (Supplement 3). S402-S412.
Status: Publicerad -
Aurelius, O., Johansson, R., Bågenholm, V., Lundin, D., Tholander, F., et al. (2015). The Crystal Structure of Thermotoga maritima Class III Ribonucleotide Reductase Lacks a Radical Cysteine Pre-Positioned in the Active Site. PLOS ONE. 10 (7).
Status: Publicerad -
Lindh, M.V., Figueroa, D., Sjöstedt, J., Baltar, F., Lundin, D., et al. (2015). Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities. Frontiers in Microbiology. 6.
Status: Publicerad -
Lundin, D., Berggren, G., Logan, D.T., Sjöberg, B. (2015). The Origin and Evolution of Ribonucleotide Reduction. Life. 5 (1). 604-636.
Status: Publicerad -
West, C.E., Rydén, P., Lundin, D., Engstrand, L., Tulic, M.K., et al. (2015). Gut microbiome and innate immune response patterns in IgE-associated eczema. Clinical and Experimental Allergy. 45 (9). 1419-1429.
Status: Publicerad -
Baichoo, S., Botha, G., Jaufeerally-Fakim, Y., Mungloo-Dilmohamud, Z., Lundin, D., et al. (2015). H3ABioNet computational metagenomics workshop in Mauritius : training to analyse microbial diversity for Africa. Standards in Genomic Sciences. 10.
Status: Publicerad -
Lindh, M.V., Sjöstedt, J., Andersson, A.F., Baltar, F., Hugerth, L., et al. (2015). Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling. Environmental Microbiology. 17 (7). 2459-2476.
Status: Publicerad -
Poole, A.M., Lundin, D., Rytkoenen, K.T. (2015). The evolution of early cellular systems viewed through the lens of biological interactions. Frontiers in Microbiology. 6.
Status: Publicerad -
Dupont, C.L., Larsson, J., Yooseph, S., Ininbergs, K., Goll, J., et al. (2014). Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition. PLOS ONE. 9 (2).
Status: Publicerad -
Hugerth, L.W., Muller, E.E.L., Hu, Y.O.O., Lebrun, L.A.M., Roume, H., et al. (2014). Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia. PLOS ONE. 9 (4).
Status: Publicerad -
Herlemann, D.P.R., Lundin, D., Labrenz, M., Jürgens, K., Zheng, Z., et al. (2013). Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria. mBio. 4 (3). 1-9.
Status: Publicerad -
Dwivedi, B., Xue, B., Lundin, D., Edwards, R.A., Breitbart, M. (2013). A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evolutionary Biology. 13 (1). 1-17.
Status: Publicerad -
Crona, M., Avesson, L., Sahlin, M., Lundin, D., Hinas, A., et al. (2013). A Rare Combination of Ribonucleotide Reductases in the Social Amoeba Dictyostelium discoideum. Journal of Biological Chemistry. 288 (12). 8198-8208.
Status: Publicerad -
Thureborn, P., Lundin, D., Plathan, J., Poole, A.M., Sjöberg, B., et al. (2013). A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities. PLOS ONE. 8 (9).
Status: Publicerad -
Silberberg, G., Lundin, D., Navon, R., Öhman, M. (2012). Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders. Human Molecular Genetics. 21 (2). 311-321.
Status: Publicerad -
Lundin, D., Poole, A.M., Sjöberg, B., Högbom, M. (2012). Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily. Journal of Biological Chemistry. 287 (24). 20565-20575.
Status: Publicerad -
Lundin, D., Severin, I., Logue, J.B., Östman, Ö., Andersson, A.F., et al. (2012). Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?. Environmental Microbiology Reports. 4 (3). 367-372.
Status: Publicerad -
Grimberg, K.B., Beskow, A., Lundin, D., Davis, M.M., Young, P. (2011). Basic Leucine Zipper Protein Cnc-C Is a Substrate and Transcriptional Regulator of the Drosophila 26S Proteasome. Molecular and Cellular Biology. 31 (4). 897-909.
Status: Publicerad -
Lundin, D., Gribaldo, S., Torrents, E., Sjöberg, B., Poole, A.M. (2010). Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evolutionary Biology. 10 (1).
Status: Publicerad -
Neumann, N., Lundin, D., Poole, A.M. (2010). Comparative Genomic Evidence for a Complete Nuclear Pore Complex in the Last Eukaryotic Common Ancestor. PLOS ONE. 5 (10).
Status: Publicerad -
Ensterö, M., Åkerborg, Ö., Lundin, D., Wang, B., Furey, T.S., et al. (2010). A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. BMC Bioinformatics. 11.
Status: Publicerad -
Johansson, R., Torrents, E., Lundin, D., Sprenger, J., Sahlin, M., et al. (2010). High-resolution crystal structures of the flavoprotein NrdI in oxidized and reduced states – an unusual flavodoxin. The FEBS Journal. 277 (20). 4265-4277.
Status: Publicerad -
Lundin, D., Torrents, E., Poole, A.M., Sjöberg, B. (2009). RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics. 10 (1).
Status: Publicerad -
Masson, P., Lundin, D., Söderbom, F., Young, P. (2009). Characterization of a REG/PA28 Proteasome Activator Homolog in Dictyostelium discoideum Indicates that the Ubiquitin- and ATP-Independent REGγ Proteasome Is an Ancient Nuclear Protease. Eukaryotic Cell. 8 (6). 844-851.
Status: Publicerad -
Tamas, I., Wernegreen, J.J., Nystedt, B., Kauppinen, S.N., Darby, A.C., et al. (2008). Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proceedings of the National Academy of Sciences of the United States of America. 105 (39). 14934-9.
Status: Publicerad
Kapitel i bok, del av antologi (Refereegranskat)
- Berggren, G., Lundin, D., Sjöberg, B. (2017). Assembly of Dimanganese and Heterometallic Manganese Proteins. Encyclopedia of Inorganic and Bioinorganic Chemistry. John Wiley & Sons.
Artikel, forskningsöversikt (Refereegranskat)
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Muthusamy, S.D., Lundin, D., Branca, R.M.M., Baltar, F., Gonzalez, J.M., et al. (2017). Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environmental Microbiology. Wiley-Blackwell. 19 (6). 2301-2319.
Status: Publicerad
Manuskript (Övrigt vetenskapligt)
- Karlsson, C.M.G., Lundin, D., Karlsson, C., Teikari, J.E., Moran, M.A., et al. Different gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.
- Karlsson, C.M.G., Pontiller, B., Teikari, J.E., Traving, S.J., Happel, E.M., et al. Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings.
- Osbeck, C.M.G., Pontiller, B., Teikari, J.E., Traving, S.J., Happel, E.M., et al. Divergent transcriptional responses of Baltic Sea bacteria to forest and agriculture river loadings.
- Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., et al. The deep terrestrial virosphere.
- Bensch, H., Tolf, C., Waldenström, J., Lundin, D., Zöttl, M. Gut microbiome similarity in wild mole-rats : The effects of shared common descent.
- Bunse, C., Lundin, D., Lindh, M.V., Sjöstedt, J., Israelsson, S., et al. Seasonality and co-occurrences of free-living Baltic Sea bacterioplankton.