Karin Holmfeldt

My research focus on the effect of viruses on the bacterioplankton community, how they regulate their diversity, influences their mortality, and impacts the biogeochemical cycles in the ocean by transforming particulate organic material (in the form of microorganisms) to dissolved organic matter and through expression of metabolic genes. This is investigated both through experimental work on virus-host model systems as well as productivity and diversity studies on community level.

My research groups

My ongoing research projects

My completed research projects

Project: Allelobact The goal of the project is to identify specific mechanisms of action involving allelochemicals in bacterial-algal interactions to understand their role in harmful algal bloom (HAB)…

Publications

Article in journal (Refereed)

Rahlff, J., Wietz, M., Giebel, H., Bayfield, O., Nilsson, E., et al. (2023). Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. ISME Communications. 3 (1).
Status: Published
Cui, L., Balamkundu, S., Liu, C., Ye, H., Hourihan, J., et al. (2023). Four additional natural 7-deazaguanine derivatives in phages and how to make them. Nucleic Acids Research. 51 (17). 9214-9226.
Status: Published
Nilsson, E., Li, K., Hoetzinger, M., Holmfeldt, K. (2022). Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium. Environmental Microbiology. 24 (5). 2270-2281.
Status: Published
Broman, E., Holmfeldt, K., Bonaglia, S., Hall, P.O.J., Nascimento, F.J.A. (2021). Cyanophage Diversity and Community Structure in Dead Zone Sediments. mSphere. 6 (2).
Status: Published
Kauppinen, A., Siponen, S., Pitkanen, T., Holmfeldt, K., Pursiainen, A., et al. (2021). Phage Biocontrol of Pseudomonas aeruginosa in Water. Viruses. 13 (5).
Status: Published
Drobysheva, A.V., Panafidina, S.A., Kolesnik, M.V., Klimuk, E.I., Minakhin, L., et al. (2021). Structure and function of virion RNA polymerase of a crAss-like phage. Nature. 589 (7841). 306-309.
Status: Published
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: Published
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: Published
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: Published
Sulcius, S., Simoliunas, E., Alzbutas, G., Gasiunas, G., Jauniskis, V., et al. (2019). Genomic Characterization of Cyanophage vB_AphaS-CL131 Infecting Filamentous Diazotrophic Cyanobacterium Aphanizomenon flos-aquae Reveals Novel Insights into Virus-Bacterium Interactions. Applied and Environmental Microbiology. 85 (1).
Status: Published
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: Published
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: Published
Sulcius, S., Mazur-Marzec, H., Vitonyte, I., Kvederaviciute, K., Kuznecova, J., et al. (2018). Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena. Harmful Algae. 78. 69-74.
Status: Published
Lopez-Fernandez, M., Simone, D., Wu, X., Soler, L., Nilsson, E., et al. (2018). Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere. mBio. 9 (6).
Status: Published
Howard-Varona, C., Roux, S., Dore, H., Solonenko, N.E., Holmfeldt, K., et al. (2017). Regulation of infection efficiency in a globally abundant marine Bacteriodetes virus.. The ISME Journal. 11 (1). 284-295.
Status: Published
Šulčius, S., Holmfeldt, K. (2016). Viruses of microorganisms in the Baltic Sea : current state of research and perspectives. Marine Biology Research. 12 (2). 115-124.
Status: Published
Holmfeldt, K., Solonenko, N., Howard-Varona, C., Moreno, M., Malmstrom, R.R., et al. (2016). Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environmental Microbiology. 18 (11). 3949-3961.
Status: Published
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: Published
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: Published
Lara, E., Holmfeldt, K., Solonenko, N., Sà, E.L., Ignacio-Espinoza, J.C., et al. (2015). Life-style and genome structure of marine Pseudoalteromonas siphovirus B8b isolated from the northwestern Mediterranean Sea.. PLOS ONE. 10 (1).
Status: Published
Holmfeldt, K., Howard-Varona, C., Solonenko, N., Sullivan, M.B. (2014). Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera. Environmental Microbiology. 16 (8). 2501-2513.
Status: Published
Holmfeldt, K., Solonenko, N., Shah, M., Corrier, K., Riemann, L., et al. (2013). Twelve previously unknown phage genera are ubiquitous in global oceans. Proceedings of the National Academy of Sciences of the United States of America. 110 (31). 12798-12803.
Status: Published
Holmfeldt, K., Odić, D., Sullivan, M.B., Middelboe, M., Riemann, L. (2012). Cultivated single-stranded DNA phages that infect marine Bacteroidetes prove difficult to detect with DNA-binding stains.. Applied and Environmental Microbiology. 78 (3). 892-894.
Status: Published
Zweifel, U.L., Hagström, Å., Holmfeldt, K., Thyrhaug, R., Geels, C., et al. (2012). High bacterial 16S rRNA gene diversity above the atmospheric boundary layer. Aerobiologia. 28 (4). 481-498.
Status: Published
Holmfeldt, K., Titelman, J., Riemann, L. (2010). Virus production and lysate recycling in different sub-basins of the northern Baltic Sea.. Microbial Ecology. 60 (3). 572-580.
Status: Published
Holmfeldt, K., Dziallas, C., Titelman, J., Pohlmann, K., Grossart, H., et al. (2009). Diversity and abundance of freshwater Actinobacteria along environmental gradients in the brackish northern Baltic Sea. Environmental Microbiology. 11 (8). 2042-2054.
Status: Published
Riemann, L., Holmfeldt, K., Titelman, J. (2009). Importance of viral lysis and dissolved DNA for bacterioplankton activity in a P-limited estuary, northern Baltic Sea. Microbial Ecology. 57 (2). 286-294.
Status: Published
Middelboe, M., Holmfeldt, K., Riemann, L., Nybroe, O., Haaber, J. (2009). Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environmental Microbiology. 11 (8). 1971-1982.
Status: Published
Riemann, L., Leitet, C., Pommier, T., Simu, K., Holmfeldt, K., et al. (2008). The Native Bacterioplankton Community in the Central Baltic Sea is Influenced by Freshwater Bacterial Species. Applied and Environmental Microbiology. 74. 503-515.
Status: Published
Titelman, J., Riemann, L., Holmfeldt, K., Nilsen, T. (2008). Copepod feeding stimulates bacterioplankton in a low phosphorus system. Aquatic Biology. 2. 131-141.
Status: Published
Holmfeldt, K., Middelboe, M., Nybroe, O., Riemann, L. (2007). Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Applied and Environmental Microbiology. 73. 6730-6739.
Status: Published
Simu, K., Holmfeldt, K., Zweifel, U.L., Hagström, Å. (2005). Culturability and coexistence of colony forming and single cell marine bacterioplankton.. Applied and Environmental Microbiology. 71. 4793-4800.
Status: Published

Article in journal (Other academic)

Quax, T.E.F., De Paepe, M., Holmfeldt, K. (2021). Viruses of Microbes 2020 : The Latest Conquest on Viruses of Microbes. Viruses. 13 (5).
Status: Published

Manuscript (preprint) (Other academic)

Nilsson, E., Li, K., Holmfeldt, K. Nutrient driven transcriptional changes during phage infection in aquatic bacteria.
Rahlff, J., Wietz, M., Giebel, H., Bayfield, O., Nilsson, E., et al. Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick.
Holmfeldt, K., Nilsson, E., Simone, D., Lopez-Fernandez, M., Wu, X., et al. The deep terrestrial virosphere.