Evolution, Cell Biology, and Symbiosis Unit (Filip Husnik)

Research Interests

Three connecting themes that run through all aspects of our research are evolution, cell biology, and symbiosis. We are particularly fascinated by the origin and evolution of the eukaryotic cell and its endosymbiotic organelles, mitochondria and plastids, but we also focus on numerous other (more recent) symbiotic interactions among bacteria, archaea, single-celled eukaryotes (protists), plants, and animals. We try to understand how these symbioses originate, how they are maintained at the cellular level for over hundreds of millions of years, and how they eventually become either organelles or extinct. We use a variety of interdisciplinary approaches to study these complex symbiotic systems in the field, in the lab, and with computational methods. Our ultimate goal is to bridge the gap between multiple fields that rarely interact with each other and to fully understand how an intracellular organism becomes so highly incorporated into its host cell that it becomes a part of the cell, an organelle.

Research Projects

  1. The origin of mitochondria and the eukaryotic cell
  2. Endosymbiotic bacteria of protists and insects
  3. Marine microbiology and symbioses

Main Methods

Our unit mostly works with 'non-model' organisms such as protists, marine invertebrates, and scale insects (see below). Establishing new methods in these non-traditional model systems is thus inevitably a large part of our every project.

  • Light, epifluorescence, and confocal microscopy
  • Electron microscopy (TEM, SEM, FIB-SEM, SBF-SEM, EDX-SEM)
  • Chemical fixation and resin embedding
  • High-pressure freezing and freeze substitution
  • Paraffin embedding/sectioning, and histology
  • Fluorescence in-situ hybridization (FISH; with both RNA and DNA probes)
  • Immunohistochemistry and immunogold labeling
  • Fluorescence-Activated Cell Sorting (FACS) of bacteria and microbial eukaryotes
  • Live-cell staining and imaging of diverse cell compartments in microbial eukaryotes
  • X-ray microtomography (micro-CT)
  • Single-cell genomics and transcriptomics of microbial eukaryotes
  • Hi-C (chromatin capture) methods
  • Genome and transcriptome sequencing (Illumina, Oxford Nanopore, and PacBio)
  • Differential gene expression RNA-Seq analyses for host-symbiont systems
  • Genome-resolved metagenomics and metatranscriptomics
  • Amplicon sequencing with 16S rRNA, 18S rRNA, and ITS markers
  • Untargeted metabolomics and proteomics of host-symbiont systems
  • Spatial metabolomics (MALDI-MSI)
  • Subcellular proteomics (LOPIT-DC)
  • Cell dissociation of Cnidaria
  • Metabolic measurements of single cells with microsensors
  • Low-oxygen experiments in an anaerobic chamber
  • Programming software and evolutionary simulations
  • Experimental evolution of microbial symbioses
  • Environmental DNA (eDNA) sampling and analysis
  • High-throughput automated plankton imaging (PlanktoScope, Imaging FlowCytobot, FlowCam)
  • Marine sediment biogeochemistry
  • Insect microinjections (symbionts and RNAi)
  • Miscellaneous molecular biology methods (PCR, RT-PCR, RNAi, electrophoresis, etc.)
  • Phylogenomics and population genomics
  • Manipulative experiments (both indoors and outdoors) with corals and microbial eukaryotes
  • Culturing and identification of diverse insects, marine invertebrates, plants, and microorganisms
  • Marine and terrestrial fieldwork

Major reviews

Husnik F, Tashyreva D, Boscaro V, George EE, Lukes J, Keeling PJ: Bacterial and archaeal symbioses with protists. Current Biology 2021, 31(13): PR862-R877.

Husnik F & Keeling PJ. The fate of obligate endosymbionts: reduction, integration, or extinction. Current Opinion in Genetics & Development 2019, 58-59: 1-8.

Husnik F & McCutcheon JP: Functional horizontal gene transfer from bacteria to eukaryotes. Nature Reviews Microbiology 2018, 16 (2): 67-79 [ReadCube Access].


Model systems

  • mitochondria and plastids
  • symbioses of microbial eukaryotes
  • symbioses of marine invertebrates
  • insect symbioses