Haloferax volcanii: a versatile model for studying archaeal biology

Abstract

Archaea, once thought limited to extreme environments, are now recognized as ubiquitous and fundamental players in global ecosystems. While morphologically similar to bacteria, they are a distinct domain of life and are evolutionarily closer to eukaryotes. The development of model archaeal systems has facilitated studies that have underscored unique physiological, biochemical, and genetic characteristics of archaea. Haloferax volcanii stands out as a model archaeon due to its ease of culturing, ability to grow on defined media, amenability to genetic and biochemical methods, as well as the support from a highly collaborative community. This haloarchaeon has been instrumental in exploring diverse aspects of archaeal biology, ranging from polyploidy, replication origins, and post-translational modifications to cell surface biogenesis, metabolism, and adaptation to high-salt environments. The extensive use of Hfx. volcanii further catalyzed the development of new technologies and databases, facilitating discovery-driven research that offers significant implications for biotechnology, biomedicine, and core biological questions.

Keywords: Haloferax volcanii; archaea; biochemistry; biotechnology; cell biology; education; genetics; history; model organisms; molecular biology.

Fig 1

A timeline of methodological milestones that established Haloferax volcanii as a key model organism to advance the biological characterization of Archaea. Cell biology advances in Hfx. volcanii include isolating Hfx. volcanii from the Dead Sea (31), establishing efficient growth of Hfx. volcanii in minimal media (41), enabling the usage of green fluorescent protein (GFP) under high-salt conditions (43), establishing conditions under which Hfx. volcanii shows motility (44), adapting super-resolution microscopy to image individual molecules (45), using microfluidics to build mother machines (46), and developing a multicellularity assay that results in tissue-like cell complexes (47). Genetic advances played major roles in establishing Hfx. volcanii as a model archaeon, including developing the first genetic information transfer assay for an archaeon (the mating assay) (48), adapting a transformation protocol to Hfx. volcanii, making this the first archaeon transformed with a plasmid (49), developing auxotrophic selection markers and the pop-in/pop-out method to generate marker-less deletion strains (50), adopting an inducible promoter for regulated gene expression/silencing (51), as well as generating a whole-genome transposon insertion library (52) and adapting a method to silence archaeal genes: clustered regularly interspaced short palindromic repeats interference (CRISPRi)(53). Early omics approaches such as publishing a detailed map of the whole genome, including a pan-genome set of cosmid clones (54), and predicting signal peptides for Sec, twin-arginine transport, and Pil/Fla pathways (55), were followed by more advanced system-wide analyses, allowing researchers to gain insights at the molecular level. These include publishing the complete genome sequence and annotation of the Hfx. volcanii DS2 strain (56), establishing differential RNA sequencing to identify transcriptional start sites (57), adapting ribosome profiling for Hfx. volcanii (58), and combining information about its proteome in the Archaeal Proteome Project (59). PEG, polyethylene glycol.

Fig 2

Biological insights and biotechnological advances in Hfx. volcanii. (A) Scanning electron microscopy of Hfx. volcanii biofilm grown on a nitrocellulose membrane. Courtesy of John Mallon and Arthur Charles-Orzsag. (B) The three-dimensional super resolution by optical reassignment microscopy images of Hfx. volcanii multicellular clone (courtesy of Alexandre Bisson). (C) Motility halos of Hfx. volcanii wild type (top center) and transposon insertion mutants (107). (D) Hfx. volcanii encapsulated within calcium alginate beads (67). (E) Formation of a cell–cell bridge in AlexaFluor488-labeled cells (top). A tomographic slice from a reconstructed tilt series of electron cryo-microscopy (bottom). The cytoplasmic membrane (M), the surface (S) layer (S), and archaella (Ar) are indicated (108). (F) Localization of green fluorescent protein-tagged volactin in mid-log phase Hfx. volcanii rod- and disk-shaped cells (109). (G) Structural model of the heptameric α1₇-ring of Hfx. volcanii 20S core particles, the central catalytic part of the proteasome. Used with permission of John Wiley & Sons, Inc., from reference ; permission conveyed through Copyright Clearance Center, Inc. (H) Atomic resolution description of an archaeal cell surface. The S-layer lattice is completed by pentameric defects (colored darker) (98). Panels C, D, E, F, and H are adapted from references , , , , and , respectively, under the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).