Mechanisms of gene flow in archaea

Key Points Horizontal gene transfer (HGT) is essential for genome evolution across the tree of life and has an important role in archaeal speciation, adaptation, and maintenance of diversity. Many of the horizontally acquired genes in archaea are involved in metabolism and cell envelope biogenesis and therefore likely provided a selective advantage for adaptation to new environments. The transfer of DNA can also function in DNA repair by providing an intact template for homologous recombination, as has been shown for Sulfolobus spp. Classic bacterial DNA transfer mechanisms, such as transformation, conjugation and transduction, have been identified in certain archaeal species. In addition, DNA exchange through vesicles, through cell fusion and by the recently discovered archaea-specific crenarchaeal exchange of DNA (Ced) system has been observed. Several barriers prevent the transfer and incorporation of foreign DNA in archaeal species; these include physical environmental barriers, the surface layer (S-layer), CRISPR–Cas systems, restriction–modification systems and toxin–antitoxin systems. Newly identified and sequenced species will enable us to uncover more HGT events among and between archaea, bacteria and eukaryotes. With an increasing number of genetically tractable archaeal species, we will be able to elucidate the processes that underlie gene flow in archaea. Archaea are highly diverse microorganisms that inhabit various environments. This evolutionary flexibility and adaptability has been supported by abundant horizontal gene transfer. In this Review, Albers and colleagues discuss the mechanisms and consequences of archaeal DNA transfer. Archaea are diverse, ecologically important, single-celled microorganisms. They have unique functions and features, such as methanogenesis and the composition of their cell envelope, although many characteristics are shared with the other domains of life, either through ancestry or through promiscuous horizontal gene transfer. The exchange of genetic material is a major driving force for genome evolution across the tree of life and has a role in archaeal speciation, adaptation and maintenance of diversity. In this Review, we discuss our current knowledge of archaeal mechanisms of DNA transfer and highlight the role of gene transfer in archaeal evolution.