Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species

Abstract

Summary The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non‐contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV‐4. Differently from HRTV‐4, HFTV1 encodes host‐derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.

Cellular and genomic properties ofHaloferax gibbonsiiLR2-5, the host of euryarchaeal virus HFTV1

“…LR2-5, it infects Halorubrum sp. LR1-23 but not any of the endogenous Haloferax strains (Mizuno et al, 2019).…”

“…gibbonsii Ma2.38 T and Hfx. volcanii H26 (see supplementary text for information on strains) to HFTV1 was examined in parallel using a spot-on-lawn assay (Juez et al, 1986;Allers et al, 2004;Mizuno et al, 2019). Serial dilutions of the HFTV1 lysate (5 × 10 11 PFU/mL) were spotted onto lawns of the three strains of Haloferax and the plates incubated for 3 days (Figure 2).…”

“…Haloferax tailed virus 1 (HFTV1) and its host, Haloferax sp. LR2-5, originate from the saline Lake Retba near Dakar in Senegal (Mizuno et al, 2019).…”

“…The siphovirus HFTV1 has an icosahedral head of ~50 nm diameter and a long noncontractile tail of ~60 nm (Mizuno et al, 2019). Four major protein types were detected in the HFTV1 virion.…”

“…The linear, circularly permuted dsDNA genome of 38 kb encodes 70 ORFs, of which half have homology to haloarchaeal viral genes, such as the archaeal siphovirus HRTV-4 isolated from Margherita di Savoia, Italy, and of uncultivated haloviruses from the solar saltern Santa Pola, Spain (Mizuno et al, 2019). The genome is likely subjected to a headful packaging mechanism initiated from a pac site (Mizuno et al, 2019). HFTV1 has a narrow host range among the Lake Retba archaeal strains tested.…”