Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods

Abstract

The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus, Acidianus tailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts. IMPORTANCEVirus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus, Acidianus tailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life. O ur knowledge and understanding of archaeal viruses (viruses that infect Archaea) are limited. Only 117 archaeal viruses are described at some level, with only a few being characterized in any significant depth (1-4). Remarkably, these relatively few archaeal viruses have formed 16 new virus families (5) and have expanded our appreciation of virion morphology, diversity, and gene content (5-7). Known archaeal viruses infect just 16 of 98 known gen...

Electron acceptor availability alters carbon and energy metabolism in a thermoacidophile

“…Acidianus is common in acidic, high-temperature, sulfur-rich hot spring environments (Huber and Stetter, 2015), including those in Yellowstone National Park (YNP), Wyoming, USA (Segerer et al, 1986;Inskeep et al, 2010;Hochstein et al, 2016). We previously isolated an Acidianus strain (strain DS80) from a sulfur-rich, acidic hot spring in YNP (Amenabar et al, 2017).…”

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

“…Module 9 encompasses crenarchaeal viruses with large spindleshaped virions that are decorated with one or two long, tail-like appendages protruding from the pointed virion ends. The module includes Acidianus two-tailed virus, the only classified member of the family Bicaudaviridae, as well as 6 unclassified viruses and three viral genomes assembled from metagenomic data (Sulfolobales virus YNP1, Sulfolobales virus YNP2, and hyperthermophilic archaeal virus 2) (see Table S1 in the supplemental material) (27,(40)(41)(42)(43)(44). There are four signature genes in this module, including a putative integrase and the bicaudavirus MCP (not detected in metagenomic assemblies), which is unrelated to the capsid proteins of the smaller spindle-shaped viruses from modules 7 and 8 (32) Table 1 for a description of the contents of each module.…”

“…Acidianus two-tailed virus (ATV) is currently the only classified representative of this virus group and the type species of the family Bicaudaviridae (39). Many morphologically similar viruses have been isolated, and related genomes have been assembled from metagenomic data (27,(40)(41)(42)(43)(44). Unlike ATV, these viruses typically contain one tail and are often referred to as "monocaudaviruses"; however, such a taxon currently has no official standing, and accordingly, these viruses remain unclassified.…”

A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea

“…has been identified for half a century, despite the isolation of thousands of new species (5), the variety of archaeal viral morphotypes continues to expand with the description of viruses from new environments and hosts (6)(7)(8)(9)(10)(11)(12)(13)(14)(15). There are reasons to believe that the known variety of archaeal viruses represents no more than the tip of an iceberg and that comprehensive information on them may shed light on the problems of origin and evolution of viruses and virus-host interactions (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28).…”