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New Double-Stranded DNA Virus Family Identified

NEW YORK (GenomeWeb) – By profiling tail-less, double-stranded DNA (dsDNA) viruses from bacteria in ocean samples, researchers from Massachusetts Institute of Technology and Albert Einstein College of Medicine have identified a previously unappreciated family of autolykiviruses capable of killing marine bacteria.

"[T]he recovery of the non-tailed autolykiviruses represents a first step in revealing extensive missed diversity in one of the two major ancient lineages of dsDNA bacterial viruses, and suggests that their ecological and evolutionary importance for microbial systems is far greater than is currently recognized," co-senior authors Martin Polz, a civil and environmental engineering researcher at MIT, and Libusha Kelly, a systems and computational biology researcher at Albert Einstein College, and their colleagues wrote in a study published online today in Nature.

In an effort to uncover viruses that may have been missed in prior environmental analyses of tailed dsDNA viruses, the team used Illumina HiSeq instruments to sequence 241 randomly selected viruses associated with Vibrionaceae family bacteria cultured from marine samples collected off the coast of Massachusetts. The search led to non-tailed dsDNA viruses with relatively short genome sequences, spanning just 10,000 bases or so, with capsid proteins in the "double jelly roll" (DJR) lineage based on their fold patterns.

Those viral genomes "were quite different from other viruses," Polz said in a statement, noting that "we don't think it's ocean-specific."

When they began characterizing these viruses, he and his colleagues found that the genetically diverse autolykiviruses fell into a family with high levels of divergence from other virus families, particularly in their core gene sequences. Likewise, the researchers' assays indicated that the newly detected viruses have both a broad host range and potent bacteria-killing abilities.

"Ecologically, members of the Autolykiviridae have a broad host range, killing on average 34 hosts in four Vibrio [bacteria] species, in contrast to tailed viruses which killing average only two hosts in one species," the authors wrote.

Their follow-up experiments and bioinformatic analyses suggested that the DJR elements associated with the viruses can act as independently replicating episomes in their hosts or as prophages, tucking themselves in the genome of infected Vibrio bacteria. Such DJR viruses appear to be associated with bacteria and archaea from a range of environmental metagenomes, they reported, suggesting "the diversity and host associations of DJR viruses far exceeds the level that is currently recognized."

The team also noted that the Autolykiviridae family viruses may have been missed from prior viral diversity studies due to their distinct bacteria infectivity, DNA accessibility, and buoyant density profiles during sample preparation steps.

"Overall," the authors concluded, "these data suggest that viruses of the non-tailed dsDNA DJR lineage are important but often overlooked predators of bacteria and archaea that impose fundamentally different predation and gene transfer regimes on microbial systems than on tailed viruses, which form the basis of all environmental models of bacteria-virus interactions."