Viruses that infect bacteria are among the most abundant life forms on Earth. Oceans and soils, and potentially even our bodies, would be overrun with bacteria were it not for bacteriophages. A new study suggests that bacteriophages with RNA genomes play a much larger role in shaping the bacterial makeup of worldwide habitats than previously recognized.
While there are numerous studies describing the role of bacteriophages with DNA genomes in ecological processes, the role of bacteriophages with RNA genomes (RNA bacteriophages) is poorly understood. This gap in knowledge is in part because of the limited diversity of known RNA bacteriophages. This research begins to address this question by identifying 122 novel RNA bacteriophage partial genome sequences present in metagenomic datasets that are highly divergent from each other and previously described RNA bacteriophages. Additionally, many of these sequences contained novel properties, including novel genes, segmentation, and host range, expanding the frontiers of RNA bacteriophage genomics, evolution, and tropism. These novel RNA bacteriophage sequences were globally distributed from numerous ecological niches, including animal-associated and environmental habitats. These findings will facilitate our understanding of the role of the RNA bacteriophage in microbial communities. There are likely many more unrecognized RNA bacteriophages that remain to be discovered.
Hyperexpansion of RNA Bacteriophage Diversity. (2016) PLoS Biol 14(3): e1002409. doi: 10.1371/journal.pbio.1002409
Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the lim- ited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacterio- phages yielded multiple novel genome organizations. Furthermore, one RNA bacterio- phage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent.