A novel freshwater PP-like cyanophage with an unknown source endonuclease VII gene

Viruses that infect bacteria are everywhere in our water, acting as invisible regulators of the microbial world. Among these, a specific group called cyanophages targets cyanobacteria, the ancient, photosynthetic organisms often called blue-green algae. These tiny viruses play a massive role in aquatic ecosystems, helping to control algal populations, recycle nutrients, and even influence the global carbon cycle. A key mechanism in their life cycle involves swapping genetic material with their hosts and with other viruses, a process known as horizontal gene transfer. This genetic shuffling allows viruses to adapt quickly, sometimes picking up tools from completely unrelated organisms to help them survive. Understanding how these viruses acquire new genes helps scientists map the complex web of life in our lakes and oceans, revealing how evolution operates on a microscopic scale.

In a recent study, researchers isolated a new virus from the surface waters of East Lake in Wuhan, China. They named this virus PP-DH22. It specifically infects two types of filamentous cyanobacteria, Plectonema boryanum and Phormidium foveolarum. When the scientists examined the virus's genetic blueprint, they found it looked almost identical to a well-known virus called PP, which was discovered in the same lake decades ago. The two viruses share a nearly identical genome structure, size, and the same set of genes for building their protein shells and tails. However, a closer look at the genetic sequence revealed a startling anomaly that suggests this new virus has been borrowing tools from a very different source.

The researchers discovered that PP-DH22 possesses a second copy of a specific gene called endonuclease VII. This gene is a molecular tool that helps viruses repair and recombine their DNA, essentially acting as a pair of scissors that cuts and pastes genetic strands. While the first copy of this gene in PP-DH22 matched the version found in other similar cyanophages, the second copy told a different story. When the team compared the sequence of this second gene to a vast database of known viruses, it did not match its cousins in the cyanophage family. Instead, it showed a much stronger resemblance to a gene found in a virus that infects Escherichia coli, a bacterium commonly found in the intestines of humans and animals.

The genetic similarity between this second gene in the lake virus and the E. coli virus was significantly higher than the similarity between the lake virus and its own close relatives. This discrepancy points to a rare event where the virus likely picked up the gene from a completely different type of host, possibly an E. coli or a related bacterium, rather than inheriting it from a cyanophage ancestor. The researchers noted that while the virus currently only infects cyanobacteria, the presence of this foreign gene hints at a broader evolutionary history. It suggests that the virus may have the potential to interact with a wider range of bacterial hosts than previously thought, or that it has successfully integrated a foreign tool to enhance its own survival strategies.

The study confirms that PP-DH22 is a distinct member of the PP-like cyanophage family, sharing a 99.97 percent genetic identity with the original PP virus in most of its genome. Yet, this single, unexpected gene stands out as a clear marker of cross-species genetic exchange. The findings reinforce the idea that viruses are not isolated entities but dynamic participants in a global network of gene flow. By carrying a gene that looks more like it belongs to a gut bacterium's virus than to a lake-dwelling cyanophage, PP-DH22 provides a concrete example of how viruses can bridge the gap between vastly different biological worlds, reshaping their own genetic makeup to navigate the complex environments they inhabit.