Sunday, February 8, 2015

A Primer on Phages

A group of phages, in green, attacks an E. coli cell, injecting their DNA through the cell membrane. Credit Image from Eye of Science / Science Source 

Phages, more formally known as bacteriophages, are viruses that infect bacteria. They are easily as ubiquitous, universal, and essential to life on Earth as light and soil, and yet they are largely unknown. “It’s kind of phenomenal, really,” Rohwer told me recently, sounding cheerful. “The thing that even most biologists don’t get—let alone most of the rest of the world—is that phages are the most diverse things on the planet, and there are more of them than anything else, and we really don’t have a clue”—he giggled—“what they’re doing.”
Rohwer and his colleagues recently published a book, “Life in Our Phage World,” that serves as a field guide to the tiny portion of phagedom that has so far been explored. (A PDF version is available online for free.) As the book’s handsome illustrations, by the artists Ben Darby and Leah Pantéa, show, phages possess a wide array of forms and functions. They are all incredibly small; at just a few nanometres across, they lie on the border of measurability between quantum and classical physics, all but impossible to see without a scanning electron microscope. Like their hosts, phages are everywhere—in dirt, water, intestines, hot springs, Arctic ice cores. They float about, awaiting a microbial encounter, then attach themselves to their preferred targets using a remarkable array of equipment—arms like grappling hooks, tails like hypodermic needles, fibres like teeth—each of which is perfectly adapted to bind to, and then sneak genetic material through, the bacterial membrane. Once inside the cell, some phages replicate at speed, destroying the host by bursting out of it, like a fungus dispersing its spores. Others are parasitic, integrating their DNA with that of their host. Sometimes they even provide it a benefit of some kind.
The book is full of astonishing phage statistics. There are, for example, an estimated 1031—ten million trillion trillion—phages on Earth, more than every other organism, including bacteria, put together. The average teaspoon of seawater contains five times as many phages as there are people in Rio de Janeiro. According to researchers in Vancouver, these tiny viruses cause a collective trillion trillion successful infections per second, in the process destroying up to forty per cent of all bacterial cells in the ocean every single day. Following their deaths at the hands of phages, those carbon-containing microorganisms sink down into the marine sediment, effectively removing greenhouse gases from circulation.
Anything that bacteria do, from breaking down the carcasses of dead animals to converting atmospheric nitrogen into plant food, is at the mercy of the phages that infect, kill, or otherwise transform them. Phages are the puppet masters; they insure that essential biochemical processes run smoothly. But, given how recent much of the research on the importance of bacteria is—look at the flurry of excitement around the human microbiome, or the much heralded “second green revolution”—it stands to reason that our understanding of phages is even less developed. Rohwer is bullish on the possibilities. Forget the probiotic, he says; the future lies with the prophage. “We’re going to hack the human microbiome with our phages,” he says. “You are going to see people manipulating individual bacteria species in someone’s gut with a bacteriophage before too long, because it’s not very hard to do.”
It is amazing how little we really know about how nature works.  That photo above looks like some kind of viral pornography.  I didn't know these things were infecting bacteria everywhere.  It will be interesting if the science of the microbiome can live up to the expectations of some scientists going forward.

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