A New Field Guide for Earth's Wild Microbes

FREMONT, CA: There are hardly any places on Earth that aren't inhabited by microbes. They live in lakes, streams, soil, and air; they colonize our bodies and even reside in extreme environments like scalding hydrothermal vents and acidic hot springs. Yet scientists don’t know much about the majority of them. Getting a wild microbe to take root in a petri dish requires painstaking work, expert skills, and a lot of luck. It doesn't happen very often. All this changed recently.

But in November, researchers from the Department of Energy’s Joint Genome Institute announced a significant advance: They have assembled the largest catalog of microbes to date, containing over 50,000 genomes from 18,000 different microbial species- 12,000 of which have never been documented before. Their study, published in the journal Nature Biotechnology, expands this branch of the known tree of life by a whopping 44 percent.

In this new snapshot of life on Earth, scientists found many potentially useful things. Among them are thousands of new genes that encode enzymes with potential uses in medicine; scores of new strains of archaea; single-celled organisms that release carbon into the atmosphere; and a new species of the bacterium Coxiella, a genus that includes the class B bioterrorism agent Coxiella burnetii, a highly contagious bacteria that can jump from farm animals to humans causing a disease called Q Fever. They also found over 760,000 viruses and linked some of them to their bacterial and archeal hosts, further illuminating the vast interconnections in this unseen world.

The study of microbes began in the 17th century, when the Dutch microscopist Antonie van Leeuwenhoek peered through his single-lens microscope and discovered a hidden world. But in the centuries that followed, scientists have only put a small dent in identifying the full biodiversity of microbes on Earth. According to Stephen Nayfach, a bioinformatician at Lawrence Berkeley National Laboratory and lead author on the paper, the vast majority of microbes can't be grown under laboratory conditions, and that makes it nearly impossible to study many organisms using traditional methods.

One reason is that replicating the exact conditions of the biological soup needed for microbes to thrive is not easy. The quest to learn the secrets of one particular microbe buried in deep sea mud, for example, took a team of Japanese researchers 12 years. They had to find just the right combination of nutrients, gases and chemicals that allowed it to grow. The feat, which required adding a mixture of four different antibiotics to kill contaminating strains, was a major accomplishment celebrated in the scientific community. Studying this microbe, which they named Prometheoarchaeum syntrophicum after the Greek god who created humans out of mud, answered longstanding questions about how complex life on Earth evolved. But this type of effort cannot be repeated for all of the species of microbes in the world, so scientists needed to find a more efficient way.