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They were right under our noses all along – thousands of novel microscopic life forms, now unmasked by genetic analysis. Many belong to entirely new groups, as different from other microbes as an insect is from a chimpanzee.

Earth’s microorganisms are split into groups called bacteria and archaea. Together, they make up the vast majority of species on the planet, but until recently we were only able to study a tiny fraction of them.

This is because less than 10 per cent can be isolated and grown in the lab. The rest can only survive in the conditions of their native environment – be it a hydrothermal vent or the guts of a cow. Researchers call them microbial dark matter.

However, a technique called metagenomics is bringing them to light. It involves taking an environmental sample, sequencing all the DNA in it – its metagenome – then piecing together the genomes of each of the microbes present. “It’s like getting a mix-up of lots of different jigsaw puzzles, and then trying to put together the pieces of each individual puzzle,” says at the University of Queensland in Australia.

Parks and his colleagues analysed more than 1500 metagenomes that researchers worldwide had uploaded to a public database. Each contained jumbles of DNA sequences collected from environments such as soil, the ocean, hydrothermal vents, industrial effluent, and cow and baboon faeces.

Crazy new levels of stuff

Using heavy-duty computers to sift through this mess, the team ultimately reconstructed 7280 bacterial and 623 archaeal genomes – about a third of which were new to science.

The newly identified microbes added 20 major branches, or phyla, to the tree of life. “To give this context, every single insect on Earth belongs to just one phylum, and every single animal with a backbone belongs to one phylum, so this is crazy new levels of stuff,” says at the University of Sydney.

The next step will be to discover what the new microbes are like. “This study has put names on that dark matter,” says Coleman. “Now we need to figure out what it’s actually doing and how we can benefit from it.”

One way will be to scan their genomes for genes that look like those of well-known organisms. “For example, they might have a gene that looks similar to a methane metabolism gene,” says Parks. However, many of the genomes are highly novel, so it will take longer to understand them.

Antibiotic potential

The new microbes could yield novel antibiotics, which are almost always discovered in bacteria and fungi. They could also be put to use in industry and environmental management: to break down plastic pollution, or make fuel and industrial chemicals, for instance. “The better we can grasp the diversity of microbes, the more we can go looking for things that are useful,” says Coleman.

More profoundly, the expanded tree of life will help us trace our deepest origins. “All the questions we have about ancient evolutionary events – what our last common ancestor looked like, when methane metabolism arose, when oxygen-producing organisms evolved – they really benefit from having more genomes to look at and a more detailed tree,” says Parks.

But the big question is how many more species there are to find. At the moment, we simply don’t know.

Previous studies have estimated that , with . “But this is probably an underestimate, as we’ve recently found that existing methods for estimating this actually miss a lot of organisms,” says Parks.

However, the discovery of new phyla does seem to be levelling off, says his co-author at the University of Queensland. So although there are plenty more microbial species left to find, they may fill up known branches of the family tree rather than starting major new ones.

Teams are mining several other public data sets of metagenomes and already identifying tens of thousands more microbial species, says Hugenholtz. “This is just the beginning,” he says. “It’s going to go off the charts.”

“There’s still a whole lot that we don’t know,” says Coleman. “There are so many crazy environments out there, and even two patches of dirt side-by-side can have different organisms.”