Most of the life on Earth comes in the form of small, single-celled organisms. But even though we knew there was incredible diversity at the microbial level, these cells all look pretty similar under a microscope. For many of the bacterial species we've identified, the key step has been growing them in a flask so we can generate large enough numbers to study them.

Over the past decade, the advent of cheap DNA sequencing technology has helped the microbe discovery process along. Currently, we can sequence huge populations of microbes and get fragments of sequences that give us some sense of the full diversity of life. But these sequences tell us little more than the fact that a species exists. We still often know little about what it is and how it manages to make a living.

Now some researchers have managed to generate a genome sequence from a single bacterium, and they have used this technique to scan for new species in a biofilm isolated from a hospital sink. The results include the genome of a previously unrecognized phylum of bacteria, called TM6, that appears to be an obligate symbiote, perhaps living inside another cell found in the biofilm.

Researchers tend to work with bacteria that grow in a liquid culture but most bacteria don't live that way. Instead they form biofilms, a dense mesh of material that is inhabited by entire communities of bacteria and which hosts multiple species. It's easy to do some DNA sequencing to figure out how many species inhabit these biofilms, but finding out more about the species is tough, because many of them won't survive in the oxygen rich culture conditions that are typically used.

To get around this, an international team of researchers has developed a technique for isolating individual bacterial cells with a cell-sorting machine. At first, they kept isolating fragments of the biofilm rather than cells, so they ended up having to pool anywhere from 20-100 items the machine called "cells" in order to increase the chances of having a single cell present. Most of these cells were things we already knew about, so the authors started doing some quick checks of some key genes that encode ribosomal RNA. If those indicated the sample had a single cell and the cell wasn't already known, they produced an entire genome from it.

This week, the group released a paper on a genome from a group of species called TM6. The name comes from “Torf, Mittlere Schicht,” which is “peat, middle layer” in German. That's the first case instance where the ribosomal RNA for this group of species had appeared but since then it's been found in a host of environmental samples: domestic water sources, acidic cave biofilms, acid mine drainage biofilms, wastewater biofilms, soil, contaminated groundwater and subsurface sites, aquatic moss, hypersaline mats, peat bogs, and peat swamps. The ribosomal RNA had suggested it was distantly related to all the bacterial groupings we knew about, and now the genome confirms it.

Perhaps the most striking thing about it is the fact that fully 43 percent of the genes appear to encode proteins that we've never seen before. Typically, due to a combination of common descent and gene transfer, many of the genes in new species are familiar. This one is so far out, most of them don't look like anything we know about. Which, of course, makes it hard to predict what they might do.

In contrast, when it comes to familiar genes, many are missing in action. The TM6 genome seems to have a stripped down metabolism that's probably anaerobic. It doesn't seem to be able to make its own amino acids or nucleotides (protein and DNA components, respectively) and it can't make a flagella to move itself around. All of which suggests it's probably a symbiotic organism, cooperating with another species to share vital biochemicals that only one of the two can produce.

What might it be living with? Some of the genome hints that it may be a eukaryote like an amoeba. A few of the genes seem to contain sequences that are typically only found in eukaryotes (larger cells with a nucleus), suggesting they got in this new species via horizontal transfer of some DNA. This is quite common among bacteria that live inside their hosts, suggesting that TM6's host is a eukaryote. In the past, amoeba have been found in biofilms, which often carry a number of bacterial species along with them.

Overall, the genome sequences don't match up well with anything we know, suggesting that TM6 represents an entirely new phylum of bacteria. Its closest relatives are the Acidobacteria, which themselves had gone unrecognized until the 1990s. If this holds up, it will continue the bacteria's remarkable expansion. They started with just 11 phyla back in 1987, and most recent estimates now say that there are 30 bacterial phyla on the planet. TM6 is likely to make that count 31.

Who knows what we'll find when we start looking beyond a hospital sink's drain.

PNAS, 2013. DOI: 10.1073/pnas.1219809110 (About DOIs).