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In our continued effort to understand the extent of microbial diversity on Earth, we are hamstrung by one inconvenient reality: it’s hard to get a given species alone. That’s the idea behind culturing – the process that allows scientists to study a single organism in isolation, unencumbered by predators or competitors. With a cultured microbe, you can eliminate a gene and see what happens, thereby linking a specific patch of DNA to a cellular function. But the vast majority of microbes are uncultured, making it difficult to establish exactly what they’re up to in the environment and which sorts of biological functions they’re capable of.
Nonetheless, we can sequence the DNA of these stubborn organisms and see how they compare with their cultured brethren, to see who’s who on the tree of life. Typically, this is done with a specific gene – the one that builds a piece of the protein-assembling ribosome. And while this gene shows how any microbe relates to any other, it's just 1,500 bases, meaning that all of the world’s diversity is compressed and biased by a small sampling of genetic code – kind of like trying to tell two songs apart after listening to just a few notes. Get more genes, and you’ve got more sequence space with which to discriminate two seemingly identical microbes.
That’s exactly what Christian Rinke of the Department of Energy’s Joint Genome Institute and a small army of co-authors set out to do. Using the rapidly advancing technology of single-cell genomics, they sequenced the full genomes of 201 microbes. Their results were published in Nature online on July 14th, and they constitute a substantial reconfiguration of the microbial tree of life.
The idea was to go after underrepresented branches of microbial diversity - so-called Microbial Dark Matter - for which additional information would have a disproportionately large effect on the tree’s overall shape. In pursuit of these recluses, Rinke and his colleagues sampled nine different habitats that were likely to house exotic or otherwise overlooked organisms: the South Atlantic tropical gyre, the Hawaiian Pacific, the Gulf of Maine, the Homestake Mine in South Dakota, British Columbia’s Sakinaw Lake, the Great Boiling Spring in Nevada, the East Pacific Rise hydrothermal vent, sediment from the bottom of the Etoliko Lagoon in Greece, and a bioreactor.
The extended sequences provide additional data, often correcting tree placements that had been based on fewer genes. The salt loving Nanohaloarchaeota were previously placed within the Euryarchaeota, but Rinke places them alongside Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Diapherotrites in the newly christened DPANN superphylum. Specific genes also reveal unexpected capabilities among certain organisms, providing a window into their way of life. Sugar-breakdown genes point to a heterotrophic metabolism, electron transport chain genes imply a range of respiration strategies, and genes encoding defensive molecules suggest a dynamic environmental context for certain microbes.
The study vastly expands our genomic knowledge of underrepresented microbes, but it doesn’t – and can’t – address one of the other problems associated with having so few organisms in culture: gene annotations. All of the assignments of particular functions highlighted above were made by comparing single cell genome sequences with similar sequences from cultured microbes.
In essence, you’re only going to find what you’re looking for, restricted to the catalog of parts that’s been assembled from the small subset of organisms that have been cultured. A gene from an uncultured archaeon from a hydrothermal vent, for example, may be very similar to one encoding a decarboxylase enzyme of E. coli, but that doesn’t always mean they’re producing the same thing.
The real question Rinke and other microbial ecologists are after is, Which organisms are where, and what are they doing? And while a genetic approach to this question is ultimately limited by our stock of cultured lab-rats, Rinke’s data offer an important advance. Placement on a phylogenetic tree often serves as shorthand for microbial lifestyle – closely branching groups may use similar energy sources or construct similar cell structures, for example.
And so, rather than trying to distinguish The Rolling Stones from Springsteen with a few notes, now we’ve got the whole song. When it comes to the meaning of the lyrics, however, we’re still largely in the dark.
