thescientist | The tree of life is dominated by microbes, but many large branches remain uncharted because scientists have been historically restricted to studying the small fraction of species that will grow in a lab. An international team of scientists has now begun to redress this bias, sequencing full genomes from single cells to bring the “uncultured majority” into view.
In total, the team identified more than 200 new microbial species belonging to 29 underrepresented or unknown lineages. And the results, published today (July 14) in Nature, were full of new metabolic abilities and genetic surprises.
“[There has been a] strong imperative to fill in the microbial tree of life,” said Philip Hugenholtz from the University of Queensland, one of the study’s leaders. “If you have an incomplete view of evolution—vastly incomplete in the case of microorganisms—you have a vastly incomplete understanding of biology.”
By sequencing DNA directly from environmental samples, geneticists have suggested that the two microbial domains of life—bacteria and archaea—include at least 60 major lineages (phyla), but just four of these account for more than 88 percent of cultivated microbes. Of the others, around half are “candidate phyla,” whose members have never been grown in lab cultures.
To fill these gaps, the team collected samples from nine diverse habitats, including industrial reactors, hot springs, and a gold mine. The researchers gravitated towards places that were low in oxygen since these tend to harbor a greater and more interesting spread of microbes than familiar sites like our bodies.
From these samples, Tanja Woyke from the Department of Energy’s Joint Genome Institute in California isolated 9,600 individual cells and amplified the genomes of around a third of these. If any of these genomes looked like they came from new lineages, the team sequenced them completely.
They ended up with 201 full genomes representing 21 bacterial lineages and 8 archaeal ones. Some of these were candidate phyla known only by abstract codes, but the team has now given them descriptive names based on the biology of their members. For example, EM19 is now Calescamantes (“heat lovers”) because they hail from an extremely hot environment, and OD1 is now Parcubacteria (“thrifty bacteria”) for its streamlined metabolism.