A Massive Underground Find Revises the Tree of Life
So many new subterranean bacteria groups have just been found that the tree of life required a major revision.
The discovery of 47 new bacterial groups has just been reported from a single aquifer in Colorado, providing a vivid reminder of just how much life exists in the still mysterious subterranean world below our feet.
When added to 35 other new bacterial groups that were documented last year, the findings -- published in the journal Nature Communications -- double the number of the planet's known bacterial groups. As a result, dozens of new branches have just been added to the tree of life, essentially requiring a major revision of that all-encompassing diagram.
"We did not initially expect anything like the diversity that was encountered at the site," co-author Jill Banfield told Seeker, explaining that she and her team started working on the Rifle aquifer along the Colorado River in west central Colorado "over a decade ago with the objective of studying microbes that remove uranium contamination from groundwater."
Banfield is a senior faculty scientist in Berkeley Lab's Climate & Ecosystem Sciences Division and a UC Berkeley professor. As the years went on at the research site near Rifle, Colo., she and her team noticed how complex and interconnected the microbial world there was -- so they developed the research site into a model system to study underground microbiology.
The researchers found so many new microbes that they struggled over how to name them. The prior study mentioning the 35 other groups drew from past Microbiology Award winners. For this latest research, they "decided to honor well-regarded microbiologists from around the world," Banfield said. "We made sure to strike a gender balance to ensure that women were given their due."
Genome-editing pioneer Jennifer Doudna inspired Candidatus doudnabacteria, for example.
To detect such tiny microbes, the scientists sent soil and water samples to the Joint Genome Institute for sequencing. The high-tech method isolates and purifies DNA from environmental samples, and then sequences 1 trillion base pairs of DNA at a time. Banfield's lab developed tools to analyze the data, permitting the reconstruction of the genomes of more than 2,500 microbes.
The underground microbes may be tiny, but they are more important than most of us probably think.
Lead author Karthik Anantharaman told Seeker that they are involved in many essential processes, such as breaking down the components of fertilizers. Nitrate from fertilizers can enter groundwater, where it may lead to the production of one of the most potent greenhouse gases, nitrous oxide, if certain microbes are inactive.
As for how microbes deal with fertilizers and other substances, Anantharaman explained that one microbe's waste is another microbe's food. This creates a tightly interconnected system.
"It is striking," he said, "that microbes need teamwork to complete tasks. It is precisely this lack of effective teamwork that can throw processes off sync and lead to release of greenhouse gases like nitrous oxide."
Banfield added that bacterial organisms in a particular community are extremely dynamic and change rapidly with conditions, for example, local pollution. Considered globally, the microbial world hosts up to one-fifth of all biomass.
The new findings have numerous potential applications in biotechnology, the researchers said, including protein engineering and the discovery of antibiotics.
"Through study of a single aquifer, we genomically resolved as many new major bacterial groups as were previously known through traditional methods. ," Banfield said. "Through study of a single aquifer, we genomically resolved as many new major bacterial groups as were previously known through traditional methods. Their genomes are full of novel enzymes and probably encode capacities that we have not yet even imagined."
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