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Novel bacteria discovered in the KBS LTER experiment
As you walk across a grassy field or forest floor, you are stepping on millions of undiscovered organisms. Invisible to the naked eye and weighing next to nothing, their strength lies in their numbers. In one teaspoon of soil, there are approximately 100,000,000,000 organisms, most of which have yet to be identified and named.
Recently, KBS LTER researchers discovered several new species of bacteria from the phylum Acidobacteria, one of the most abundant phyla in soils anywhere in the world. Using KBS LTER soils, they were the first scientists to isolate and name these bacteria. Isolating bacteria—taking them from soil and growing them in pure colonies in the lab—is necessary for scientists to be able to study the role of bacteria in ecosystems, and to determine if they produce useful products such as antibiotics or pesticides.
The researchers chose to look for new species in the phylum Acidobacteria because even though it’s so abundant, very few of its species have been cultivated (grown) in the lab. In other words, it was one of the world’s major phyla of bacteria, but scientists basically knew nothing about it!
To isolate the bacteria, the scientists first extracted DNA from the LTER soils and sequenced (mapped) it. They were looking for a particular gene they knew the Acidobacteria to have. The sequencing method destroys all of the organisms in the soil, but it gives the scientists a “fingerprint” of the microbes in the soil. Next, they compared this “fingerprint” to a database that lists all of the bacteria known to have that particular gene—over one million organisms to date. Hundreds of microbiologists from all over the world contribute information to this database. Using this database, KBS scientists confirmed that the bacteria from the LTER soils had never been cultivated in a lab.
Finding the right conditions to cultivate bacteria takes a long time. Even though humans have been cultivating bacteria from the soil for hundreds of years, no one had been able to figure out the right conditions (temperature, moisture, food) for growing Acidobacteria in the lab. Using a new technology that rapidly screened different growing conditions, the scientists discovered that the bacteria prefer one-tenth the amount of oxygen that ambient air has. Oxygen is a double-edged sword for humans and bacteria alike. While we need it to breathe, oxygen also produces toxic particles called oxygen radicals, which is why doctors advise a diet rich in anti-oxidants. These oxygen radicals are toxic to bacteria as well. When placed in low oxygen conditions, the bacteria were better able to survive and grow. However, the scientists soon learned that unlike most bacteria, Acidobacteria are very slow growing, taking weeks for a colony to become large enough to study.
This slow growth may have important consequences for how much carbon can be stored in soils, an issue directly linked to global climate change. Soils have the potential to mitigate—reduce the severity of—global climate change by storing carbon and keeping it out of the atmosphere. This is commonly referred to as soil carbon sequestration. Because the Acidobacteria grow much slower than most soil bacteria, scientists believe they may behave differently in how they store and release carbon. This is just one example of the huge impact these millions of soil bacteria have on ecosystems and human life.