Microbial Wonders
Stephanie McPherson for TEI
Microscopic organisms make up more than half the biomass on Earth, and Klaus Nüsslein, Associate Professor of Microbiology, is investigating how they work. “They own this planet. There is more biomass in microbes than there is in plants,” says Nüsslein. The hundreds of thousands of microbe species live and work together. It is near impossible to find one species living on its own. “They live together in the amount of a billion in [a gram of] soil. So how is that possible?” Nüsslein is focusing on three major areas of study to understand how microbes function in their various ecosystems, with emphasis on stressful environments.
The first area of research focus is the deep underground layers of organically rich sediments such as shale and coal, invaluable to the production of energy. Currently, companies drill wells and extract the materials using less than environmentally ideal processes. Nüsslein is interested in using microbes to produce methane gas from the wells without removing sediment. Since food sources are scarce in this deep subsurface, microbes found here have been forced to evolve alternate methods of energy intake. They have developed a way of eating organic materials in the rock and, in the process, emitting methane gas. “Instead of surfacing this rock, you could surface the gas,” Nüsslein says. “And this country sits on huge reserves of this kind of organic matter. Again, it’s fossil fuel, but microbes would help transfer this unreachable fuel from this type of rock into a gas we can use.”
The major question to be answered is how the microbes are able to live off these materials. To date, no one has figured out the exact process through which microbes metabolize the rock. “A microbe is tiny. It sits in front of these long chains of carbon. What scissors do they use to cut out a piece?” Nüsslein asks. He is trying to determine which microbes are doing the work, and exactly how the process occurs. He is examining the chain of reactions within the microbe communities to see the steps taken from coal to gas. He is also examining different sizes of coal, big chunks to pulverized bits, to determine whether or not surface area effects methane production. Nüsslein also is analyzing the presence of lipids in the rocks to see if microbes are living off the fatty molecules.
In another project co-funded by the National Science Foundation and the U.S. Department of Agriculture, Nüsslein is studying microbial diversity in the Amazon Rainforest to determine if it mirrors the biological diversity of rainforest plants and animals. Nüsslein and his collaborators at the University of Oregon, Michigan State University, the University of Texas, and the University of Sao Paulo are asking if, when a rainforest is cleared for farmland, the microbial diversity decreases. They also plan to monitor whether or not the diversity returns when the farmland is no longer in production and evolves into a secondary rainforest. “Does it ever come back to the same functions?” Nüsslein asks. “Will it be an active, healthy ecosystem? Will it be as strong as it was before, or will it never be the same?” The team is taking soil samples from a farm in Rondônia, Brazil to determine what microbes reside in the soil samples. Because of the immense microbial diversity, identifying all species present would be difficult. Instead, they are analyzing 400,000 DNA samples at a time for ID purposes, focusing on two strands of microbes dominant in a range of soils whose functions are widely known. One microbe thrives in nutrient limiting conditions while the other has a large genome, which allows it to thrive in environments rich in nutrients. The team will analyze the genomes to see if any beneficial shifts occur from rainforest to farmland ecology. Nüsslein hopes the data gathered will indicate the stress levels occurring within the changing environments.
Another field of research interest is bioremediation, the practice of using biomass to reduce toxins in the environment. One project pairs Nüsslein with researchers in Civil and Environmental Engineering to develop a more efficient means of removing the toxin perchlorate from ground water. Perchlorate is a chemical used to deliver oxygen during reactions and can be found in explosives such as roadside flares, fireworks and military weapons. When consumed in drinking water, it can block the human thyroid gland and is particularly dangerous for pregnant women and newborns where it can cause serious problems in neurodevelopment.
The Massachusetts Military Reservation in Bourne, Massachusetts is currently dealing with perchlorate contamination by pumping the water from the ground and passing it through filters filled with resin. This method cleans effectively, but creates other problems. “You have this resin, this granulated chemical substrate that is loaded with perchlorate,” Nüsslein says. “Where do you put it?” It is usually dumped in a landfill, but that does not really solve anything. It’s also costly, in monetary and energy terms, requiring the removal of large tanks full of resin. Nüsslein knows certain microbes use perchlorate for energy, so he wants to employ the microscopic communities to remediate the problem. Nüsslein and his team have created a small, trash can-sized test filter in which microbes are placed along with elemental sulfur. As the water flows through the reactor, the microbes feed on the sulfur and use the perchlorate, effectively reducing the contaminants present in the water. “We tell the engineers what the microbes really like and the engineers build systems and test them out to optimize them, and together we develop this project,” says Nüsslein. He says the project is already seeing success and could be commercially viable in three or four years.
Another bioremediation project has Nüsslein working on acid mine drainage, namely at Davis Mine in Rowe, Mass. After its collapse, the mine filled with groundwater which started to leak as acid streams near its opening, but further downstream the acid was neutralized and the water became more and more clear. Together with hydrologists, engineers and geologists Nüsslein examined the water, trying to determine the cause of the self-cleaning. Eventually, the team realized it was due to the work of acidophiles, or acid-loving microbes. There was an overwhelming microbial diversity in the acid mine area, but Nüsslein and his team eventually pinpointed the natural filter. A large group of microbes called sulfate loving bacteria were able to “breathe” the sulfate which, when combined with the water, was creating sulfuric acid. By removing the sulfate, they removed the acid. The stream was also rich with heavy metals, and the microbes took care of that issue as well. “They take the sulfate and turn it into H2S, or sulfide,” Nüsslein says. “If this H2S reacts with any dissolved metal, they make a strong chemical bond, crash out as sediment and will remain stable. They don’t dissolve again.” A member of Nüsslein’s research group has been working on ways to support these acid-loving microbes. By understanding how the tiny organisms work, they hope to make the filter process more efficient and applicable to other similar sites around the world. “Engineers say we harness the power of the microbes,” Nüsslein says. “We say we harness the knowledge of the microbes, because we try to understand what the microbes are doing. We don’t just use them as tools.”
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