A University of Nebraska–Lincoln research team has identified new microscopic players in the global carbon cycle, a discovery that paints a clearer picture of carbon flow through the environment and provides key information for the sustainable development of bioenergy sources.
A recent publication in Communications Earth and Environment is among the first studies to show that methanogens — microorganisms ubiquitous in low-oxygen environments like lakes, wetlands, aquifers, freshwater habitats, a variety of soils and even permafrost — can propel their growth by consuming hydrogen and dissolving calcium carbonate, one of Earth's most abundant minerals. This metabolic process produces methane, which is both a biofuel and a potent greenhouse gas.
"This is one of the first demonstrations of microbial dissolution of calcium carbonate at a higher pH," said Karrie Weber, professor of biological sciences and Earth and atmospheric sciences.
Weber and Nicole Fiore, a lecturer and former graduate student in biological sciences, led the Husker team. The paper culminates more than a decade of work at the university, including contributions from many graduate and undergraduate students, and postdoctoral researchers.
By pinpointing the carbonate-dissolving microorganisms, the team has challenged the prevailing belief that carbonate minerals — which contain roughly 80% of the Earth's carbon — are stable at elevated pH levels. This potential instability means that in certain locations — where there is subsurface carbon sequestered as carbonates and conditions that support microbial life — the sequestered carbon may be converted to methane, especially in underground hydrogen energy reservoirs.
"Something to consider, when looking at these kinds of strategies, is whether there are methanogens present and the extent to which they might be able to undo what we are doing with mineral sequestration," said Fiore, whose National Science Foundation Graduate Research Fellowship funded a portion of the work.
The work started with a mud sample from alkaline saline wetland soil in Lincoln. The researchers already knew that any methanogens in the sample would consume hydrogen — but they did not know if the microbes could dissolve calcium carbonate to generate methane. To answer this question, they created special culture conditions that included hydrogen and calcium carbonate, an environment designed to weed out microorganisms not capable of using the carbonate.
A small community of microorganisms survived the culture process, the genomes of which the researchers constructed using a technique called genome-resolved metagenomics. The community contained not only methanogens, but five types of bacteria. The team was able to visualize these microbes using Nebraska's CARS (coherent anti-Stokes Raman scattering) microscope, part of the Laser Assisted Nano Engineering Lab. The work demonstrated that the microbes were attached to the carbonate mineral's surface.
In a departure from other studies exploring this question, the Husker team strictly controlled the pH level — the acidity or basicity — of the culture. This is because carbonate minerals change state when pH levels fluctuate. By holding pH steady, the team ensured that mineral dissolution could be more definitively attributed to the microorganisms' metabolism rather than the culture's shifting chemistry.
Methanogens' metabolism has consequences in the bioenergy realm. Researchers are increasingly interested in using natural hydrogen as a clean fuel — Nebraska, in fact, is home to the United States' first well drilled to find naturally occurring hydrogen. Weber said it is important to determine the extent to which microbial processes may impact subsurface hydrogen reservoirs. Another avenue to explore is whether the methane that methanogens produce can be harnessed as an alternative natural gas, in addition to subsurface hydrogen.
The next step, Weber said, is determining which other carbonate materials methanogens are capable of dissolving and searching for biosignatures that confirm the dissolution process is happening in the environment — not just in the laboratory. The team believes it is likely occurring worldwide, as both carbonates and the same type of methanogens are side by side in many locations across the globe.
"This is local research with global significance," Weber said.
In addition to Fiore's NSF grant, the work was supported by a NASA Nebraska Space Grant and funding from the Nebraska Center for Energy Sciences Research and the NSF-funded Center for Root and Rhizobiome Innovation.
Other Husker authors are Xi Huang, research assistant professor in electrical and computer engineering; Yongfeng Lu, Lott Distinguished Professor of electrical and computer engineering; Nicole Buan, professor of biochemistry; Dan Miller, adjunct faculty in agronomy and horticulture and a Lincoln-based research microbiologist with the U.S. Department of Agriculture; former postdoctoral researcher Sanjay Antony-Babu; and former students Anthony Kohtz, Donald Pan and Caitlin Lahey.
