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Biological Sciences Division
Research Highlights

October 2015

The Difference a Day (or Night) Makes

Studying the diel cycle gives rise to new hypotheses about microbial community behavior

earth in day and night with microbial mat sample
The diel cycle—the 24-hour period encompassing night and day—impacts the behavior and interaction of microbial communities within mats that grow in hot springs. Understanding these impacts can help efforts to use such communities to produce biochemicals and bioenergy.

Anyone who has encountered slime built up on a shower curtain has experienced nature's ability to generate a thriving microbial community where most macro organisms, such as humans, would find little sustenance. But how a microbial community self-assembles is often mysterious to researchers who want to harness the abilities of these communities to produce chemicals and energy that can be substituted for those originating from fossil fuels. What researchers do know is that if they want to use microbial communities to produce biochemicals and bioenergy, they need to learn how those community members interact.

Results. In a study recently published in Frontiers in Microbiology, PNNL scientists Young-Mo Kim, Jim Fredrickson, and Tom Metz demonstrated the effect that sunlight or the absence thereof over a 24-hour period-the diel cycle-has on the production of chemicals used as metabolites in the microbial mats of Mushroom Springs in Yellowstone National Park. The microbial mats, which are layered accretions of microorganisms, look like slimy bright green floor mats growing in and around the hot springs. These microorganisms are able to grow in waters that are 60-65 degrees Celsius, about the drinking temperature of tea.

researchers in lab
PNNL scientists Young-Mo Kim (right) and Erin Baker prepare microbial samples for omics analyses. Kim is the first author of a recently published study that demonstrated the effect that the diel cycle has on microbial mats of Mushroom Springs in Yellowstone National Park. Enlarge Image.

Earlier research established that these mat communities are highly dependent on exposure to light. The microorganisms living in the top layer of the mats, mostly cyanobacteria, use energy from the sun to create sugars using photosynthesis. PNNL team members and collaborators at Montana State University, Penn State, Temple University, and the University of Copenhagen were able to detect the accumulation of storage molecules for photosynthesis products during the day. They also observed glycolate during peak sunlight and lactate in the afternoon and evening. Glycolate is an indicator of high levels of photosynthesis, whereas lactate is created during fermentation, suggesting that some mat organisms were using fermentation as a source of energy during the afternoon.

Although some of these results matched predictions gleaned from earlier studies, some were more surprising.

"We were expecting fully that glycolate would show peak abundance at midday based on previous studies by our collaborators," Metz said. "But we did not expect a peak in lactate during the afternoon since it would normally occur in the evening." Metz thinks this has to do with how the cyanobacteria prevent sun damage.

"One of the new hypotheses that we came up with is that in the afternoon, when the light intensity is the greatest, some of the organisms doing photosynthesis might be so bombarded with light that they might have to shut down their light-harvesting mechanisms just to protect themselves," he said.

Why It Matters. According to Kim, "The reason many scientists do genomics and transcriptomics on Yellowstone microbial communities is because they are not very complex, so we can detect which molecules came from which organism." Studying what segments of DNA (genes) are present in the community (the community's genome), as well as what genes are being activated (the transcriptome) will often show the metabolic potential of a community. However, researchers can't know if that potential is being realized without measuring the metabolites. Additionally, many of the chemicals circulating in the mat can be used by different community members, creating symbioses that could be leveraged for future industrial processes. 

Methods. Kim and Metz used metabolomics, the study of the full array of metabolites produced by an organism, to investigate how microbial mat communities feed themselves and exchange nutrients. When prior studies showed changes in gene expression for metabolism between daytime and nighttime in the Mushroom Springs mat, it was an opportunity for scientists like Kim.

"We wanted to confirm that those changes were real," he said. The PNNL researchers took samples from the mat over a 24-hour period and ultimately detected 104 metabolites.

What's Next? Metz and Kim will continue studying the metabolites that flow through microbial communities to determine what principles govern their interactions. "Principles," said Metz, "that are hopefully fundamental to any microbial community and, once learned, can be manipulated for the benefit of people through the production of biofuels and other commodity chemicals."


Sponsors: This research was supported by the Genome Science Program (GSP), U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER), under the PNNL Foundational Scientific Focus Area. Funding was also provided by the National Science Foundation and the Montana Space Grant Consortium. Portions of this research were enabled by capabilities developed as part of the PNNL Pan-omics Program under support from the BER GSP. Metabolite measurements were performed in EMSL, a national scientific user facility sponsored by BER and located at PNNL.

Research Team: Young-Mo Kim, Thomas O Metz, and James K Fredrickson (PNNL); Shane Nowack, Millie T Olsen, Eric D Becraft, Jason M Wood, and David M Ward (Montana State University); Vera Thiel and Donald A Bryant (Penn State); Isaac Klapper (Temple University); and Michael Kühl (University of Copenhagen).

Reference: Kim Y-M, S Nowack, MT Olsen, ED Becraft, JM Wood, V Thiel, I Klapper, M Kühl, JK Fredrickson, DA Bryant, DM Ward, and TO Metz. 2015. "Diel Metabolomics Analysis of a Hot Spring Chlorophototrophic Microbial Mat Leads to New Hypotheses of Community Member Metabolisms." Frontiers in Microbiology 6:209. DOI: 10.3389/fmicb.2015.00209.

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About Omics: Omics is a term appended to biological technologies that attempt to characterize the entire set of molecules belonging to a subject or system of interest. Metabolomics, for example, is the study of all of the metabolites within a study's scope, be it a cell, an organism, or a microbial community. The goal of proteomic, genomic, and transcriptomic technologies, respectively, is to characterize the proteins, genes, or activated genes (transcripts) within a study's scope of interest. Used together, omics can provide a detailed picture of the system under study, giving researchers a powerful tool to control the outputs of that system.

Yellowstone Hot Springs: The hot springs at Yellowstone National Park are famous in microbiology circles because they were where the microorganism Thermus aquaticus was first discovered. T. aquaticus's ability to thrive at high temperatures allowed researchers to develop the technology used to increase trace amounts of DNA to amounts that can be used for a variety of analysis techniques. DNA amplification has been crucial in many fields, from biotech to forensics, and ultimately netted its creator a Nobel Prize.