Extreme Living: How Microbial Communities Fare in Hot Springs

Devaki Bhaya still remembers her first visit to Yellowstone National Park. 

Bhaya and family trekked to Yellowstone Park with Montana State University professor Dave Ward, where Ward wanted to bring state-of-the-art molecular tools to study hot spring ecology. Yellowstone features more than 10,000 hydrothermal features including hot springs. 

Ward, along with distinguished microbiologists such as Tom Brock and Dick Castenholz, made landmark discoveries about life in these inhospitable, early Earth-like areas. 

“Our first visit was just mind-blowing, and it seemed like we had stepped into a primeval world of steam and sulfurous vapors, capricious hot springs, and boiling mud pots,” said Bhaya, a senior scientist at Carnegie Science on the Stanford University campus. “And of course, I was drawn to the range of colorful complex biofilms at the edges of the hot springs.” 

Bhaya realized that Yellowstone provided the perfect location to test out some particular scientific questions: 

• How do microbes live in and adapt to these hostile environments, particularly the scalding high temperatures? 
• Could molecular tools be used to analyze the functions and interactions of these ancient resilient communities? 

She even wondered if these microbial communities may help reveal secrets about the origins of life itself. 

Bhaya led research looking at how cyanobacteria in extreme conditions affect microbial communities living in Yellowstone hot springs. This research was funded by the National Science Foundation (NSF) and more recently by a user project at the Environmental Molecular Sciences Laboratory (EMSL). 

Bhaya recently spoke about her research on extremophiles—the organisms that not only live, but thrive, in extreme environments like hot springs—on an episode of the National Public Radio Short Wave podcast. 

EMSL User Research on Extremophiles 

Several years ago, a group of researchers including Bhaya received NSF funding to examine how extremophiles adapt to high temperatures. Among other discoveries, they found to their surprise that cyanobacteria in these hot spring communities have dynamic or fluid genomes. They noted several examples of horizontal gene transfer likely facilitated by active transposons, which are DNA that move from one location to another within a gene. In one instance, they found evidence of the acquisition of a​n entire​ nitrogen fixation module by horizontal gene transfer. They were able to show that this allowed cyanobacteria to grow in this nutrient poor environment. 

To extend their molecular ecology studies, the research team wanted to know how community members collaborated to share resources such as light and metabolites. 

Bhaya was awarded access to EMSL instrumentation and expertise through the EMSL Exploratory Research proposal call for her project, "Diel dynamics and physical interactions of phototrophic isolates from a hot spring microbial mat." 

Through this research, the team sought to study the effects of cyanobacteria on microbial function and to develop a predictive understanding of the impacts on the cycling of metabolites and nutrients on other biological and biogeochemical processes. They used a binary consortium of two abundant organisms, an autotrophic cyanobacterium Synechococcus (recently renamed Thermostichus sp.) and Chloroflexus sp., a filamentous photoheterotroph. 

Bhaya ​and group ​used EMSL’s Aquilos 2 dual beam cryogenic focused ion beam scanning electron microscope to probe the interactions between microbes under specific light conditions. 

“Access to such an instrument allowed us to generate images that were very useful,” Bhaya said. 

Results and Next Steps for Extremophile Research 

Bhaya’s EMSL project gave her insights into how these phototrophic organisms move in response to light and how they might organize themselves into spatially structured biofilms to optimize light utilization. The research was recently published in the journal Proceedings of the National Academy of Sciences (PNAS). 

Bhaya and the research team now plan to detail the interactions between two major phototrophic organisms of a microbial community and gain insight into their individual behaviors that can inform a larger model of community behavior. Thermophilic phototrophic communities can serve to unveil links between energy production and the living environment. The team is also exploring the role and activity of other less well understood community members, including the unexplored role of viruses and plasmids in biofilms. 

“We are also currently writing up a manuscript that focuses on proteomic data generated at EMSL,” Bhaya explained. We hope this will set the stage for a more complex project that develops methods to probe complex consortia.” 

“Actually, looking back on almost two decades of working with extremophiles, I can’t help but notice how our understanding of interactions in microbial communities has become more nuanced, often based on new technologies, and propelled us to ask new questions,” Bhaya reflected. 

Read the published research on the user project.