NAU study lead author Bram Stone: 'What happens in the lab and what happens in wild soil are often worlds apart'

Northern Arizona University researchers recently found new evidence that shows most bacteria is slow growing in wild soil. According to a release by the university, a study published in The ISME Journal, found that most bacteria in the wild grows slowly, while fast growing bacteria is not as prevalent.

“What happens in the lab and what happens in wild soil are often worlds apart, and we need to be testing and challenging ideas about bacteria and microbes from the lab with what we see in the field,” said lead author Bram Stone, who conducted the research at NAU’s Center for Ecosystem Science and Society (Ecoss) and is now a Linus Pauling Postdoctoral Fellow at Pacific Northern National Laboratory. “Many of our society’s most urgent questions about carbon storage and how soils will respond to climate change rely on understanding better how microbes act in nature.” 

The report said that researchers uncovered evidence that challenges the conventional understanding of bacterial lifestyles in wild soil. This offers new insights into the work of microbial ecology and its role in carbon storage and the health of soil. 

This research could significantly help in understanding climate change impacts, as well as in creating strategies to preserve ecosystem functionality. Typically scientists have categorized bacteria into two major lifestyle groups. One is adapted to be competitive and fast-growing, and the other characterized as slow-growing and resistant to starvation. However, the NAU-led research shows that most bacteria grows slowly in the wild.

The NAU researchers used a technique called quantitative stable isotope probing (qSIP) to gather data for their study. This technique employs stable isotopes labeled with an extra neutron to track the fate of water or sugar molecules through the soil. By analyzing wild soil samples treated with labeled water or sugar and sequencing the DNA at different time points, the team could track microbial growth and community changes in response to isotopic labeling.

Bruce Hungate, director of Ecoss and a co-author of the study, expressed enthusiasm about the potential implications of conducting microbiology in the field. 

"It's so exciting to me that we can get the data in nature, rather than speculate," Hungate said. "Being able to conduct microbiology in the field like this means we can reasonably scale up to predict fluxes for an entire ecosystem or region, all while retaining the high taxonomic resolution available from modern sequencing." 

The researchers' discovery aligns with a shift in other scientific fields towards statistically derived trait spectrums, rather than categorizations. Stone compared this to the transition from the Myers-Briggs test to the trait-based spectrum of "the Big Five" personality factors in psychology. 

"Our goal is to identify the most salient microbial traits that determine actual behavior in the soil and that determine things like energy flow," Stone explained. "And we want to express those traits numerically. With a tool like that, we can make better predictions of how microbial communities react to climate change, pollution, or a new crop rotation in an agricultural field."

The researchers' findings highlight the vital role of microbial communities in soil ecosystems. Climate change continues to be a major issue and sustainable solutions are constantly being sought after, and this research shows that understanding the dynamics of bacterial lifestyles in the wild soil becomes is increasingly crucial. This research could lead to further studies and also shows the need for new scientific approaches to address challenges due to climate change.

Collaborators on the study include researchers from Lawrence Livermore National Laboratory, Pacific Northwest National Laboratory, University of California-Irvine, West Virginia University, and the Institute for Environmental Genomics at the University of Oklahoma. The study received support from grants provided by the U.S. Department of Energy's Biological Systems Science Division Program in Genomic Science and the LLNL 'Microbes Persist' Soil Microbiome Scientific Focus Area, as well as from the National Science Foundation.