In a recent study, researchers utilized both statistical methods and experimental approaches to reveal that soil pH significantly influences the composition of microbial communities. However, they also found that the management of toxicity released during nitrogen cycling ultimately determines the final makeup of these communities.
An established idea in ecology posits that physical conditions dictate the survival of organisms. However, current scientists have begun to suspect there are additional factors influencing the formation of microbial communities within soil.
Recently, a team of researchers found through statistical methods and experiments that soil pH plays a crucial role in shaping microbial community composition. Nevertheless, addressing the toxicity that arises during nitrogen cycling is what ultimately dictates the final microbial community.
Co-lead author Karna Gowda, an assistant professor of microbiology at The Ohio State University, stated, “The physical environment impacts the nature of microbial interactions, which in turn affects how the community is assembled. While professionals in the field understood the importance of these elements, concrete evidence was lacking. We are contributing more specificity and mechanisms to this concept.”
This research enhances our understanding of the microbial aspects of global nitrogen cycling and may offer a fresh perspective on nitrous oxide emissions, a powerful greenhouse gas, according to Gowda.
The findings of this research were recently published in Nature Microbiology.
Microorganisms play a vital role in maintaining soil health by recycling nutrients and are especially critical in transforming nitrogen into forms that are accessible to plants. These underground organisms are also intricately connected, engaging in predation, chemical exchanges, and contributing to community well-being.
For this investigation, Gowda and his team analyzed a global dataset of topsoil samples. They sequenced the genomes of the microbes present and examined key soil characteristics, including nitrogen and carbon levels, as well as pH, which indicates soil acidity.
“Our goal was to identify trends that were widespread and would manifest globally across diverse environments,” Gowda explained.
With billions of bacteria found within individual soil samples, the researchers relied on the genetic makeup of microbial populations to ascertain their specific functional roles.
The team focused on genes that were indicative of which bacteria contributed to denitrification, a process that converts nitrogen compounds from usable forms into nitrous oxide and dinitrogen gas, which is then released into the atmosphere. A bioinformatics analysis revealed that soil pH was the most significant environmental factor linked to the presence of these organisms.
To validate the statistical findings, the researchers carried out laboratory enrichment experiments, simulating various growth conditions for natural microbial communities.
During the denitrification process, specific enzymes play critical roles in the conversion of nitrate into different nitrogen-containing compounds. One such product, nitrite, is more harmful in acidic soils (low pH) compared to neutral soils (higher pH).
The experiments demonstrated that the levels of strains containing enzymes called Nar, associated with the production of toxic nitrite, and strains with enzymes called Nap, responsible for consuming nitrite, varied according to the soil’s acidity.
“At lower pH, we observed an increase in Nar and a decrease in Nap. Conversely, as the soil pH approached neutral levels, the pattern reversed,” Gowda noted. “This indicates that distinct groups of organisms thrive at either acidic or neutral pH, but the situation is more complex. It’s not solely environmental conditions dictating these patterns; the interactions among various organisms play a crucial role as well.”
“This signifies that pH consistently influences the interactions between organisms within the community, primarily concerning the toxicity of nitrite. It emphasizes how different bacteria collaborate to prosper in diverse soil pH environments.”
This discovery was both novel and pivotal, Gowda remarked. Although bacteria and other microorganisms are commonly driven by survival instincts, their dependence on one another for safety highlights significant implications for environmental health, according to the research.
“While the effects of individual fitness clearly impact various contextual patterns, interactions among organisms are likely essential in explaining patterns across a range of other contexts,” the authors noted.
Comprehending how environmental factors and interactions influence nitrous oxide emissions could lead to innovative strategies for reducing this potent greenhouse gas, stated Gowda. Denitrifying bacteria are critical contributors to nitrous oxide in agricultural soils. While earlier studies have concentrated on the behavior of these nitrate-emitting organisms in differing pH environments, examining their ecological interactions could unveil new methods to decrease emissions.
This research was funded by the National Science Foundation, the University of Chicago, the National Institute of General Medical Sciences, a James S. McDonnell Foundation Postdoctoral Fellowship, and a Fannie and John Hertz Fellowship.
The co-authors of the study include Seppe Kuehn, Kyle Crocker, Kiseok Keith Lee, Milena Chakraverti-Wuerthwein, and Zeqian Li from the University of Chicago; Mikhail Tikhonov from Washington University in St. Louis; and Madhav Mani from Northwestern University.
