Soil pH and toxicity influence microbial community composition in new study

Though a founding concept of ecology suggests that the physical environment determines where organisms can survive, modern scientists have suspected there is more to the story of how microbial communities form in the soil.

In a new study, researchers have determined through both statistical analysis and in experiments that soil pH is a driver of microbial community composition – but that the need to address toxicity released during nitrogen cycling ultimately shapes the final microbial community.

The physical environment is affecting the nature of microbial interactions, and that affects the assembly of the community. People in the field understood these two things must be important at some level, but there wasn’t a lot of evidence for it. We’re adding some specificity and mechanisms to this idea.”

Karna Gowda, co-lead author, assistant professor of microbiology, The Ohio State University

The work helps clarify the microbial underpinnings of global nitrogen cycling and may provide a new way to think about emissions of nitrous oxide, a potent greenhouse gas, Gowda said.

The research was published recently in Nature Microbiology.

Microbes keep soil healthy and productive by recycling nutrients, and are particularly important for converting nitrogen into forms that plants can use. Underground organisms living in the same environment are also highly interconnected, preying on each other, participating in chemical exchanges and providing community benefits.

For this work, Gowda and colleagues used a dataset from a worldwide collection of topsoil samples, sequencing the genomes of microbes present in the samples and analyzing important characteristics of the soil – such as nitrogen and carbon content and pH, a measure of soil’s acidity.

“We wanted to look at trends that were widespread and that would manifest around the planet across very different environments,” Gowda said.

With billions of bacteria present in a sample of soil, the researchers relied on the genetic makeup of microbial communities to determine their functional roles.

The team zeroed in on genes that identified which bacteria were involved in denitrification – converting nitrogen compounds from bioavailable forms into nitrous oxide and dinitrogen gas that’s released in the atmosphere. A bioinformatics analysis showed that soil pH was the most important environmental factor associated with the abundance of these organisms.

To test the statistical finding, the researchers conducted lab enrichment experiments, running a natural microbial community through different conditions of growth.

During denitrification, specific enzymes have roles in the conversion of nitrate into various nitrogen-containing compounds. One of these forms, nitrite, is more toxic in acidic soil (low pH) than it is under neutral conditions with higher pH.

The experiments showed that strains with enzymes called Nar, linked to creating toxic nitrite, and strains with enzymes called Nap, linked to consuming nitrite, fluctuated based on the acidity of the soil.

“We found more of Nar at low pH and less of Nap, and vice versa as the soil pH moved toward neutral,” Gowda said. “So we see two different types of organisms prevalent at acidic versus neutral pH, but we also find that that’s actually not explaining what’s going on. It’s not just the environment that’s determining who’s there – it’s actually the environment plus interactions between more organisms in the community.

“This means that pH is affecting the interaction between organisms in the community in a more or less consistent way – it’s always about the toxicity of nitrite. And this highlights how different bacteria work together to thrive in varying soil pH levels.”

That finding was novel and important, Gowda said. Bacteria and other microorganisms are known to be driven by a will to survive, but they also rely on each other to stay safe – and that cooperation has implications for environmental health, the research suggests.

“While individual fitness effects clearly play a role in defining patterns in many contexts, interactions are likely essential to explaining patterns in a variety of other contexts,” the authors wrote.

Understanding how interactions and the environment affect nitrous oxide emissions could provide new insights into reducing this potent greenhouse gas, Gowda said: Denitrifying bacteria are key sources and sinks of nitrous oxide in agricultural soils. While past studies have focused on the behavior of these nitrous oxide-emitting organisms in different pH conditions, considering their ecological interactions may offer new strategies to lower emissions.

This work was supported by the National Science Foundation, the University of Chicago, the National Institute of General Medical Sciences, a James S. McDonnell Foundation Postdoctoral Fellowship Award, and a Fannie and John Hertz Fellowship Award.

Co-authors include Seppe Kuehn, Kyle Crocker, Kiseok Keith Lee, Milena Chakraverti-Wuerthwein and Zeqian Li of the University of Chicago; Mikhail Tikhonov of Washington University in St. Louis; and Madhav Mani of Northwestern University.