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,” said co-lead author Karna Gowda, assistant professor of microbiology at The Ohio State University. “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.” 

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. 

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