Can soil microbes survive climate change?

Around the world, the dire impacts of climate change and human-caused environmental alterations are placing enormous strain on living organisms, including plants, animals, and even microbes. 

Amid this turbulence, scientists are seeking to understand which species are adaptable enough to thrive in varied environments, and which are tethered so tightly to their niches that they are at risk of extinction?

Generalist and specialist species

Traditionally, ecologists categorize organisms into two broad types. Think of it as a spectrum: on one end, we have the “generalists” – hardy creatures able to thrive in diverse environments and habitats. 

By contrast, the “specialists” at the opposite end possess narrow survival criteria, often rooted in very specific environments. 

The iconic panda bear is a perfect example of a specialist. With its exclusive bamboo diet, its existence hangs precariously on the fate of this single plant species.

Beyond the visible life forms, there is a microscopic realm teeming with life beneath our feet and inside of us. Which category do the soil microbes belong to?

To investigate, Michelle Afkhami’s biology lab at the University of Miami College of Arts and Sciences embarked on a groundbreaking study. 

Focus of the study

The research, which is now published in the journal Nature Ecology & Evolution, centered on prokaryotes – a vast microbial group encompassing all bacteria and archaea.

“The idea behind the project was to find out whether these microbes can exist within a narrow or broad range of conditions along many different environmental dimensions,” said Damian Hernandez, a former graduate student in Afkhami’s lab who is now a postdoc preparing for a biology fellowship with the National Science Foundation. 

“Specifically, we wanted to know whether microbes are typically multidimensional specialists, multidimensional generalists, or use different strategies on different environmental dimensions—and what effect that could have on their roles within communities.”

“The environmental dimensions we used to determine whether the microbes are generalists or specialists were based on multiple environmental conditions in the soil in which they live, for example, leaf litter, temperature, water, and nutrients.”

What the researchers learned 

For two years, the team meticulously dissected the DNA sequences from over 200 soil samples gathered from various U.S. locations by the National Ecological Observatory Network. 

Their analysis of over 1,200 prokaryotes yielded unexpected revelations. Contrary to prior assumptions, a staggering 90% of the microbes exhibited either “multidimensional generalist” or “multidimensional specialist” traits.

This means a microbe that’s a generalist in one environmental aspect extends its versatility across all aspects. Conversely, a specialist microbe remains specialized across every environmental axis. 

Study implications 

While this is a breakthrough in understanding microbial communities, the discovery also raises alarms. 

The specialist microbes, despite their vital roles as ecosystem engineers – nurturing plant growth, detoxifying soil, breaking down complex carbons, and replenishing soil nutrients – are vulnerable to environmental shifts. These microbial “community organizers,” despite their high functionality, face an uncertain future in our rapidly changing world.

“We found that microbes can be very restricted on where they can exist,” said Hernandez, who is the first author of the study. 

“The generalist microbes are very flexible and can withstand a wider range of conditions. But the specialist microbes are sensitive to many different environmental conditions because they are restricted on multiple environmental axes and thus any changes in the environment may hinder their survival.”

“Hypothetically, if an ecosystem is structured by microbes that are specialists, then those ecosystems are more likely to be sensitive to environmental change,” he said.

Which microbes will survive?

Afkhami confirms that the findings present an interesting argument on how microbes can survive in a changing climate.

“As we learned from the study, microbes that are generalists can live across a wide range of habitats, and this can mean that those microbes may be resilient to climate change or habitat fragmentation because they are likely to tolerate changing environmental conditions. They are also very dominant within microbial communities,” she said. 

“This is very concerning because what we also learned in the study is that microbial specialists are highly connected within the microbial network and can be considered as keystone species for maintaining and driving the diversity and function of the microbiome,” said Afkhami. 

“In this study, we can start to understand – across a wider sense in the microbiome community – some of their biological functions, their roles in the microbial community, and how they will respond to global changes on the planet.”

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