Examining the Biology of Microbes and Their Response to Global Changes

Around the world, organisms are experiencing unprecedented levels of stress from habitat destruction, climate change, and several other human-driven changes to the surrounding.

Examining the Biology of Microbes and Their Response to Global Changes
Dots on the map indicate where soil samples were collected across the U.S. by NEON. Image Credit: University of Miami

Forecasting and reducing the effects of this growing stress on organisms, and the environmental services on which one relies, needs comprehension of why few species could exist in an extensive range of environments while others exist in just a few habitats.

As far as the scientific world of ecology is concerned, scientists frequently try to sort organisms on the planet into two categories: generalists and specialists.

Generalists have the potential to survive throughout several environmental conditions and habitats, while specialists are highly restricted or limited to particular conditions for survival. For instance, the panda bear feeds just on bamboo inside a specific habitat.

The restriction is for their habitat range and also their diet, and if the bamboo plant turned out to be extinct, panda bears might become dead as well.

Image Credit: paulista/Shutterstock.com

Image Credit: paulista/Shutterstock.com

However, what about the microbial world of unseen organisms found in all the places on Earth, from the human gut to the soil under the feet? Into which category do they fall?

For the answer to be discovered, a group of graduate and postdoc students in Associate Professor Michelle Afkhami’s biology laboratory at the University of Miami College of Arts and Sciences learned the DNA sequences of prokaryotes, a group of microbes that include all archaea and bacteria.

The study outcomes are now available in the journal Nature Ecology & Evolution.

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.”

Damian Hernandez, Study First Author and Former Graduate Student in Afkhami’s Lab, University of Miami

Hernandez continued, “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,” added Hernandez.

At present, Hernandez is a postdoc preparing for a biology fellowship with the National Science Foundation.

In collaborative measures two years in the making, the team of students examined more than 200 soil samples gathered by the National Ecological Observatory Network (NEON) from sites across the United States.

Among over 1,200 prokaryotes that have been analyzed, Hernandez and the team discovered something quite astonishing. They discovered that the majority (90%) of the microbes were either multidimensional specialists or multidimensional generalists.

If a microbe was a generalist throughout one environmental axis, it was almost always a generalist throughout all other axes; and if it was a specialist on one environmental axis, it specialized throughout all axes.

Besides offering significant knowledge into how microbial communities have been structured, this breakthrough offers a few of the first proofs for multidimensional specialization and generalization in any kind of organism.

We found that microbes can be very restricted on where they can exist. The generalist microbes are very flexible and can withstand a broader 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.”

Damian Hernandez, Study First Author and Former Graduate Student in Afkhami’s Lab, University of Miami

Hernandez added, “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.

Afkhami verifies that the findings present a fascinating argument on how microbes could 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.”

Damian Hernandez, Study First Author and Former Graduate Student in Afkhami’s Lab, University of Miami

On the contrary, the team discovered that specialist microbes could be highly vulnerable to environmental change. Also, microbes classified as specialists appear to be significant “community organizers” as a result of their high functionality inside the microbial world.

For instance, the research group found out that specialist microbes are more probably to be those that could detoxify the soil, promote plant growth, digest complicated carbons present in the soil, and also add nutrients to the soil.

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,” stated Afkhami.

Afkhami added, “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.”

Source:
Journal reference:

Hernandez, D. J., et al. (2023) Multidimensional specialization and generalization are pervasive in soil prokaryotes. Nature Ecology & Evolution. doi.org/10.1038/s41559-023-02149-y.

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