A Mountain of Discoveries in Biodiversity

Microorganisms are the final frontier of biodiversity. To learn more about the ecology and evolution of these tiny organisms we studied a mountain range that has inspired ecologists for over a century.

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Some of the earliest research in ecology involved naturalists describing patterns in plant and animal biodiversity across the landscape. In the 19th century early American ecologists, such as Clinton Hart Merriam, began documenting which species lived in different regions across our country. Traveling on expeditions to Florida, Alaska, the Colorado Plateau, and many other regions across north American, Merriam documented and characterized animal species, many previously unknown to science. 

Clinton Hart Merriam (1855-1942), American naturalist and pioneer of the “life zones” concept.

Since then much progress has been made in determining not only where species live but how the local environment influences the functional traits of plants and animals. Traits that determine how organisms interact with each other and impact the environment. While hugely informative, 19th and 20th century descriptions of biodiversity are incomplete because the most diverse subset of organisms in these environments — microbes — were left uncharacterized. Only recently have we developed the tools needed to study microbial communities. As a result, microorganisms are the final frontier of biodiversity. With thousands, maybe millions, of undescribed species the opportunity for discovery is endless but is also riddled with challenges. 

In our recent paper, we use a new tool, developed by members of our team, (quantitative stable isotope probing, qSIP) that allows us to measure the traits of undescribed microbial species within their natural communities. This method tracks “heavy” elements into the DNA of microorganisms, allowing us to determine the growth and carbon assimilation (key traits) of individual species. With new tools such as qSIP in hand we are now, in the 21st century, able to begin catching up with plant and animal ecologists. Most recently we set out to answer a fundamental question of nature vs nurture—Are the traits of microorganisms hard-wired by genes handed down over evolutionary time, or are they more malleable and sensitive to their surroundings? If traits are determined by nature, the activities of microbial species and families should be consistent across environmental variation. In contrast, if nurture is more important, traits will be dependent upon the contemporary environment. 

To answer this question, we needed to study microbial species in multiple ecosystems, and I found myself in the perfect place for it: at the base of the majestic San Francisco peaks that give a picturesque backdrop to Northern Arizona University (NAU) and the city of Flagstaff. Humphrey’s Peak is the highest point in the state at nearly 13,000 feet above sea level. From this peak the land slopes steadily downward toward the Grand Canyon, reaching an elevation of 5,500 feet in only 20 miles.

The San Francisco Peaks

More than a century before we started our experiment, these volcanic peaks were inspirational to Clinton Merriam when he performed a survey of the mountains in 1889. 

During my time as a postdoc at NAU, I got to know these mountains. When ascending to Humphry's Peak, the hot dry air typical of Arizona gradually gets cooler, more humid — a refreshing change reminiscent of higher latitudes.

Coauthors Morrissey and Hayer summit Humphreys Peak, the tallest of the San Francisco Peaks outside Flagstaff AZ.

Having seen these ecosystems, I can imagine Clinton hiking up the mountainside, witnessing the Ponderosa Pines gradually give way to Fir, Spruce, and Aspen trees. Merriam’s expedition in northern Arizona led him to develop his “life zones” concept to describe the changes in species composition that occur in response to shifts in temperature and moisture along the elevation gradient. 

In his 1890 book* Clinton wrote, “it may be said that in ascending from the hot and arid Desert of the Little Colorado to the cold and humid summit of the mountain no less than seven zones are encountered, each of which may be characterized by the possession of forms of life not found in the others” and he illustrated these life zones. 

* From Merriam and Stejneger 1890

Now, more than a century later, our research team hoped this elevation gradient could help us understand how temperature and moisture, so influential in shaping the plant and animal communities, impact the biodiversity Merriam couldn’t see: the microbes inhabiting the soil beneath his feet.  We collected soil from four sites along the elevation gradient Merriam described, and that now bears his name. Following in his footsteps, our publication also has an illustration depicting the zones we studied. 

Diagram of sampling locations in our study within four distinct ecosystem or “life zones” differing in temperature and precipitation. Illustration by Victor Leshyk

Just as with the plants and animals above ground, we found patterns in the biodiversity of soil microorganisms along the elevation gradient. However, perhaps owing to the diversity of microbial communities, we were able to identify hundreds of species present at all four sites, enabling us to determine whether the functional traits of microorganisms are determined more by their evolutionary history or local environment. 

Similar to what is observed for plant and animal species, we found that evolutionary history (i.e. “nature”) explained more variation in the traits of microbial species than did the local environment (i.e. “nurture”). Specifically, evolutionary history, as assessed by taxonomy, explained up to 65% of the variation in trait values, while the variation explained by the ecosystem never exceeded 20%.  Even across this broad climatic gradient in temperature and elevation the traits of microbial species remained relatively consistent. Consistency in the traits of microbes (growth and carbon assimilation) that influence nutrient cycling and biogeochemical processes may have practical value. For instance, predicting how microbial species influence soil carbon cycling may help us enhance modeling approaches and reduce uncertainty when forecasting soil carbon feedbacks to global change. 

The ecosystems that once inspired an early great American naturalist continue to reveal nature’s secrets to a new generation of ecologists. As microbial ecologists we may be a little behind — after all, unlike shifts in dominant vegetation, patterns in microbial biodiversity are not readily visible on the landscape. But with new tools, microbial ecologists are venturing into this final frontier of biodiversity to gain a more complete understanding of how the species composition of “life zones” influences the ecosystem processes in our changing world.

* Merriam, C. H., & Stejneger, L. H. (1890). Results of a Biological Survey of the San Francisco Mountain Region and Desert of the Little Colorado, Arizona: 1. General Results with Special Reference to the Geographical and Vertical Distribution of Species. 2. Grand Cañon of the Colorado. 3. Annotated List of Mammals, with Descriptions of New Species. 4. Annotated List of Birds (No. 3). US Government Printing Office.

Ember M Morrissey

Assistant Professor, West Virginia University