Waimea Valley’s natural beauty has long drawn admirers, with its picturesque waterfall, flourishing botanical gardens and river pushing through sand dunes to a sparkling bay.

This fall a team of researchers from the University of Hawaii at Manoa will be focusing on what the naked eye can’t see at the North Shore watershed in hopes of revealing secrets to ecological and human health.

With $1 million from the W.M. Keck Foundation, which funds pioneering research, the UH faculty members will map the microbial communities that underpin the valley’s varied ecosystems and explore how they function.

“They are going to be identifying the microbes from the top of the watershed all the way down to the ocean — what are those communities like, how do they interact with the plants and animals that are there?” said Margaret McFall-Ngai, principal investigator on the project.

Once dismissed as “germs,” microbes such as bacteria and fungi play vital roles in maintaining the health of plants, animals and ecosystems — but more research is needed to understand how that happens. The UH scientists believe it is the first time an entire watershed, from ridge to reef, will be studied in this way.

“The microbial communities that live in and on us confer our health, and similarly the microorganisms that live in the watershed will be at the very basis of the health of that watershed,” said McFall-Ngai, who directs UH’s Pacific Bio­sciences Research Center.

The team’s experiments could lead to revelations that ultimately help scientists harness the power of microbes to restore habitats, boost food production and improve human health.

“Microbes comprise, arguably, the greatest untapped natural resource on our planet,” the researchers wrote in their proposal.

Waimea Valley is seen as the perfect spot to study complex microbial networks because so much ecological diversity is packed into its 13 square miles. The traditional Hawaiian land division encompasses an entire water cycle in a compact area, relatively isolated from the rest of the world.

“Hawaii is basically the only place we can do this type of study,” said Nicole Hynson, co-principal investigator. “If you were to go somewhere like California, a single watershed is going to span hundreds of miles. In Hawaii we have these very strong environmental gradients restricted to very small geographic areas.”

As the elevation drops nearly 2,000 feet from the back of the valley to sea level, heavy rainfall gives way to a dry coast, and soil chemistry and temperatures shift. Human impact is just as varied: Visitors flock to the world-famous beach and botanical gardens, but the deep interior of the valley is largely untouched.

“We know that most macro­organisms (plants and animals) are born microbe- free, for the most part, and they accumulate these microorganisms over time from the environment,” Hynson said. “But so far that environment has kind of been the black box. … We are interested in how changes in environment affect these microbial communities and in turn the health of the hosts that inhabit these environments.”

The Keck project team at UH includes Hynson, a physiological ecologist, and Joanne Yew, a chemical ecologist, both of the Pacific Biosciences Research Center; Anthony Amend, microbial ecologist and associate professor of botany; Camilo Mora, ecological modeler and associate professor of geography and environment; and Craig E. Nelson, aquatic systems microbiologist with the Center for Microbial Oceanography.

“The W.M. Keck Foundation is noted for its support of cutting-edge, high-risk, high-reward science that more risk-averse federal agencies are less inclined to fund,” said UH President David Lassner. “This award recognizes the capacity UH has built with truly world-class microbiome researchers.”

The scientists will experiment with two “model hosts,” a species of vinegar fly known as Drosophila melanogaster and a wild strawberry plant, Fragaria vesca, both well established locally.

“These will be the equivalent of lab rats for the study,” Hynson said. “What we really want to test through field and lab experiments is how does a change in microbial diversity influence the health of the host. … Ultimately, what we really want to get to is prediction.”

The project seems daunting, given the incredible array of microbes and wildlife from Waimea’s mountainous rainforest to its coral reef. But McFall-Ngai said the “phenomenal cohort” of young researchers recruited by UH has the tools to tackle it.

“We have this huge frontier out here, and it’s so vast and so immense we could probably just say, ‘My God, that’s impossible,’” she said. “We have these bold junior faculty who have an idea how to do this. They know how to ask a circumscribed question and how to impose highly rigorous sampling methods as well as analysis methods.”

Working with Waimea Botanical Garden staff, who have documented its treasures, also gives them a big leg up on the project, formally known as “Establishing a Hawaiian Watershed as a Model Microbiome Mesocosm.”

“They have lots of survey data about what kinds of plants, animals and fish are found throughout the valley,” Hynson said. “We’ve been really able to hit the ground running because they have such a great base line of information.”

McFall-Ngai is a leading light in microbiome research. Last month she received a $5 million MERIT award from the National Institutes of Health, an honor that provides long-term support to outstanding investigators with stellar records of scientific achievement and is renewable after five years.

In December she landed a $1 million professorship grant from the Howard Hughes Medical Institute to revamp the way biology is taught at the undergraduate level by creating a curriculum recognizing the microbial world as the basis of the health of all ecosystems.

“We used to think that animals and plants were the major things, and now we know the vast diversity of the biosphere is microbial,” McFall-Ngai said. “That is the biggest change in our view since Darwin.”