Tarah Sullivan is fiercely insistent that we are all interconnected. The Washington State University soil microbiologist and ecologist says that understanding those connections is key to a healthy future.

“I know it sounds a little hokey,” the mother of two daughters apologizes without backing down: “Microorganisms connect everything everyday in every way. We absolutely could not survive on the planet without active and healthy microbiomes, in humans and in the environment.”

Sullivan’s work focuses on how microbial communities in soil impact heavy metal biogeochemistry. Many metals are important micronutrients for both plants and animals—but too much of a good thing can make plants sick. And some metals are toxic and need to be removed or sequestered so they don’t enter the food chain.

“By enhancing soil health and its microbial communities, can we increase micronutrient uptake in order to improve the nutrient quality of the crop? Or just to survive under toxic conditions?” One way to do this would be to induce microbes to secrete chelating molecules that bind metals and micronutrients. In the case of iron, for example, chelation makes the metal bioavailable. Other toxic metals, like cadmium and aluminum, are sequestered in ways that don’t interfere with the plant’s growth.

The petri dish problem

The challenge with studying chelation, and other microbe-mediated processes in the soil, is something microbiologists call the Great Plate-count Anomaly. “We know that what we can grow in the lab,” Sullivan says, “is probably about .01 percent of what is actually out there.”

Bacteria like to grow in soil, air, water, in our guts, hair, skin—pretty much anywhere except in petri dishes. No matter what you try to feed them, most just won’t survive. This is a problem with single-organism studies in general, and only underscores Sullivan’s point about everything being interconnected. There are all sorts of reasons why it is so difficult to culture microorganisms in vitro.

One is the idea of “helper” organisms. “Bacteria and fungi never live in isolation,” Sullivan says. “They are all working together and cooperating.” One microbe might secrete a chelating molecule that others don’t. As those chelators move through the local soil environment, everybody potentially benefits. What Herbert Spencer said of Darwin’s theory of evolution now has to be revised: It’s not survival of the fittest single organism that matters, but rather the fitness of communities that enables survival.

“Now that we know how important the microbial communities are,” she says, “we can look at ways of using them to sequester a metal or translocate that metal up into the biomass of the plant so it can be harvested or landfilled or burned for biochar or what have you.” Indeed, it may even be possible to soon plant a “hyperaccumulating” crop, one that sucks up nickel, zinc, or copper from soil and yields a harvest of valuable metals.

“Our burgeoning population is creating a waste stream that is just not being dealt with,” Sullivan says. “Microbial communities can maybe help so that we can recycle out the metals” from electronics, cars, and appliances. “Bacteria are even able to break down certain plastics.”

Soil microbes aren’t just necessary for the health of the plants we eat, they may also affect flavor. Consider terroir, that nearly impossible-to-pin-down combination of soil profile, vine type, growing conditions, and winemaking processes that determine a wine’s character. Recent work by wine chemist Tom Collins, now at WSU, and his colleagues, suggests that microbial communities associated with grapes, and particular to their local environment, have an influence on the final product.

The unwanted bloom

Soils are far from the only place where the invisible world plays a critical role. WSU limnologist Stephanie Hampton is an expert on fresh water and its microbes. She points out that many microorganisms perform life-critical environmental services.

“We don’t see it but, all the time, microbes are taking toxins and breaking them down, taking excess nutrients and turning them into stuff we don’t even notice in water. There is all of this processing that microbes are doing in water that keeps us safe and keeps us healthy. It’s only when it goes really out of whack that we notice the microbial world,” Hampton says and adds, laughing, “and we blame the microbes.”

And out of whack the microbes can indeed go. It may be parallel to what happens in the human gut. A course of antibiotics, for instance, administered with good intentions, may wipe out the gut biota, giving Clostridium difficile just the opportunity it’s been waiting for. C. diff, as it is unaffectionately known, can cause unrelenting diarrhea and cramps in sufferers. So too with cyanobacteria which, given the opportunity, forms spectacular blooms in lakes and oceans.

“In Lake Erie a couple of summers ago,” Hampton relates, residents of Toledo, Ohio, had to find other sources of fresh water, as their normal source was contaminated by “toxic outbreaks of cyanobacteria. These blooms are resulting from both cyanobacteria taking up some of the nutrient runoff [of fertilizers] as well as responding to warmer temperatures [due to a climate change]. We’re trying to rethink algal blooms in light of the interactions of these communities of bacteria, algae, and viruses that are all interacting with each other” and their environment.

Hampton, too, points out that the single-organism approach isn’t working when it comes to understanding why a bloom sometimes produces toxins while at other times and places it doesn’t. The more modern approach, she says, is the “ecological or ecosystem perspective. An ecologist would look at a big bloom and say, OK, we know the nutrients are here, the light is just so, and the temperature is within this range—but who else is there?” What other organisms are interacting to incite a bloom?

One of the confounding factors for any ecologist, in soil, water, or anywhere, “is the way that some of our pharmaceuticals and personal care products are inadvertently affecting those microbial communities,” Hampton says. “If we take an antibiotic and we pee out the excess, that is typically not something that our sewage systems remove. And same is true for caffeine, which is now everywhere, in all of our water bodies.”

Even in Lake Baikal, the world’s largest body of fresh water. Remote as it is, in a roadless wilderness deep in Siberia, caffeine, nicotine, and the residues of pharmaceuticals are present. “It’s only been more recently that people have started to say, Wait a minute, what are these chemicals doing to bacterial and algal communities, and to microscopic animals and fish, and the larger animals that are ingesting them as well.”

A rift lake, Baikal is incredibly deep and contains roughly 20 percent of the planet’s fresh water. As deep as it is, its near-shore environment is wondrously rich. “Something like 30 to 50 percent of the plants and animals are endemic; they evolved there and that’s the only place they are,” Hampton says. “That diversity is concentrated on the nearshore and in the sediments at the bottom of the lake. But the nearshore is also where you get the human impact, that’s where you get your sewage.”

That’s an environmental and an economic concern, Hampton explains, as a big algal bloom turns off tourists “because the beach becomes slimy.”

“In Lake Baikal, you see these big branching sponges that live 30 or 40 years,” says Hampton, who has dived in the lake to collect samples. “There are extensive sponge forests. What our Russian colleagues are seeing is these sponges becoming diseased. It’s not clear what is happening. The Russians think it might have to do with sewage. But whether that’s a direct change caused by the nutrients or whether it’s something else in the sewage causing these diseases, we don’t know, but there has been some recent work on how the microbiome of these sponges has changed.”

A sponge is a supraorganism, as it is a symbiotic arrangement of photosynthesizing bacteria, other microorganisms, other sponges, and sometimes animals, such as crabs. Like organisms in all the world’s lakes, those in Baikal are having to deal with a warming planet.

“What you see in Baikal is a shortening of the ice season,” Hampton says. “We’re just beginning to try to understand how that is affecting the dynamics of algae that are photosynthesizing under the ice relative to those photosynthesizing in the summer” and how those changes affect the flow of nutrients throughout the yearlong cycle of freeze and thaw.

Finding the microbial plateau

Someday we may understand enough about ecosystem-wide processes, like nutrient flow and how microbial communities use nutrients to clean up plastics, sequester carbon, or metabolize and recover the rare-earth metals from our electronic gadgets currently tossed in landfills. It’s a big maybe but it’s an idea that drives Sullivan’s work.

“Think of the microbial growth curve in a closed system, like a Petri dish,” Sullivan urges. She quickly sketches a graph on a scrap of paper. The Y axis is growth—of a community of microbes, in this case, but she also means humans—and the X axis is time. The curve climbs the X axis quickly, then plateaus.

The plateau, she says, is a state of equilibrium in which population and available essential resources are in balance. “But, like our planet, it’s a closed system,” she repeats, and draws a vertical slash down the right side of the graph.

“Crash and burn: lack of resources, and waste products have built up to toxic levels.” The community of microbes dies off rapidly. “Humans are doing this right now,” she says grimly.

“That’s why I have this interest in microbiology.” The mother of two sighs, and concludes, “I can’t solve the world’s problems, but I can chip away at them.”

Learn More

Tarah Sullivan

Stephanie Hampton

“A Mother’s Microbial Gift”