Conservation Tends to Ignore the Most Common Type of Life

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Conservationists pride themselves on protecting all of Earth’s life, not just the flashy panda bears and tigers. The field has focused on obscure desert pupfish, insects, and modest little herbaceous plants. But conservationists seldom put bacteria on a tote bag, even though most life is microscopic. Earth has something like a trillion species of bacteria, fungi, archaea, and protozoa—the families of life grouped under the general heading of “microbes.” The sea is a soup of microbes, the soil a wonderland of imperceptible life; even the air is alive. Hundreds of millions of viruses and tens of millions of bacteria that float through the air are deposited on every square meter of Earth every day. We’re living in an “English drizzle of microbes,” Kent Redford, a consulting conservationist in Maine who previously held a top post at the Wildlife Conservation Society, told me.

The word microbes is sometimes used synonymously with germs, but there’s a growing understanding that most microbes are not the enemy, and that they keep everything on the planet—including humans—alive. Animals without the right microbiome can sicken and even die. Plants, too, require microbial partners to flourish. Microbes are the glue that holds ecosystems together (sometimes quite literally: Soil clumps into particles in part because of mucus that microbes secrete.)

But though microbes are ubiquitous, some communities of microbes could be at risk of extinction. In Yellowstone National Park, visitors are forbidden from entering many of the hot springs and geysers, in part to protect the rare microbial communities that call them home. Unique microbial ecosystems in subglacial Antarctic lakes that have been isolated for millions of years are carefully sampled using methods least likely to contaminate them with organisms from beyond the ice.

The conservation movement, however, pays little attention to microbes: As of 2012, only 2 percent of academic papers on conservation focused on these organisms. “Many conservation organizations are largely uninterested in extending their work to microbes,” according to Redford, who just published a plea in the journal Conservation Biology for conservationists to consider the microbial world. But by ignoring microbes, conservationists are ignoring most of life, ancient and fascinating lineages that are valuable in their own right—and essential to all flourishing on Earth.

Conserving microbes is different from conserving sea otters. A single microbial species or subspecies is not usually the focus of concern. Microbes are actually kind of hard to eradicate because microbes are fantastically numerous, reproduce quickly, and can swap genes with their neighbors, they adapt well to environmental change. There’s a lot of “functional redundancy” in the microbial world. If pollution or climate change or an herbicide knocks out one kind of bacteria that moves nutrients or carbon around in an important way, there are often hundreds of other types of bacteria that do the same thing.

Rather than worrying that climate change or agricultural methods will make an individual species of bacteria go extinct, Redford’s concern is more that these forces will wipe out or radically change microbial communities—with complex and hard-to-predict consequences for the larger ecosystem. For example, wild trout eggs are covered in a complex mix of bacteria that can come from more than a dozen different families. When climate change heats up stream water, that can radically alter the types of bacteria that live on the eggs, or reshuffle which types are common and which types are rare. And this new community might also be toxic to the trout eggs themselves, endangering the trout. “Whether you want to conserve microbes for their own sake or not, you’re not going to succeed at the things you do want to do” unless you take them into account, Redford told me.

Taking microbes into account can help more traditional conservation targets, such as rare animals. For example, many translocations or reintroductions of species done in the name of conservation fail—and in some cases, that might be because the microbial context was not taken into account. Studies have shown that animals in captivity often have very different microbiomes than wild animals of the same species. Redford asked me to imagine taking a zoo zebra from Paris and letting it loose in Serengeti National Park, in Tanzania. “It had a Parisian-zoo microbiome for eating French hay and pelletized alfalfa. And then all of a sudden, its microbiome was asked to digest Serengeti grasses.” It might get sick or simply fail to absorb the needed nutrition from its food.

Conservationists don’t always ignore microbes: Some who are working on reintroducing the endangered Yangtze sturgeon even “trained” their captive fish on more wild, unprocessed foods in an effort to shift their gut microbiome to a more natural ecology—and they saw improved survival rates over untrained sturgeon. Plants have a microbiome too, and many partially rely on other fungi in and on their roots to help them absorb nutrients and water. Translocated plants without the right root fungi are much more likely to die after being outplanted. Researchers working on prairie restoration in Indiana found that introducing the right fungi during restoration increases plant diversity by about 70 percent.

Considering microbes as factors in the survival of plants and animals is becoming more common, especially as the tools needed to detect and sequence microbial genes are becoming more affordable. But there’s less work on conserving microbes themselves. In part, that’s likely because conservationists already have so much on their plate. Conservationists also find microbes tough to work on because they don’t fit neatly into species boxes—and species are the core units of conservation. We typically measure “biodiversity” by counting species; we know we’ve failed when a species goes extinct. America’s central policy tool for protecting the nonhuman world is called the Endangered Species Act. And yet, bacteria, protists, viruses, and other miniature beings don’t come in easy-to-distinguish species. They evolve quickly, hybridize readily, and even share genes with other lineages.

“They’re all busy using horizontal gene transfer to move genetic elements around to each other quite happily,” Redford said. And sometimes they live in mixed-lineage groups called biofilms, physically attached, communicating with one another, and operating almost like a single organism. You may be intimately acquainted with biofilms if you have ever scraped plaque off of your teeth. Conservationists simply struggle to incorporate this frothy, dynamic riot of life into their familiar frameworks. They can’t count or make lists of endangered microbe species.

I asked Redford to imagine a world where his plea was heeded and microbes were fully incorporated into the work of conservation and restoration. What would it look like for someone managing a trout stream? First, he said, a conservationist would be able to use a handheld environmental-DNA detector to get an overall picture of the microbial communities in the water, in the trouts’ guts and gills, on the surface of aquatic plants, and in other specific niches. To make the best of that sort of information, she would need to develop a much more sophisticated understanding of how the unseen world of the microbes influences what we can see: the shading willows, hovering damselflies, and swirling trout. Perhaps her data could also help locate a rare strain of bacteria in the stream that she wants to protect, and she could learn that it needs cool water to thrive. Someday, we might be planting willows to shade streams to keep bacteria cool.

Conservation in general is moving away from simply putting things “back the way they used to be” and toward helping dynamic ecosystems adapt to changing conditions. Working with microbes fits that new model because there’s less concern about stopping them from changing and evolving. It would be impossible anyway; they are just too damn fast. But that embrace of adaptation also opens the door to the possibility of influencing the trajectory of microbial communities—or even incorporating engineered microbes into ecosystems. Sewage-treatment plants already employ diverse communities of bacteria, archaea, and protozoa to clean up water—and even to turn sewage into bioplastic. Meanwhile, a recent study identified a bacterium that can actually break down plastic completely—destroy it for good—and turn it into carbon dioxide. Learning how to manage ecosystems so bacteria that eat plastic flourish might be a conservation strategy of the future.

The goals of conservation have always been both selfish and altruistic. We want to save species and protect ecosystems because they keep us alive and happy, but we also want to protect the nonhuman world for its own sake. Both goals potentially apply to microbial conservation too. Bacteria, archaea, and microscopic fungi can improve our lives. But Redford also believes that they are valuable in and of themselves, that neither size nor membership in the animal kingdom ultimately determines moral value. Microbes are unique forms that have evolved over millions of years, just as the whale or panda has.

The idea that we spend each moment of our lives moving through a universe of millions of individuals and collectives with inherent moral worth is enough to give one ethical vertigo. It is hard enough to determine how to do right by the plants and animals we share the Earth with. What, if anything, do we owe the fungi and bacteria that invisibly shape our lives?