Classification Challenge: Documenting Microbes, Biodiversity’s Hidden Treasure

The impulse to classify life seems hard-wired in our species, a relic perhaps of an ancient need to forage in landscapes rife with poisonous roots, fruits, shoots and fungi. Not that the need has disappeared. You get just once chance to mistake Amanita phalloides—aka the “death cap”—for the delectable paddy straw mushroom (Volvariella volvacea).

Linnaeus’ Systema Naturae
introduced the modern framework for classification, helping scientists categorize life as a first step to understanding it. Taxonomists have now described roughly 1.5 million species, just a fraction of the true measure of the planet’s biodiversity.

Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges. A recent census effort, published last summer, placed the estimate at around 8.7 million species on land and sea, with the vast majority still awaiting description.

The paper raised a stir, not least because its estimate of microbial diversity was so low (for bacteria, about 10,000 species), to the consternation of many, including UC Davis professor Jonathan Eisen, an evolutionary biologist and microbe ambassador. But I’ll return to that in a moment.

Taking stock of the number of species on the planet helps biologists predict how losing them might impact ecosystems. But we’re losing species faster than biologists can discover and describe them, let alone identify the conditions they need to survive.

As a somber report published a few years ago made clear, the Convention on Biological Diversity’s push to reduce the rate of biodiversity loss by 2010 has largely failed. Several categories of animals skirt the brink of extinction while threats to ecosystem health, from nitrogen pollution to overfishing, continue unabated.

Peter Kareiva, chief scientist for The Nature Conservancy, described our failure in an essay:

“Biodiversity on Earth continues its rapid decline. We continue to lose forests in Africa, Asia, and Latin America. There are so few wild tigers and apes that they will be lost forever if current trends continue. Simply put, we are losing many more special places and species than we're saving."

Kareiva’s point was not that we should all hang our heads in defeat, or dig in our heels and fence off more and more land from our ever-expanding ecological footprint. He suggested something more radical: recognize the resilience of nature—not “nature” with a capital “N” but nature as a complex system of physical forces and chemical processes—and our place in it.

Embrace your inner microbe

And here’s where microbes come in.

Consider this: by the numbers, you’re more microbe than human. Microbes outnumber you by at least 10 to 1. Your eyelashes, hair, saliva and skin offer prime habitat to a multitude of microorganisms. What looks like a body part to you looks like a niche to microbes. When you type, you leave a unique microbial fingerprint on your keyboard.

But the real action takes place in your gut, Microbe Megalopolis, population 100 trillion, give or take a few. And here’s where it gets interesting. Your gut microflora and mine differ. And these variations can spell the difference between health and disease.

David Relman, a Stanford microbiologist and “microbiome” pioneer, told a reporter that the diversity and individual variation of our gut microbial communities suggests that “one of the most important ecosystems on the planet might be the human body.”

Researchers have now implicated the microbiome in allergies, autoimmune disease, obesity, and a variety of other conditions. And it all started with one study that showed that when you transplant a microbial community from one mouse to another, the phenotype--traits associated with that community, in this case, obesity--goes with it, explains Eisen. “That changed everything. Until that paper came along no one had shown that microbes played that big a role.”

We know microbes are the most abundant life form on Earth. But that doesn’t mean we can take them for granted. Many of their natural habitats—both landscapes and organisms—are disappearing. When host organisms disappear, the microbes will go with them. The reverse could also be true.

Most captive breeding programs to restore endangered species to the wild concentrate on genetic diversity as the key to survival. “But no one’s really saying we need to worry about their microbes too,” says Eisen. “No one’s focusing on whatever we need to do to make sure they have the right microbial community with them.”

An improbable field guide

About 6,000 to 8,000 species of bacteria have been described so far, but biologists like Eisen think there may be hundreds of thousands or even billions of niches to exploit. Trying to count microbe species is a losing proposition, he thinks. But trying to characterize microbe diversity by thinking in terms of niches isn’t. Microbes exploit different niches just like any other organism, from Darwin’s finches to Arctic foxes.

A self-described “bird nerd” since he was 7 years old, Eisen thinks the best way to get a handle on the seemingly intractable diversity of microbial life on the planet is to think in terms of field guides. Document everything you know about different types of microbes, their niches, range, biology, genetics and ways to identify them. That becomes both a reference and an organizational framework for gathering and making sense of the mountains of data, mostly genetic, gathered from the places microbes live.

Using “metagenomic” tools, scientists sift through reams of genetic material extracted from environmental samples by matching gene sequences to known organisms or, if nothing matches, to something roughly similar.

DNA is obviously different from skeletons, bones and fossils, Eisen says, but the classification, clustering and taxonomy methods are no different from what ecologists, archeologists and paleontologists have been doing for thousands of years.

Even so, the microbe field guide is a tad more ambitious than any field guide to birds. The enormity of the task was perhaps best expressed by metagenomic pioneer Julian Davies in a quote beloved by microbe hunters: “Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science.”

It’s hard to overstate microbes’ importance to the planet. They drive the global carbon and nitrogen cycles that make life possible, regulate climate, purify groundwater and detoxify waste. If it weren’t for the ancient forebears of ocean-dwelling cyanobacteria, which pumped oxygen into Earth’s atmosphere after emerging some 3.5 billion years ago, we probably wouldn’t exist.