Almost 2/3 of Earth's Biodiversity Is Bacteria

In this new 'tree of life' diagram, bacteria dwarf everything else. For context, all plants, animals and other multicellular beings fit into the eukaryotes section at lower right. (Image: Jill Banfield and Laura Hug/UC Berkeley/University of Waterloo)

Humans excel at nearly everything but humility. We tend to see ourselves as the apex of evolution, ruling a planet we conquered long ago. Yet despite all our material wealth, and Madonna's 1984 wisdom, we are living in a bacterial world.

If you doubt the dominance of bacteria, see the diagram above. It's a new "tree of life," published this week in the journal Nature Microbiology, and it reveals how unbelievably biodiverse bacteria are compared with all other life on Earth.

A tree of life, also known as a phylogenetic tree, is a map of how life has evolved and diversified, illustrating evolutionary relationships like branches on a family tree. The image below is an iconic example, sketched in 1837 by Charles Darwin:

These trees have always fallen well short of their ultimate goal, even today, since the 2.3 million species known to science so far may only represent 20 percent of Earth's total biodiversity. We're still fumbling around in the dark, trying to describe and categorize a biosphere we can barely see.

Our vision is improving, though, with new ways to study tiny life forms. The latest tree is a major expansion, factoring in more than 1,000 new kinds of bacteria and archaea found in the last 15 years. (Archaea are single-celled creatures that used to be classified as bacteria. They're now deemed one of three domains of life, the others being bacteria and eukaryotes.)

Straight from the dolphin's mouth

The 1,000 new bacteria and archaea were discovered in a variety of environments, including a hot spring at Yellowstone National Park, a salt flat in Chile's Atacama desert, meadow soil, wetland sediments and the inside of a dolphin's mouth.

Many of the newfound microbes couldn't be studied in a lab because they rely on other organisms to survive, either as parasites, scavengers or symbiotic partners. Scientists can only detect them now by searching for their genomes directly in the wild, rather than trying to grow them in a lab dish. (They're labeled "candidate phyla radiation" on the new tree of life, in purple at the upper right of the diagram.)

"What became really apparent on the tree is that so much of the diversity is coming from lineages for which we really only have genome sequences," says co-author and University of Waterloo biologist Laura Hug in a statement. "We don't have laboratory access to them; we have only their blueprints and their metabolic potential from their genome sequences. This is telling, in terms of how we think about the diversity of life on Earth, and what we think we know about microbiology."

These "uncultivable bacteria" are not only common, the researchers say, but seem to represent about a third of all biodiversity on Earth. Other bacteria account for another third, leaving "a bit less than one-third" for archaea and eukaryotes, the latter of which contains all multicellular life — including plants, fungi and animals.

"This incredible diversity means that there are a mind-boggling number of organisms that we are just beginning to explore the inner workings of that could change our understanding of biology," says co-author Brett Baker, a marine scientist at the University of Texas-Austin and previously the University of California-Berkeley.

It's a small world after all

We clearly still have a lot to learn about life on Earth, but this is nonetheless a big leap for humans' understanding of the biosphere and our place in it. Our species has long felt separate from and superior to other life, as depicted in this 1579 "Great Chain of Being." Even after Darwin published "On the Origin of Species" in 1859 — which included an updated tree of life, and upended the way humanity sees itself — early portrayals of evolution were often still shaped by a human-centric point of view.

In 1879, German biologist and philosopher Ernst Haeckel published "The Evolution of Man," which featured the tree of life drawing below. Haeckel was a luminary in evolutionary science, but like many early thinkers in that field, he also painted his own species as the pinnacle of evolution, as in his arrangement of this tree:

This 1879 tree was part of a long-term shift in the way we classify nature. (Image: Ernst Haeckel/Wikimedia Commons)

As evolutionary science continued evolving over the years, the tree of life grew more complicated. It began to emphasize molecular methods over the observation of physical traits, and to focus more closely on less obvious life forms like bacteria. It was time for another phylogenetic shakeup by the late 20th century, when American microbiologist Carl Woese introduced the three-domain system of life:

This modern tree divides life into three domains: bacteria, archaea and eukaryotes. (Image: Wikimedia Commons)

Here's another, more recent version, based on completely sequenced genomes. It was released in 2006 as part of the Interactive Tree of Life:

Based on sequenced genomes, this 2006 tree shows eukaryotes in red, archaea in green and bacteria in blue. (Image: iTOL)

In 2015, the Open Tree of Life project released the most comprehensive tree to date, mapping the links between all 2.3 million named species. The circular graphic below illustrates the first draft, using colors to represent the proportion of each lineage in U.S. biological databases (red is higher; blue is lower). See the full view here.

This map is just a selection of the full Open Tree, which links 2.3 million species so far. (Image: opentreeoflife.org)

With most of Earth's biodiversity still unidentified by science, the tree of life is far from finished. Many more changes lie ahead, and while it can be humbling to see humans and other animals dwarfed by microbes, denial wouldn't do us any good. They run this show whether we like it or not, and as the authors of the new diagram point out, bacteria can teach us a lot about our planet — and ourselves.

"The tree of life is one of the most important organizing principles in biology," says Jill Banfield, co-author and geomicrobiologist at UC-Berkeley. "The new depiction will be of use not only to biologists who study microbial ecology, but also biochemists searching for novel genes and researchers studying evolution and earth history."