• P.K. Peterson

Meet Your Ancient Ancestors: New Light on the “Tree of Life”

Whenever I found something remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people be informed thereof. - Antonie van Leeuwenhoek, 17th century Dutch inventor of the microscope, Father of Microbiology

“If you don't know history, then you don't know anything. You are a leaf that doesn't know it is part of a tree."

- Michael Critchon, American physician, author, and filmmaker

Bacteria have been on this planet since the beginning of life some 3.8 billion years ago. Few stories in biology are as mind boggling as those about bacteria. Moreover, few scientific discoveries are more intriguing than those defining the “Tree of Life.” If you’ve ever wondered, “Where did we (Homo sapiens) come from?,” you’ll find the answer in this Germ Gems post.

The Tree of Life. In his 1859 book “On the Origin of the Species,” Charles Darwin first formulated the “Theory of Evolution by Natural Selection” postulating that the origin of species is rooted in competition, the so-called “survival of the fittest.” Darwin’s theory was highly controversial when first proposed, and it remains so to this day…albeit for very different reasons. In the past century-and-a-half, understanding of evolution has evolved enormously. In particular, the pivotal role played by microbes in evolution has come to light.

Although he is considered the “Father of Evolution,” Charles Darwin didn’t consider microbes in his thinking about evolution. Of course, this isn’t at all surprising as few scientists took microscopic creatures seriously until the “Germ Theory of Disease” emerged in the last half of the 19th century. Nonetheless, in his Origin of Species, Darwin did include an illustration of a “tree” depicting branching and extinction through time and referred to the genealogical relationships among all living things as “the Tree of Life.” But germs were nowhere to be found on Darwin’s “tree.”

Modern day thinking about the “Tree of Life” is credited to University of Illinois microbiologist Carl Woese. Depicted below is a modified version of Woese’s 1970s phylogenetic “Tree of Life.” It contains three major life forms or “domains”: Bacteria, Eucarya, and Archaea, a domain discovered by Woese. The distinguishing feature of all Eucarya, the domain that includes humans, is that their cells possess a nucleus. All members of both the Bacteria and Archaea domains are single-celled microbes that lack a nucleus.

In 2016, a team of researchers led by University of Dusseldorf Professor of Molecular Evolution William Martin hypothesized that there was a microscopic last universal common ancestor (LUCA) and placed LUCA at the base of the “Tree.” Subsequently, using a supercomputer and new methods to generate genome sequences, Jillian Banfield and her colleagues at the University of California Berkeley recently proposed a new view of the Tree of Life that includes 92 Bacteria phyla, 26 Archaea phyla, and five Eucarya supergroups.

Following these seminal discoveries related to the Tree of Life, the nature of LUCA was recently discovered. In a publication in Science this May entitled, “A rooted phylogeny resolves early bacterial evolution,” Gareth Coleman and his colleagues at the University of Bristol provided evidence from a model of the evolution of 11,272 gene families that a bacterium, dubbed LBCA (“last bacterial common ancestor”), is at the root of the “Tree.” The other two domains, Archaea and Eucarya, developed down the line, arising from Bacteria. This means that plants and animals are all descendants of ancient Bacteria. (Studies of the Earth’s oldest fossils suggest that Bacteria appeared about 3.8 billion years ago.)

The Coleman group also found that most gene transmissions have been vertical (that is, from parents to offspring of the same species), but that horizontal gene transfer (HGT) occurs in a large majority of gene families. Although HGT is more likely to be successful between closely related than distantly related species, it does occur between species as divergent as those found in different domains of life. Thus HGT is a process of acquiring new genes and is a major driving force leading to genomic variability that contributes to evolution.

Microbes are everywhere. Our planet’s first living species and our ancient microbial ancestors were extremophiles (from the Latin extremus, meaning “extreme,” and the Greek philia, meaning “love”). These microbes lived and reproduced in hostile environments, such as extreme heat, cold, acidity, and salinity. They continue to populate our planet today. Extremophiles have been found living in the cold and dark, in a lake buried a half mile deep under the ice in Antarctica; in the deepest spot on Earth, at the bottom of the Mariana Trench in the Pacific Ocean; and inside rocks up to 1,900 feet beneath the sea floor, under 8,500 feet of ocean.

Archaea are famous for colonizing hot springs and hydrothermal vents. A recent report in Nature Communications showed that such archaeans recycle carbon without producing methane (a plus for Earth’s climate). And in another publication in Nature Communications, researchers revived microbial cells from 101.5-million-year-old sub-seafloor sediment, a severely nutrient-limited environment almost devoid of food. Finally, according to an article last year in Popular Science, yeast and E. coli can thrive in conditions that might exist on alien planets. Thus, it’s not at all surprising that the search for life in outer space is targeting microbes that can withstand unbelievably withering conditions.

If the microbial mastery of the ecosystems mentioned above doesn’t impress you, I recommend an article by Jordan Cepelewicz in the May 24, 2021 issue of Quantamagazine, “Radioactivity May Fuel Life Deep Underground and Inside Other Worlds.” Scientists who’ve used sophisticated technologies to tunnel kilometers below the continents and deep marine sediments have found that these “uninhabitable” environments are home to an astronomical number of microbes, estimated at 10 to the 30th or 30 nonillion (for comparison, the observable universe contains 10 to the 22nd stars). If that’s not astonishing enough, researchers discovered that a form of radioactivity called radiolysis is important for sustaining this subsurface life.

Appearance of complex life (Eucarya). Archaea look similar to bacteria but that’s where the resemblance ends. Both groups of these prokaryotes had planet Earth all to themselves for more than 2 billion years when the first eukaryotes emerged. Scientists believe that the nucleus and other organelles, such as mitochondria (the source of cell energy), that reside inside eukaryotic cells formed when one prokaryotic organism engulfed another.

According to an article in May of this year in Nature News, “The mysterious microbe that gave rise to complex life,” there’s been a recent surge in research interest in Archaea. The painstaking studies of Buzz Baum, an evolutionary biologist, and his cousin David Baum, a professor of botany, have provided convincing evidence that it was a tentacled archaeon that did the engulfing. In what looks like an ancient love story between an archaeon and a bacterium, Buzz Baum commented, “We are part bacteria, part archaea, part new inventions. It’s better together.”

Viruses, the “dark angels” of evolution. Viruses are the most abundant biological entities on Earth. Nonetheless, viruses aren’t considered members of the “Tree of Life.” This has nothing to do with their extremely small size (100 million viral particles of the novel coronavirus, SARS-CoV-2, can fit on a pinhead). Rather, they are “treeless” because viruses lack their own metabolism and must rely on the cells that they infect as their source of energy.

In most cases, the cells that viruses infect are bacteria, and as was discussed in the June 10, 2020 Germ Gems post, “Viruses that Eat Bacteria: Fighting Fire with Fire,” viruses called bacteriophages (that is, “bacteriaeaters”) kill an astounding number of bacteria. For example, 40% of all bacterial cells in the ocean are eliminated by bacteriophages every single day. (Phages provide the same service in the human gut where they outnumber bacteria about 10:1.)

Biologists think that viruses emerged on Earth about the same time as Bacteria and that they have been co-evolving with bacteria ever since. For an excellent review of the crucial role that viruses have and continue to play in evolution, I recommend David Quammen’s January 14, 2021 National Geographic article, “How Viruses Shape Our World.” While almost all of our attention to viruses these days is riveted on the relatively small number of species that are human pathogens, according to Quammen, “Mammals may carry as many as 320,000 species of viruses . . . many viruses bring adaptive benefits, not harms, to life on Earth, including human life . . . Viruses, it turns out have played crucial roles in triggering major evolutionary transitions.”

We’ve learned in recent years that about 5-8% of the human genome is from a group of viruses called retroviruses. (HIV is an example of a retrovirus). That is, our genome is also partly their genome. Somehow, the genome of our human ancestors learned how to adapt to these viruses. They’re not “dark angels” at all.

Many infectious diseases specialists consider the global emergence of bacteria that are resistant to antibiotics to be the single biggest infectious diseases threat to our species. Bacteriophages are increasingly being used as a treatment of life-threatening infections caused by antibiotic-resistant bacteria. My guess is that human survival, that is, our fitness, in what is an increasingly challenging environment will benefit from learning how the “masters of hostile environments” that is, microbes, have pulled it off. After all, our ancient ancestors, Bacteria, Archaea, and viruses, have been working on sustaining their survival for the past 3.8 billion years.

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Main Page images courtesy of Shuxian Hu, MD. Dr. Hu is a scientist in the Neuroimmunology Research Laboratory at the University of Minnesota.


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