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  • Writer's pictureP.K. Peterson

Earth’s Microbiome Is in Peril: Sweating the Small Stuff

“If microbial life were to disappear, that would be it — instant death for the planet.”

- Carl Woese, American microbiologist and pioneer of phylogenetic taxonomy of 16S ribosomal RNA


“We’re starting to see scary signals that there may be this large microbial extinction event under way that we barely noticed."

- Colin Averill, forest microbiologist, ETH, Zurich, Switzerland



The Earth’s microbiome—a hidden community of microbes (bacteria, archaea, fungi, protozoa, and viruses) that make extraordinary contributions to our planet, such as, maintaining major life-sustaining cycles of carbon, hydrogen, nitrogen, and oxygen—is in trouble. Critical components of it are under threat of extinction. Therefore, microbiologists around the world are developing strategies to preserve this vital member of our planet’s ecosystem. In today’s Germ Gems post, I focus on this extraordinarily important, but often overlooked component of the environment.

The environmental movement. This past Saturday (April 22) was Annual Earth Day. Since its founding in 1970, the day brings millions of people together around the globe who are involved in the environmental movement. (The year 1970 is a watershed date for environmental health in the U.S. as on December 2, 1970, President Richard Nixon’s administration created the Environmental Protection Agency “to protect human health and the environment.”)


A pecking order of microbiomes. The term “microbiome” is derived from the ancient Greek words mikros (“small”) and bios (“life”) and refers to a community of microorganisms found living together in any given habitat. In 1988, John Whipps first defined the term for horticulture as “a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties encompassing not only the microorganisms but also their theatre of activity.” We now know that all plants and animals form associations (microbiomes) with microbes—bacteria, archaea, fungi, protozoa, and viruses.


For over 100 years, scientists considered the plant microbiome a key determinant of plant health and food productivity. But at the end of the last century, the application of new molecular techniques in phylogenetic taxonomy greatly accelerated the studies of microbiomes associated with animal health.


Microbiologist and Nobel Prize laureate, Joshua Lederberg, sparked enthusiasm for studies of the “Human Microbiome.” In 2000, he described it as “an ecological system of commensal, symbiotic, and perhaps pathogenic microorganisms that reside in the human body.” In order “to improve understanding of the microbiota involved in human health and disease,” in 2007 the U.S. National Institutes of Health launched the “Human Microbiome Project.” Similar scientific initiatives occurred around the world. In the past two decades, studies of microbiomes have revolutionized the entire discipline of Microbiology. (In previous Germ Gems posts, I have highlighted many of the discoveries, especially those involving the role of the gut microbiome in human health and disease.)

The status of the Earth’s microbiome. Microbes are breathtakingly remarkable for their combined weight and staggering number. To quote Swiss forest microbiologist and ecologist Colin Averill, “[W]e usually sweat the big stuff: plants, fish, reptiles, birds and mammals. But these are perhaps just the tip of the iceberg. All told, there are perhaps 7.7 million species of animals, around 8 percent of which are insects and other arthropods, including arachnids and crustaceans. But there are at least 6 million species of terrestrial fungus and up to a trillion species of bacterium and archaeon, collectively known as prokaryotes. On top of that, there are about 200,000 species of complex unicellular microorganisms called protists, such as slime molds. These latter two groups make up the majority of Earth’s biodiversity.”


Despite the staggering number of microbes, a growing number of microbiologists around the world are warning that microbes that are vital to life on Earth are no longer regarded as impervious to threats of extinction (a predicament mirrored by many animals and plants).The first suggestion that the microbial underpinning of life on Earth was threatened appeared in 2007 when French investigators at the Pierre and Marie Curie University in Paris published a study in which they challenged the idea that there is always a vast reservoir of every species, including of microorganisms, that can repopulate any habitat at any time.


Why is the Earth’s microbiome threatened? Scientists working on climate change may be the ones who most acutely observe the impact of major disruptions in the Earth’s microbiome. As I described in my June 15, 2022, Germ Gems post, “Microbes and Climate Change: the Ugly, the Bad, and the Good,” climate change fuels not only vector-borne and water-borne infections, but on the positive side, it can also provide new insights and technological innovations that improve adaptations to a warming world.

Awareness of the threats to Earth’s microbiome. Learning of the threat of extinction of vast numbers and kinds of microorganisms in the Earth’s microbiome should be enough to keep all of us awake at night. I take solace in knowing that there are scores of microbiologists who believe it is not too late to arrest and reverse the decline. But there’s no room for complacency.


Whether or not we believe that “[t]he secret to saving our planet may be lurking in the dirt under our feet,” as is suggested in an article in October 2022 in Nature Microbiology, I find it of historical interest that the concept of “microbiomes” originated in the field of horticulture. But no matter who leads the campaign to save the Earth’s microbiome, it’s clearly a time for “all hands and brains on deck.”


According to forest ecologist, Colin Averill “this is our final wake-up call. A functioning Earth without a functioning microbiome is nearly unimaginable.” Let’s hope this message is heard loud and clear every day of the year, including “Earth Days.”

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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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