Microbes are ‘unknown unknowns’ despite being vital to all life, says study

A new study has highlighted how little is known about microbes – the hidden majority of life on Earth.

Life on the planet relies on an enormous quantity of bacteria, fungi and other tiny organisms. They generate oxygen, keep soils healthy and regulate the climate. Microbes play a crucial role in food production, such as cheese, beer, yoghurt and bread.

But despite their importance to human life and the health of the Earth, a new scientific paper has shown our “profound ignorance” of microbial biodiversity and how it is changing.

“We have no idea whether global microbial diversity is increasing, decreasing, or staying the same,” said David Thaler, a biologist at Basel University and author of the paper. “Most scientific papers tell us new facts. This is a different kind of paper; it does not answer anything but asks a new question.”

Many plant and animal populations are rapidly decreasing, with about 1 million species at risk of extinction, according to a 2019 UN-backed report. Plants and animals are counted over time to monitor how their populations change.

Microbes are often found in extreme environments – surviving at the bottom of the ocean, frozen deep inside glaciers and even inside a toxic volcanic lake – making them hard to study. Although poorly understood, bacteria and other tiny organisms are widespread in the deep biosphere below the Earth’s surface.

Prof Frederick Cohan, a microbial ecologist at Wesleyan University, Connecticut, who reviewed the study prior to publication, said that although animal and microbe extinctions may go hand in hand, new bacterial species could form at such high rates that they may be increasing regardless of plant and animal extinctions.

“When a mammal species goes extinct, we should expect that all the microbes that depend primarily or exclusively on that species should also go extinct,” he said.

“On the other hand, microbial ecologists like me who study the diversity of extremely closely related bacteria find that there are always new bacterial species being formed. There are always new ways for bacteria to divvy up the existing resource to allow for new species.”

Kelp microbes with each colour representing a different microbial community.
Microbial communities on the surface of kelp. Around 90% of the ocean’s total weight of organisms is microbes. Photograph: Tabita Ramirez-Puebla and Jessica Mark Welch/Marine Biological Laboratory

The paper considers how to study changes in global microbial biodiversity, including by monitoring small sequence changes similar to those used to track Covid-19 variants, and analysing the molecular machinery of gene transfer. Researchers hope the study will inspire others to investigate.

“Socrates called ignorance of what we do not know ‘profound ignorance’. This kind of ignorance was also termed ‘unknown unknowns’ by former US defence secretary Donald Rumsfeld. This paper identifies what is, or was, as of now, a biological unknown unknown,” said Thaler.

Jesse Ausubel, director of the Rockefeller University’s programme for the human environment, a sponsor of the study, said: “Linnaeus started his Systema Naturae in 1735, almost 300 years ago, and we still do not have a complete list of the plants and animals species that he started to catalogue. It will not be easy to do something similar with probably 1,000 times as many microbes and measure the changes.”

Microbes in the human body have been linked to conditions from obesity and type 2 diabetes to food intolerances and anxiety. But the consequences for the planet of humanity’s ignorance about how microbial life is changing is also unclear, the study finds.

About 90% of the ocean’s total weight of organisms is microbes, according to the 2010 Census of Marine Life. Microbes are critical in carbon capture, they breakdown organic matter and form the basis of the food web.

Kelp microbes with each colour representing a different microbial community.
Kelp microbes. These tiny organisms sit at the bottom of food chains, breaking down organic matter so it can be used by other living things. Photograph: Tabita Ramirez-Puebla and Jessica Mark Welch/Marine Biological Laboratory

Viruses such as Covid-19 and other microbes, such as the Yersinia pestis bacterium responsible for bubonic plague, can cause illnesses and are increasingly linked to the destruction of the natural world. Understanding changes in the abundance and diversity of microbes is important for understanding the health of the planet.

“There is no agency yet monitoring the state of the microbial world, and no WWF or Nature Conservancy for microbes. Perhaps one day soon we will realise and rectify our neglect and lift our respect for the diversity of microbial life,” said Ausubel.

Find more age of extinction coverage here, and follow biodiversity reporters Phoebe Weston and Patrick Greenfield on Twitter for all the latest news and features

The Guardian

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