COVID catastrophe sparks new focus on microbes and their evolution

[Editor's note: This story originally was published by Real Clear Science.]

By Jesse H. Ausubel & David S. Thaler
Real Clear Science

With alarms sounding about the declining diversity and populations of plants and animals, we post a related concern with equally profound implications: is the variety of microbial life, including viruses, changing too, and if so, in which direction and how fast? As plant and animal numbers shrink, some specialized microbes associated with them might vanish, too. But is there a net overall reduction occurring? If so, is it good or bad news or irrelevant for our species?

During COVID lockdowns, we began holding weekly Zoom discussions on these questions with colleagues across ten time zones. We realized we simply have no idea of the global trend of microbial biodiversity, and one of us (DST) has now published "Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?" in the journal Frontiers in Ecology and Evolution.

The consequences of the ignorance may be profound. Microorganisms maintain Earth's breathable atmosphere. Homo sapiens depends in other ways on many other ecological services performed microscopically, including nutrient recycling, plant growth, water purification, and waste decomposition, not to mention enabling our creation of wine and beer, bread and cheese, and other foods.

Microbes are a Great Power, mightier than the greatest nations. Let's treat them with due respect, and try to assess much more expertly what they are doing and, if the metaphor is apt, what they want.

Botanists and zoologists can measure changes in many populations of the larger plants and animals with relative ease: count the diversity and abundance of many species in a given timeframe, then compare a subsequent count.

Attempting the same in relation to global microbial biodiversity is another matter. For starters, microbial "species" might total one trillion, more than one hundred times the number of humans and one hundred thousand times the kinds of larger "macrobial" species. We cannot send each variety of microbe a census form to complete.

Large fractions of the microbial world exist in hard-to-access, rare, or extreme environments, such as the soils and seafloor. The deeper, the less we know.

Then there is the challenge of establishing and maintaining a baseline library of nucleotide (DNA and RNA) sequences which define microbial species.

Moreover, some or all parts of microbial diversity may be increasing rapidly, meaning surveys may never catch up to this dynamic process.

The hundreds of variants turning up these days in the SARS-CoV-2 virus causing COVID-19 illustrate dramatically the pace of change within microscopic communities. While a new bird or beetle might enter the scene every few thousand years, or in bursts during the rare big shifts in geology, uncounted new microbes arrive daily. Microbial evolution did not stop when plants and animals came on the scene. Microbes quickly evolve to fit new niches we offer them. In deep mud, our guts, and new environments we build such as sewers, microbes continue to evolve in relation to each other. There is so much to discover, and not all of it existed last week.

The Swedish naturalist Linnaeus set out to make a complete list of the species of plants and animals in 1735, and after almost 300 years ago we still do not have a complete catalogue. It will not be easy to do something similar with orders of magnitude more microbes, and to measure the changes. Even an object the width of a human hair may host a massive community of diverse microbes.

Molecular technologies offer an obvious way to look for answers, and two approaches suggest themselves: The first is to focus on what modulates and what promotes microbial evolution. The other is to see how we might harness single molecule or single cell and viral (DNA and RNA) sequencing to assess variation within species. So the challenge we face to assess the pace and direction of change in microbial biodiversity is hard -- but not impossible.

One intriguing possibility is that our macrobial "team" consisting not only of humans but of all the other animals and plants that we can see with our naked eyes may constitute a shrinking proportion of the biosphere. When considered in the context of the microbial majority, learning how our team is faring relative to other elements in this evolving and sometimes perilous environment would surely be prudent.

Consider the volume of Earth compared to the rest of the universe and how Earth’s fraction of the total universe shrinks as the universe expands. Plant and animal species form clusters in the vast space of the possible sequences of DNA. Think of ‘species’ in terms of stars and galaxies, where individuals are stars and species are galaxies.

An analogy may apply to a shrinking share for humans and other macrobes of an ever-expanding sequence space. It is humbling to think that even as humans and a few species under our direct control (cows, pigs, chickens) now dominate the mass of terrestrial vertebrates, our team may be shrinking as a proportion of biological information space.

We cannot yet offer sure ways to census microbes globally, but can frame the rate of change of microbial biodiversity as a fascinating and likely important question on which science can make progress.

No agency yet monitors the state of the microbial world -- no World Wildlife Fund scans microbes. Perhaps one day soon, though, we will realize and rectify our neglect and lift our respect for the diversity of microbial life, and importantly, determine which way it is headed. Let’s respect microbes as a Great Power.

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