Microbial extinction is happening

Another extinction catastrophe has been signalled by an article by Graham Lawton in New Scientist in April 2023 describing the loss of microbial biodiversity. For a long time, microbes were assumed to be universally distributed through the air and thus common everywhere. It is only since 2007 with the development of DNA sequencing technologies that the true diversity of microbes, including bacteria, fungi and protists, has become apparent. There are at least 6 million species of terrestrial fungus, but only 140,000 have been fully characterised. For up to a trillion species of prokaryotes like bacteria, DNA-based microbial surveys are only beginning. Protists, complex unicellular organisms like slime molds, number 200,000. This represents the majority of the Earth's biodiversity.

Microbes are essential to life on Earth. A gram of soil can contain a billion single-celled organisms of tens of thousands of different species, and its fungal strands would extend for hundreds of kilometres. Microbes are the main decomposers, breaking down organic matter. They drive the cycles of carbon, hydrogen, nitrogen, oxygen, phosphorus and sulphur. Recent studies have shown that bacterial genomes vary by location, showing that they can evolve in isolation. A common wood-decaying fungus has been shown to have nine subspecies. Many microbes are specific to their host plant or animal, such as an endangered plant found to have six species of fungi only on its leaves. If the host goes extinct, so do all the associated specific microbes.

A large microbial extinction event may already be underway. Species of soil fungi that produce mushrooms have diminished by nearly half in the Netherlands over 30 years, and more generally by 45 percent across Europe in the past century. The main causes are probably air pollution, and intensive forest management that removes the food of wood-decaying fungal species. Since most species are undescribed, they will go extinct without our knowing it. Not only are fungi decreasing in abundance, but the same common ones come to dominate and more exotic ones disappear, with intense homogenisation. Recent studies have shown that microorganisms are sensitive to the same pressures as higher organisms, including habitat loss, invasive species, pollution and wildfires. Warnings that the recent decline in insect populations would be catastrophic for planetary ecosystems, show that a microbial apocalypse would be even worse. You can't overemphasise the importance of microbes.

A first priority is to identify where microbial diversity is highest so that conservation efforts can be started. Then we need to include restoring microbial populations as part of efforts at soil regeneration and reforestation. When planting a tree, we need to plant the associated native microbiome. This has been shown to increase plant growth by an average of 64 percent. While fungi are getting more attention, other microbes are not yet the focus of conservation attention. As with the rest of biodiversity loss, we need to act quickly, as this may be our last chance to avoid catastrophe.

Another report by James Dinneen on 10 June shows that microbes on coral reefs appear to be more varied than the microbiomes of the rest of the planet's ecosystems combined. Coral reefs have a third of marine species of plants and animals. A study sampling 99 reefs across the Pacific looking at only three species of corals and two species of fish found more than half a million unique sequences of DNA from bacteria and archaea, distinct across different parts of the ocean. Extrapolating to all the other species of corals and fish would put the diversity six times higher, greater than some estimates of the microbial biodiversity of the entire planet. In the complex coral reef ecosystem, microbes are involved in many different kinds of processes. With the threatened collapse of coral reef ecosystems from climate change, microbial extinction may be even more significant and irreversible.

SOURCES: Graham Lawton, "The hidden extinction", New Scientist 258(3434):46-49. 15 April 2023.
James Dinneen, "Coral reef microbe community is staggeringly diverse", New Scientist 10 June 2023, p. 13