The diversity of bacteria on Earth may be vastly underestimated


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Illustration: Aïda Amer/Axios

A two-year expedition to coral reefs in the Pacific Ocean detected half a million types of microbes, the latest estimate in the quest to quantify the planet's microbiome.

The big picture: There is intense debate among scientists about how many different types of bacteria and other microorganisms live on Earth — information that could aid conservation of species and fragile ecosystems brimming with biodiversity.

  • The microbiome supports other life on Earth through symbiotic relationships that provide nutrients, protects its hosts from pathogens and performs other essential roles.
  • Past efforts to characterize the microbiome have largely focused on a single species or a particular area. But there is a trend toward trying to do large-scale projects, says Emiley Eloe-Fadrosh of the Department of Energy's Joint Genome Institute.
  • The crowd-sourced Earth Microbiome Project analyzes samples from around the world and the National Ecological Observatory Network collects samples from 81 freshwater and terrestrial sites across the U.S.

What's new: The Tara Pacific Expedition, between 2016 and 2018, collected nearly 5,400 samples from three types of coral, two fish species and plankton at each of 99 coral reefs. The researchers then sequenced a specific region of DNA in the microbes and found more than 500,000 unique sequences, a proxy for species in this study.

  • When the researchers extrapolated the findings to the total number of fish and coral species in Pacific Ocean reefs, the total microbiome diversity rose to 2.8 million types of bacteria — within the current estimate of between 2.2 million and 4.3 million for the entire planet, they write in Nature Communications.
  • The microbiomes in the different areas sampled were distinct, and plankton in the water had more diverse microbiomes than marine animals.

Yes, but: There is debate about how to define a true species of microbe. Unlike with plants and animals, the physiology and morphology of bacteria can't be easily separated and most can't be grown in a lab and analyzed.

  • In the study, researchers analyzed their data with a widely used cutoff of 97% similarity in the genetic sequences to determine whether something is a species. But there are examples of microbes that have even higher genetic similarity but their genomes encode proteins with different functions so they could be considered different species, says Eloe-Fadrosh, who wasn't involved in the study, adding the reverse can also be true.
  • Even if the same species aren't present, their functions — for example, carbon or nitrogen cycling — could be redundant. "That changes the picture of how you can actually estimate diversity," says Eloe-Fadrosh, who uses metagenomic sequencing of the total genetic content of microbes to estimate their diversity in permafrost, soil and other environments.

The intrigue: The immense diversity of the microbes on the reefs may offer "ecological insurance" for coral, fish and other inhabitants, Pierre Galand, a researcher at Sorbonne University in France and a co-author of the study, said in a press briefing.

  • If some bacteria have similar functions, then one bacteria that doesn't survive due to environmental conditions could potentially be replaced by another, he told Axios in an email
  • "The large diversity of the reef microbiome may thus be important because it could help mitigate environmental perturbations," he said. "It's a theory ... [and] will be the focus of future studies."

What's next: The researchers said they plan to look at how environmental factors affect the microbiome.

  • "There's no direct link or correlation now between the decline in the coral reef and a change in the microbiome," said expedition leader Serge Planes of the University of Perpignan in France in the press briefing, adding that is "mainly because we know so little