Undercover Cells: New Estimate of the Microbes Beneath the Continents

Researchers compiled hundreds of studies of the types and numbers of microbes living in the terrestrial subsurface and carefully scaled the results to come up with estimates of the total number and mass of microbes living beneath continents.

Scientists have proposed that the majority of microbes on Earth live in the vast, dark subsurface, but estimates of their numbers vary widely. Microbes in the subsurface might far outweigh the cells at the surface, or, they might just constitute a sizeable majority. During the past two decades, next-generation sequencing, which enables researchers to get a snapshot of a microbial community by sequencing all of the DNA in an environmental sample, has become more affordable and more widely used. Additionally, more scientists have undertaken explorations of the subsurface through coring and underground sampling. These advances are helping scientists to get a better handle on the numbers and diversity of cells in the subsurface.  

In a new review in Nature Geoscience [1], DCO members Cara Magnabosco (Flatiron Institute, USA), Li-Hung Lin (National Taiwan University, Taiwan), Hailiang Dong (Miami University, USA), Malin Bomberg (VTT Technical Research Centre of Finland), Karsten Pedersen (Microbial Analytics Sweden), Thomas Kieft (New Mexico Institute of Mining and Technology, USA), and Tullis Onstott (Princeton University, USA), and colleagues, make new estimates of the number and biomass of cells living beneath the continents. The researchers compiled cell counts and next-generation sequencing data from sampling locations around the world and used advanced analysis techniques to scale local counts to a global approximation. They estimate that 200 to 600 octillion microbes (2 to 6x1029 cells) live in the continental subsurface.

Magnabosco embarked on this effort after completing her dissertation on microbes living deep within gold and diamond mines in South Africa. She wanted to know if the microorganisms she was seeing in her samples lived elsewhere in the subsurface. Onstott, her co-author and former advisor, had already begun compiling studies of subsurface diversity and microbial abundance for his book, Deep Life, so Magnabosco and her co-authors expanded the database to include data from more than 200 publications, with 3,800 measurements of cell concentrations in the continental subsurface.
The existing data sets had some significant gaps. Most data sets came from shallow locations in North America. But, by using data sets from all seven continents and taking into account surface temperature, global heat flow, depth, and rock type across the continents, the researchers were able to scale local biomass estimates to make a comprehensive estimate of biomass worldwide. To improve their accuracy, they performed cross validation, where they split their microbial data set into a “training set” and a “test set.” First they fed the training set into a software program to develop a model of global subsurface continental biomass (see the visualization below). Then they used the test set to assess and improve the model’s predictions. 

Barring any surprises in cell abundance from under-sampled regions in the Southern Hemisphere, the researchers estimate that 200 to 600 octillion microbes live in the continental subsurface. These cells represent about four to 13 petagrams of carbon, (each petagram is about one billion tons, or more than five million blue whales), which is approximately four to 10 times less than earlier estimates. Previous calculations may have overestimated the number of subsurface cells by extrapolating cell counts from groundwater samples, and by basing estimates on only a handful of sites. Not only do these cells constitute an underground reservoir of organic carbon, but their metabolic activities also impact the cycling of carbon in the subsurface. 

The researchers also attempted to estimate the total dizzying diversity of microbes in the subsurface, but the number of species was harder to pin down, in part because scientists can’t always agree on what constitutes a microbial species. “I think this is one of the first times anyone has really looked at combining a lot of different environments in the continental subsurface and tried to think about how many species there might actually be,” said Magnabosco.

Now that Magnabosco and her colleagues have developed a global map of cell concentrations by depth for the continental subsurface, she hopes that other researchers will incorporate the information into their own models. Additionally she is interested in linking this map to existing ecological and evolutionary models to understand how microbial communities grow and interact in the subsurface on a global scale. 

“We hope that this is a stepping stone,” said Magnabosco. “As people generate more and more data throughout the continental subsurface, we’ll be able to make even better, more precise estimates in the future.” She also encourages scientists to investigate the populations of other types of organisms in the subsurface. “To get the full picture of microbial diversity in subsurface ecosystems, fungi and viruses and other small eukaryotes will be especially important.”

Main image: Magnabosco and colleagues collect fluid samples 1.3 kilometers underground during a 2013 trip to Beatrix Gold Mine to investigate the diversity and abundance of deep microbes in South Africa. Credit: Gaetan Borgonie

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