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Microbes' activities underground are no longer a mystery thanks to new technology

A recent breakthrough is empowering scientists to unveil the secret underground activities of microbes, shedding light on their astonishing capabilities and their vital contributions to our planet.

Barren landscapes in sun-scorched places like Death Valley, California are a testament to the extremes our planet can harbor, a place where the mere concept of life seems improbable.

But appearances can be deceiving. Deep beneath the cracked, parched surface, scientists have opened a window into a world pulsating with microbes and their hidden activities.

Microbes activities in extreme environments

Microbes, the minuscule powerhouses behind many of Earth’s fundamental processes, thrive in seemingly impossible environments. From hydrothermal vents to nuclear waste sites, they have evolved remarkable adaptations.

But studying those living in truly extreme settings, like the depths of Death Valley, presents a special set of challenges. Researchers could look at the genetic blueprints of these microbes, but this data only revealed their potential capabilities.

The critical question of how active those capabilities were at a given moment — in other words, what those microbes were actively doing to survive — remained largely unanswered.

This activity level is essential for understanding their influence on global cycles like the movement and transformation of carbon, an element crucial to life.

New method reveals microbes activities

A team of researchers at the Bigelow Laboratory for Ocean Sciences has achieved a remarkable feat. They’ve developed a way to directly link the genetic code of individual microbes with their moment-by-moment activities.

This provides an unprecedented glimpse into the real-time functioning of microbes in their natural environments, like seeing how a car engine operates while it’s in motion, not just while it’s parked.

The “Genomes to Phenomes” project

This innovation is the result of the bold and ambitious “Genomes to Phenomes” project. It’s a testament to the potential for insights when experts from diverse fields – marine science, desert research, and genetics – join forces.

The project’s power lies in its combination of cutting-edge techniques:

Single-cell genetic sequencing

This technique begins by isolating single microbes and deciphering their individual DNA sequences. This provides a detailed genetic blueprint, revealing the potential functions a microbe is capable of based on the genes it possesses. It like a parts list for a machine – we can see what the machine could potentially do, but not if it’s currently switched on.

Flow cytometry

Adapted from its use in medical science, flow cytometry allows researchers to analyze microbes from water samples collected in the depths. Researchers treat each microbe with a special dye that lights up under a laser during certain internal reactions.

The brightness of the light corresponds to how active those reactions are. This is where things get exciting because it tells us which of the ‘machines’ on our parts list are not just present, but are actually switched on and running.

Combining techniques

Previously, when studying microbes in extreme environments, scientists were limited to just a genetic parts list. They could see what genes a microbe had, but not whether or how it was actually using them. This new method bridges that gap.

Now, researchers can directly measure the activity of specific microbes deep beneath the surface. This reveals which microbes are the key players in their environment and exactly what roles they play in essential processes, like breaking down and transforming carbon, impacting vast, global systems.

Subterranean microbial world activities

Armed with this toolkit, the team descended nearly half a mile beneath Death Valley’s surface, targeting a groundwater aquifer.

Lacking oxygen, this environment would be uninhabitable to most life forms. Yet, the scientists detected a community of microbes specially equipped to survive these conditions.

Using their method, they were able to perform a kind of microbial census, identifying not only the most abundant species, but crucially, which ones were the most active players in this underground ecosystem.

Activities of microbe Candidatus Desulforudis audaxviator

The research revealed one bacterium, Candidatus Desulforudis audaxviator, to be the star of the show. This organism has evolved to use sulfate for energy – a kind of ‘breathing’ that replaces the need for oxygen, giving it an edge in this oxygen-barren zone.

“Previously, we had to assume that all cells were operating at the same rate, but now we can see that there is a wide range of activity levels between individual members of the microbial communities,” explained Melody Lindsay, the lead researcher on the study. “That helps us understand what these microbial communities are capable of and how that might influence global biogeochemical cycles.”

The reach of innovation

Having started with oxygen-using microbes in the ocean, the scientists are now successfully applying their method to other challenging environments.

From the sediments of Maine’s coastline to the depths of the ocean floor, this technique is pushing the limits of our knowledge.

Even more excitingly, it holds the potential to inform our search for life in the subsurface environments of other planets.

“Right now, we’re getting all of these point measurements around the world, and they do help us better understand what microbes are up to, but we need to scale it up,” said Lindsay. “So, we’re thinking about how to apply this method in new places, even potentially on other planets, in expanded ways.”

This method marks the beginning of an exciting new era in microbial research. The discoveries made remind us that life finds a way, even in seemingly impossible environments, and that organisms too small to see play incredibly influential roles in Earth’s most fundamental processes.

Broader implications of knowing microbes activities

This innovative technique has broad applications, making it a powerful tool for various research areas and environments:

Oceanographic studies

The method has proven effective in subsurface land studies. It shows promise for marine research. It’s ideal for investigating microbes in deep-sea sediments and water columns. These are areas where traditional sampling struggles.

Environmental monitoring via microbes activities

Researchers can use this method to monitor environmental health by analyzing the microbial communities and their activity levels in polluted water sources or soils. This could help in assessing the impact of contaminants or changes in environmental conditions.


The technique’s ability to identify and analyze life forms in extreme environments makes it promising for astrobiology, especially in the search for life on other planets or moons within our solar system that have subsurface oceans or ice layers, like Europa or Enceladus.

Medical and biotechnological research

While not its initial application, the method’s principles could be adapted for studying microbial communities in the human body or in industrial processes. This could improve understanding of microbiomes’ roles in health, disease, or biodegradation.

Climate change studies

By examining how microbes in various environments respond to changes in conditions, researchers can gain insights into how global warming and other climate change factors affect microbial-driven processes like decomposition and carbon cycling.

The study is published in Proceedings of the National Academy of Sciences.


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