Deep beneath Earth’s surface lies a largely unexplored ecosystem known as the Critical Zone. The Critical Zone is a region of soil extending from the ground surface to the bottom of the groundwater zone, and forms a dynamic interface where rock, water, air, and life interact. These deep soils contain much lower amounts of carbon and nutrients than surface soils, yet host microbial populations comparable in size to those aboveground. Scientists don’t understand how microorganisms survive and function under such starved conditions.
To determine how microbes survive in the Critical Zone, researchers investigated a little-known group of bacteria that scientists have repeatedly detected in deep soils worldwide. These bacteria, known as the CSP1-3 phylum, were first identified in geothermal systems at Yellowstone National Park in 2006. Since then, they’ve also been found in oxygen-limited deep soils, oxygen-rich topsoils, and other nutrient-poor environments, but scientists don’t know what they are or what they’re doing there.
To find out, the researchers collected samples from 7 deep soil cores extending to depths of 20 meters (about 65 feet) from Shaanxi Province in China and western Iowa in the USA. They extracted mixtures of environmental DNA from the samples and sequenced them to piece together draft genomes for the microbes living there. They analyzed these genomes, referred to as metagenome-assembled genomes, to identify where the CSP1-3 microbes were living, what they were eating, how they cycle nutrients in deep soils, and which adaptations help them survive in these environments.
The researchers found that CSP1-3 are particularly abundant in deep soils, accounting for more than 10% of all microbes they detected in 30 out of 86 individual layers of soil below 5 meters (16 feet). In some deeper soil layers, like from depths of 17 meters (56 feet) and 22 meters (72 feet), CSP1-3 made up as much as 60% of the microbial population. The team also used a method that measures how much DNA is being copied inside the cells to estimate that approximately 50% of CSP1-3 cells in these deep soils are actively replicating.
Based on their metagenome-assembled genomes, the researchers suggested that CSP1-3 bacteria survive in deep soils by relying on a flexible metabolism. They identified genes that allow these bacteria to switch between making their own food, called autotrophy, and consuming organic matter from the environment, called heterotrophy. This mode of metabolism, known as mixotrophy, allows the bacteria to adapt to fluctuating nutrient availability.
The researchers also found genes that allow CSP1-3 bacteria to utilize a variety of energy sources, including carbon monoxide (CO) and hydrogen (H2), which are abundant in deep soils. They also discovered genes that allow the microbes to generate energy whether oxygen is present, absent, or unreliable, which is useful in environments where oxygen levels fluctuate. Additionally, they have genes to synthesize a sugar that acts as an energy reserve, called trehalose, which further helps them endure resource-limited environments, as well as genes associated with carbon, nitrogen, and sulfur processing.
Next, the team analyzed 521 genomes collected from various environments worldwide, including aquatic habitats, topsoil, and deep soils, to trace the evolutionary history of CSP1-3. The genomic analysis revealed that their ancestors originated in aquatic environments before transitioning to topsoil and eventually deep soils. This transition was marked by significant genomic changes, including the acquisition of genes for carbohydrate and energy metabolism, which helped them adapt to habitats on land.
The researchers concluded that CSP1-3 bacteria are genetically adapted to life in deep, nutrient-poor soils, since they have genes linked to streamlined metabolisms and low-energy survival. The authors noted that CSP1-3’s role in energy and elemental cycles in deep soils could impact global environmental processes by enhancing soil fertility and nutrient availability, and helping to stabilize deep soil ecosystems. Their ability to utilize gases for energy in nutrient-limited environments also offers insights into how microbes survive in extreme conditions, further informing planetary protection efforts. However, they also noted that further research is required to determine exactly how these deep-soil microbes influence soil chemistry and ecosystem function over time.
