Beneath the Earth’s surface lies a largely unexplored ecosystem known as the critical zone. This unique area of soil stretches from the Earth’s surface to the base of the groundwater zone, acting as a dynamic interface where rock, water, air, and life converge. Despite their low content of carbon and nutrients compared to surface soils, the microbial communities found in these deep soils are remarkably diverse. Scientists are still uncovering how these microorganisms manage to thrive under such nutrient-scarce conditions.
To explore how microbes survive in the critical zone, researchers focused on a little-known group of bacteria identified globally in deep soils. Known as CSP1-3 Gate, these bacteria were first discovered in 2006 within a geothermal system in Yellowstone National Park. Since then, they have been found in various oxygen-limited and nutrient-poor environments, yet their exact role and characteristics remain mysterious.
Researchers collected soil samples from seven deep soil cores spanning 20 meters (approximately 65 feet) in Shaanxi province, China, and western Iowa, USA. By extracting and sequencing environmental DNA from these samples, they pieced together draft genomes of the microorganisms inhabiting these depths. Through metagenomic analyses, they aim to uncover where CSP1-3 microbes live, their dietary habits, their nutrient cycling processes, and the adaptations that facilitate their survival.
Analysis revealed CSP1-3 bacteria were abundant in deeper soils, comprising over 10% of all microorganisms found in 30 out of 86 soil layers below 5 meters (16 feet). In some layers, such as those at 17 meters (56 ft) and 22 meters (72 ft) deep, CSP1-3 accounted for up to 60% of the microbial population. Using DNA copy-counting methods, researchers estimated that nearly 50% of CSP1-3 cells in these deep soils were actively replicating.
Based on the assembled metagenomes, the research indicated that CSP1-3 bacteria utilize a flexible metabolism to thrive in deep soils. They identified genes that allow these bacteria to alternate between two methods of obtaining energy: autotrophy, which involves producing their own food, and heterotrophy, which entails consuming organic matter from their environment. This adaptability, referred to as mixotrophy, allows them to respond to varying nutrient availability.
Additionally, researchers uncovered genes enabling CSP1-3 bacteria to utilize diverse energy sources such as carbon monoxide (CO) and diatomic hydrogen (H2), both prevalent in deep soils. They also identified genes allowing these microbes to generate energy under varying oxygen conditions, providing an advantage in environments where oxygen levels fluctuate. Genes related to sugar synthesis, such as trehalose, contribute further to their endurance in resource-limited conditions, alongside genes linked to carbon, nitrogen, and sulfur management.
The team analyzed 521 genomes from diverse environments globally, including aquatic habitats, topsoil, and deep soil, to trace the evolutionary lineage of CSP1-3. Genome analysis indicated that these bacteria’s ancestors originated in aquatic settings before transitioning to topsoil and ultimately to deep soil, with significant genomic changes that augmented their carbohydrate and energy metabolism to facilitate adaptation to terrestrial ecosystems.
The researchers concluded that CSP1-3 bacteria are evolutionarily suited to thrive in deep, nutrient-poor soils due to their specialized metabolism and low-energy survival strategies. They posited that CSP1-3 plays a crucial role in energy and nutrient cycling, potentially influencing global environmental processes by enhancing soil fertility and nutrient availability, thereby stabilizing deep soil ecosystems. The ability of these microorganisms to utilize gaseous energy in nutrient-deficient environments offers compelling insights into their survival strategies under extreme conditions, contributing to ongoing planet protection efforts. However, further investigations are necessary to fully comprehend how these deep soil microbes impact soil chemistry and ecosystem functions over time.
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Source: sciworthy.com
