Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface

Area of Science:

• Microbiology
• Environmental Science
• Genomics

Background:

• Microbes inhabit diverse subsurface environments, necessitating adaptations to sense and respond to their surroundings.
• Extracellular sensor systems, particularly two-component systems (TCSs), are crucial for microbes to perceive environmental cues and regulate intracellular responses.

Purpose of the Study:

• To investigate the variation of microbial extracellular sensor systems, specifically TCSs, across different subsurface niches.
• To understand how environmental conditions influence the evolution and abundance of microbial sensor systems in the deep Earth.

Main Methods:

• Analysis of metagenomic data from multiple Deep Mine Microbial Observatory (DeMMO) subsurface sites.
• Quantification of sensor histidine kinases (HKs), a component of TCSs, across different geochemical and microbial diversity gradients.

Main Results:

• TCSs, indicated by HKs, were detected across all sampled subsurface and surface sites.
• HK abundance was higher in subsurface fracture fluids than surface fluids and inversely correlated with microbial diversity (r² = 0.81).
• HK frequency showed a strong positive correlation with dissolved organic carbon (r² = 0.82), suggesting nutrient availability drives sensor system evolution.

Conclusions:

• Abiotic and biotic properties of ecological niches significantly influence the diversity and abundance of microbial sensor systems.
• Microbes in dynamic nutrient environments may require more diverse TCSs compared to those in stable, low-nutrient settings.
• Further integrated metagenomic and geochemical studies are essential to fully elucidate the drivers of microbial sensor evolution in the deep subsurface.