250 / 2025-04-15 21:05:18

Mineral-mediated Microbial Nutrient Acquisition: Insights from Biological Nitrogen Fixation and Enzymatic Organic Matter Decomposition

mineral,microbe,nitrogen fixation,organic matter,molybdenum,reactive oxygen species (ROS)

Theme 1: Novel Tools and Techniques in Geobiology > Session 1f: Geobiology at Molecular-, Nano-, and Atomic Scales

Nitrogen is a vital nutrient for life on Earth, and biological nitrogen fixation plays a crucial role in converting atmospheric nitrogen (N₂) into bioavailable ammonia (NH₃). This process relies on nitrogenase enzymes, which primarily use molybdenum (Mo) as a cofactor, although iron (Fe) and vanadium (V) can serve as alternatives. While the origin of nitrogenase was once debated, evidence suggests that Mo-based nitrogenase dates back to the Archean, despite the low concentrations of Mo in early oceans. Less efficient Fe and V nitrogenases are thought to have evolved about a billion years later, with Mo possibly being less bioavailable than Fe and V in certain environments, thus enabling activation of these alternative enzymes. Although hydrothermal vents may supply some trace metals, the bioavailability of mineral-bound Mo is crucial for nitrogen fixation in shallow seas and coastal environments, where ancient diazotrophs could access it. We examined the bioavailability of Mo, Fe, and V in minerals and rocks by incubating them with anaerobic diazotrophs. The results demonstrated that these microorganisms were able to extract metal ions from minerals to express nitrogenase genes and fix nitrogen through various mechanisms. The efficiency of nitrogen fixation was influenced by the rate of microbial weathering of minerals, with some bacteria secreting metallophores—metal-binding compounds that facilitate metal acquisition from minerals. Methanogens, which do not produce metallophores, were still able to utilize Mo from minerals and rocks for nitrogen fixation, likely due to the metal-chelating compounds and redox reactions on mineral surfaces. However, metallophores produced by other bacteria likely inhibited methanogen growth, suggesting competition for trace metals. These findings underscore the significance of mineral-bound transition metals in supporting biological nitrogen fixation in ancient environments.



Extracellular enzymes catalyze the rate-limiting steps of organic carbon decomposition. Although the enzyme activities have been incorporated into predictive biogeochemical models, they exhibit a range of catalytic, kinetic, and stability properties across different environments. Mineral surfaces are known for their ability to adsorb enzymes, but their effects on enzyme activity are not well studied. Moreover, oxygenation of mineral-bound Fe(II) generates reactive oxygen species (ROS), yet it is unknown whether and how this process alters the activity and functional lifespan of extracellular enzymes. We explored the extent to which interaction with primary silicates and secondary minerals affects the activity and longevity of extracellular enzymes under both oxic and anoxic conditions. The enzyme activity was correlated with the capacity-related properties of minerals (controlling space for adsorption), including specific surface area (SSA) and the SSA-normalized amount of BG adsorption, but not with the functional properties (controlling the mechanisms of adsorption) such as surface charge. Enzyme conformational change is a function of SSA-normalized amount of adsorption, suggesting that spatially more distributed enzyme molecules would have a higher probability of encounter with the substrate than the congested molecules. Under anoxic conditions, enzyme adsorption to mineral surfaces decreased its activity but prolonged its lifespan. Under oxic conditions, ROS was produced, with the amount of •OH, the most abundant ROS, being positively correlated with the extent of structural Fe(II) oxidation in reduced minerals. •OH decreased enzyme activity and shortened its lifespan via conformational change and structural decomposition of enzyme. These results suggest that under oxic conditions, the ROS-induced inhibitory role of Fe(II)-bearing minerals outweighed their adsorption-induced protective role in controlling enzyme activity. These results disclose a previously unknown mechanism of extracellular enzyme inactivation, which have pivotal implications for predicting the active enzyme pool in redox-oscillating environments.