Aeppli, M. | Search bioRxiv

bioRxiv2026

Microbial carbon metabolism is linked to organic matter chemistry across soil systems

Soil microbial growth and respiration play a critical role for soil organic carbon dynamics. Yet, we lack understanding of the main controls of soil microbial carbon metabolism at large scales. Here, we investigated whether and how the chemical composition of microbially available organic matter affects soil microbial carbon metabolism across soil systems. We linked soil microbial growth and respiration rates as well as carbon use efficiency (quantified with 18O stable isotope probing) to the chemical composition of extractable organic matter (characterized with reversed-phase liquid chromatography coupled to Fourier-transform ion cyclotron resonance mass spectrometry) along a geoclimatic gradient of 33 Chilean temperate grassland soils. We found that biomass-normalized rates of growth and respiration were primarily positively linked to aliphatics such as carbohydrate-, proteinaceous- and amino sugar-like compounds, and secondarily to unsaturated lignin-like compounds. Respiration was positively linked to compounds with carbon in a reduced oxidation state, suggesting carbon-conserving catabolism, while growth appeared unrelated to the oxidation state of carbon. This suggests that other mechanisms than mere energetic constraints control microbial growth rates in aerated soils. Our findings demonstrate that information on the chemical composition of bioavailable organic matter can provide insights into the processes that govern the fate of carbon across different ecosystems. Key pointsO_LIWe investigated if bulk soil microbial growth (18O stable isotope probing) and respiration is linked to the chemical composition of extractable organic matter (LC-FT-ICR MS) along a geoclimatic gradient of temperate grasslands. C_LIO_LIHigher rates of microbial carbon turnover were positively linked to aliphatic and unsaturated compounds. C_LIO_LISpecific (i.e., biomass-normalized) respiration was positively linked to compounds with carbon in a reduced oxidation state, suggesting carbon-conserving catabolism. C_LIO_LISpecific growth was unrelated to the oxidation states of substrate carbon, suggesting that soil microbial substrate use for anabolism may not be determined by direct energetic constraints. C_LI

microbiology↗

bioRxiv2025

Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils

Alpine riparian zones span topographic gradients from wet soils on the plain near streams to drier soils on adjacent slopes. These differences in soil moisture are generally associated with shifts in soil redox state from anoxic on the plain to oxic on the slope. In anoxic plain soils, soil organic carbon (SOC) may accumulate due to thermodynamic constraints on microbial activity. Here, we used shotgun metagenomics to examine how microbial diversity and functional potential varies across differing redox conditions on plain and slope soils in two catchments in the Swiss Alps. We complemented these analyses with soil physicochemical characteristics and information on the chemical composition of organic matter. Plain soils had higher SOC stocks and higher relative abundance of phenol compounds relative to slope soils, consistent with SOC preservation and preferential mineralisation of easily degradable organic compounds under anoxic conditions. Microbial communities in plain soils further exhibited greater taxonomic and functional diversity, including an increased potential for anaerobic respiration pathways. Genes for nitrate, iron, and sulfate reduction were linked to Chloroflexota, Acidobacteria, and Desulfobacterota phyla, respectively. Based on NMDS correlations, electron accepting capacity, calcium content, and pH shaped microbial community composition. Slope soils, by contrast, supported less diverse microbial communities, determined mainly by electron donating capacity and clay content. Our work demonstrates how soil redox conditions and microbial functional potential shape carbon cycling across landscape positions in alpine riparean zones. This mechanistic understanding is critical to anticipate changes in carbon cycling in alpine ecosystems in a changing climate.

microbiology↗