Microbial Carbon Use Efficiency in Soil Ecosystems

Microbial carbon use efficiency (CUE) quantifies the fraction of organic carbon taken up by soil microorganisms that is converted into biomass rather than respired as carbon dioxide. As a central regulator of soil organic carbon (SOC) dynamics, CUE integrates microbial physiology, community composition and environmental constraints to determine how much carbon is stabilised in soils. Variations in temperature, moisture, nutrient availability and substrate quality all influence CUE, creating spatial and temporal heterogeneity in soil carbon retention. Understanding the drivers of microbial CUE is therefore fundamental to predicting soil feedbacks to climate change, guiding land-use practices and improving the representation of microbial processes in biogeochemical models. Recent advances have combined global data synthesis, experimental manipulations and modelling frameworks to reveal how CUE responds to climatic factors, management regimes and community traits, highlighting its global significance for carbon storage and agricultural sustainability.

Research from Nature Portfolio

Global analyses have demonstrated that microbial CUE is a dominant determinant of SOC storage, outweighing factors such as carbon inputs, decomposition rates or vertical transport. By integrating large-scale datasets with process-explicit modelling and deep learning, researchers established that CUE explains spatial variation in SOC at a magnitude at least four times greater than other evaluated drivers. This work further revealed a positive correlation between CUE and SOC content across diverse ecosystems, emphasising the potential of CUE as a predictor of carbon persistence under changing climates.

In a decade-long field experiment on a wheat–maize system, researchers examined how conservation agriculture interacts with warming to shape microbial mechanisms of soil carbon accrual. Under no-tillage with crop residue retention, warming promoted linear increases in microbial growth and CUE, driven by shifts in fungal community composition. Enhanced fungal necromass was identified as the strongest predictor of SOC gains, illustrating how management and climatic factors jointly regulate microbial physiology and long-term soil carbon formation.

Research from all publishers

A global study using stoichiometric modelling across natural ecosystems revealed that CUE is determined by the single most limiting resource—temperature, water, plant-derived carbon or soil nutrients—within each climate zone. Higher CUE prevailed in arid and cold regions limited by physical conditions, whereas nutrient limitations in tropical and temperate zones corresponded with lower CUE. This resource-specific dependence suggests that changes in precipitation, temperature or anthropogenic nutrient inputs may drive asymmetric responses in soil carbon retention across latitudes.

A management-focused review of agroecosystems highlighted key ecological drivers of microbial CUE in agricultural soils, including the roles of soil environment as a trait moderator, microbial community interactions and spatiotemporal dynamics across the soil profile. It emphasised how amendments, crop rotations and tillage practices can alter CUE conditions, and called for mechanistic, trait-based approaches to resolve unknowns in microbial responses. Such insights are essential for optimising land management strategies aimed at enhancing soil carbon sequestration through microbial processes.

Microbial Carbon Use Efficiency in Soil Ecosystems publication trend

The graph below shows the total number of articles in microbial carbon use efficiency in soil ecosystems across all publications each year (not limited to Nature Index journals).

Technical terms

Microbial carbon use efficiency (CUE): The proportion of organic carbon taken up by microorganisms that is allocated to biomass growth rather than respired as carbon dioxide.

Soil organic carbon (SOC): The reservoir of carbon compounds in soil derived from plant and microbial residues, critical for soil fertility and climate regulation.

Conservation agriculture: A land management system that employs minimal soil disturbance, continuous soil cover and crop rotations to enhance soil health and carbon storage.

Stoichiometric modelling: A quantitative approach that predicts microbial carbon use efficiency based on the balance of fundamental resources such as carbon, nutrients and moisture.

References

1. Microbial carbon use efficiency promotes global soil carbon storage. Nature (2023).
2. Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming. Nature Communications (2024).
3. Limiting Resources Define the Global Pattern of Soil Microbial Carbon Use Efficiency. Advanced Science (2024).
4. Managing Agroecosystems for Soil Microbial Carbon Use Efficiency: Ecological Unknowns, Potential Outcomes, and a Path Forward. Frontiers in Microbiology (2019).