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Updated: Sep 15, 2025

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

Published on: July 16, 2017

Functional regimes define soil microbiome response to environmental change.

Kiseok Keith Lee^1,2,3, Siqi Liu⁴, Kyle Crocker^1,2,3

¹Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.

|July 16, 2025

Summary

Soil microbiomes exhibit distinct metabolic responses to environmental changes, identified through a new modeling approach. These functional regimes reveal how soil communities adapt to pH perturbations and nutrient availability.

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Area of Science:

Soil science
Microbiology
Environmental science

Background:

Soil microbiomes are crucial for global nutrient cycling.
Understanding soil metabolic responses to climate change is challenging due to soil complexity.

Purpose of the Study:

To reveal functional regimes defining soil responses to environmental change.
To model soil metabolic activity under perturbations.

Main Methods:

Dynamic measurements of respiratory nitrate metabolism.
Modeling using biomass activity and nutrient availability.
Analysis of over 1,500 soil microcosms subjected to pH perturbations.

Main Results:

Identified three distinct functional regimes governing soil responses to pH perturbations: acidic, nutrient-limited, and resurgent growth.
A minimal model with two parameters accurately predicted nitrate utilization dynamics.
Mechanisms for each regime were validated through various experimental approaches.

Conclusions:

Soil functional regimes are widespread in pH-perturbed soils.
These regimes provide a framework for understanding soil microbial responses to environmental change.