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Updated: Jul 15, 2026

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
A method for extracting plant roots from soil which facilitates rapid sample processing without compromising
D B Metcalfe1,2, M Williams1, L E O C Aragão3
1University of Edinburgh, School of Geosciences, Edinburgh, UK.
Abstract:
This study evaluates a novel method for extracting roots from soil samples and applies it to estimate standing crop root mass (+/- confidence intervals) in an eastern Amazon rainforest. Roots were manually extracted from soil cores over a period of 40 min, which was split into 10 min time intervals. The pattern of cumulative extraction over time was used to predict root extraction beyond 40 min. A maximum-likelihood approach was used to calculate confidence intervals. The temporal prediction method added 21-32% to initial estimates of standing crop root mass. According to predictions, complete manual root extraction from 18 samples would have taken c. 239 h, compared with 12 h using the prediction method. Uncertainties (percentage difference between mean, and 10th and 90th percentiles) introduced by the prediction method were small (12-15%), compared with uncertainties caused by spatial variation in root mass (72-191%, for nine samples per plot surveyed). This method provides a way of increasing the number of root samples processed per unit time, without compromising measurement accuracy.
