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Related Experiment Video

Updated: Jun 15, 2026

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

A low-cost pipeline for soil microbiome profiling.

Anita Bollmann-Giolai^1,2, Michael Giolai³, Darren Heavens²

¹John Innes Centre (JIC, Norwich, UK.

Microbiologyopen

|November 23, 2020

Summary

We developed a low-cost genomic DNA extraction method for soil microbiome studies. This method provides high-quality DNA suitable for various sequencing applications, reducing costs for researchers.

Keywords:

DNA cleanup amplicon library construction gDNA extraction microbiome soil

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

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Published on: July 16, 2017

Area of Science:

Environmental microbiology
Molecular biology
Bioinformatics

Background:

Genomic DNA extraction and library preparation are costly bottlenecks in microbiome research.
Soil samples present challenges due to inhibitors, impacting DNA quality and yield.
Existing commercial kits are expensive, limiting large-scale studies.

Purpose of the Study:

To develop a low-cost genomic DNA extraction method for soil samples.
To create an efficient Illumina-compatible amplicon library preparation workflow.
To benchmark the new method against commercial kits for soil DNA extraction.

Main Methods:

A novel, cost-effective genomic DNA extraction protocol for soil was established.
An Illumina-compatible two-step amplicon library preparation workflow for 16S and ITS rRNA genes was developed.
The method was evaluated against two commercial kits (MoBio PowerSoil®, MP Biomedicals™ FastDNA™ SPIN) and a published non-commercial method using four soil types.

Main Results:

The new method yielded high-quality genomic DNA comparable to commercial kits in both quantity and purity.
DNA fragment sizes averaged approximately 10 kb, suitable for long-read sequencing technologies.
Amplicon sequence variant analysis showed good correlation with commercial kit results.

Conclusions:

The developed low-cost method provides high-quality soil genomic DNA suitable for amplicon sequencing.
This approach significantly reduces costs, enabling large-scale microbiome studies.
The extracted DNA is also suitable for advanced applications like shotgun metagenomics and long-read sequencing.