Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

A comparison of hard and soft direct methods for DNA extraction from soil

Patrick Hill, Mathieu F Dextraze, David Kroetsch, Christopher N Boddy
doi: https://doi.org/10.1101/2022.03.07.483395
Patrick Hill
1Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
2Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mathieu F Dextraze
2Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Kroetsch
4School of Environmental Science, University of Guelph, Guelph, N1G 2W1 Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher N Boddy
1Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
2Department of Chemistry and Biomolecular Sciences, Centre for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada
5Department of Chemistry and Biomolecular Sciences, Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, K1N 6N5 Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: cboddy@uottawa.ca
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Nucleic acid extraction is the first step in molecular biology studies of soil bacterial communities. The most common used soil DNA extraction method is the direct, hard extraction Mobio method, which uses bead beating to lyse bacteria. In this study we compared the Mobio method with a soft, enzymatic lysis extraction method. Next generation sequencing (Illumina and Pyrosequencing) of amplicons generated from four 16S primer pairs and DNA from 12 soils and 3 composts was used to compare the two extraction methods.

Four bacterial orders, the delta proteobacterial Desulfuromonadales and gamma proteobacterial Pseudomonadales, Enterobacteriales, and Alteromonadales were more common in amplicons from soft extracted DNA, sometimes by two orders of magnitude. These groups can be a significant fraction of the bacterial population. For example the Pseudomonadales made up to 16 % and Enterobacteriales 10% of amplicons from Soft extracted DNA. The JG30-KF-CM45 order was under extracted by the enzymatic lysis extraction method. Results differed more by primer choice than extraction method and the phylogenetic resolution of differences between extraction methods changed with primer choice.

Given how often Mobio extraction is used, these proteobacterial orders are probably under-represented in the studies of soil bacteria that use nucleic acid methods. Further improvements in soil DNA extraction are needed. Amplicons sequencing studies should use a range of different primers to confirm the phylogenetic resolution of their results.

Importance Several large scale studies of soil bacteria that compare thousands of soil samples across continents have used the Mobio method for DNA extraction. Large scale studies like these are increasing with the recent establishment of the Global Soil Biodiversity Observation Network (Soil BON), which also uses the Mobio method. The results of this work will be used to make policy decisions about how to manage the soil and may be a guide for bioprospectors. As the Mobio method is so widely used, it is important to know its limitations. Studies that use the Mobio method underestimate the fraction of several proteobacterial groups. Most notably the Enterobacteria and Pseudomonas can be under extracted by 10-100 fold. The degree of under extraction varies with different soils.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted March 08, 2022.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
A comparison of hard and soft direct methods for DNA extraction from soil
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
A comparison of hard and soft direct methods for DNA extraction from soil
Patrick Hill, Mathieu F Dextraze, David Kroetsch, Christopher N Boddy
bioRxiv 2022.03.07.483395; doi: https://doi.org/10.1101/2022.03.07.483395
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
A comparison of hard and soft direct methods for DNA extraction from soil
Patrick Hill, Mathieu F Dextraze, David Kroetsch, Christopher N Boddy
bioRxiv 2022.03.07.483395; doi: https://doi.org/10.1101/2022.03.07.483395

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4667)
  • Biochemistry (10332)
  • Bioengineering (7653)
  • Bioinformatics (26277)
  • Biophysics (13497)
  • Cancer Biology (10663)
  • Cell Biology (15389)
  • Clinical Trials (138)
  • Developmental Biology (8480)
  • Ecology (12800)
  • Epidemiology (2067)
  • Evolutionary Biology (16817)
  • Genetics (11378)
  • Genomics (15451)
  • Immunology (10591)
  • Microbiology (25141)
  • Molecular Biology (10187)
  • Neuroscience (54317)
  • Paleontology (399)
  • Pathology (1663)
  • Pharmacology and Toxicology (2889)
  • Physiology (4331)
  • Plant Biology (9223)
  • Scientific Communication and Education (1585)
  • Synthetic Biology (2551)
  • Systems Biology (6769)
  • Zoology (1459)