Successive DNA extractions improve characterization of soil microbial communities.

Mauricio R Dimitrov,Johannes A Van Veen,Eiko E Kuramae,Annelies J Veraart,Hauke Smidt,Mattias De Hollander

doi:10.7717/peerj.2915

Mauricio R Dimitrov, Johannes A Van Veen + Show 4 more

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https://doi.org/10.7717/peerj.2915

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Abstract

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.

Highlights

Microorganisms are key to various biogeochemical processes that drive life on Earth (Falkowski, Fenchel & Delong, 2008)
For almost all soil samples, DNA extractions performed with both kits yielded the highest DNA concentration in E1, except for clay 2 (PS extraction) and sandy 3, which showed the highest DNA yield in E2 (Table S2)
DNA extraction of clay 1 was similar for both kits, where the highest amount of DNA was extracted in E1, with E2 and E3 showing lower DNA concentration compared to previous extractions (Figs. 2A and 2C; Table S2A)

Summary

Introduction

Microorganisms are key to various biogeochemical processes that drive life on Earth (Falkowski, Fenchel & Delong, 2008). Besides being essential drivers of biogeochemical processes, soil microorganisms. How to cite this article Dimitrov et al (2017), Successive DNA extractions improve characterization of soil microbial communities. The introduction of culture independent methodologies has revolutionized the way soil microbial communities are studied. Extracting and characterizing DNA has become ordinary in most soil microbial ecology studies (Delmont et al, 2012; Navarrete et al, 2015; Pan et al, 2014; Tahir et al, 2015). Constant improvements and accessibility of high throughput sequencing technologies have allowed researchers to characterize soil microbial communities in an unprecedented way and at ecologically relevant scales and resolution of time, space and environmental conditions

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