Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

Abstract

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

“…The recently developed Illumina MiSeq platform can yield more detailed information of microbial community with greater throughput but less cost (Caporaso et al 2012;Nelson et al 2014). Illumina-based sequencing has found applications in characterizing the bacterial community in various natural and man-made environments, such as drinking water biofilter (Liao et al 2014), biofilm on drinking water distribution pipe (Wu et al 2014), anaerobic digestion sludge (Yang et al 2014), tropical rainforest leaf litter , river water (Staley et al 2013), soil (Rubin et al 2013), and mangrove wetland sediment (Jiang et al 2013). In addition, Illumina-based sequencing has also had several applications to characterize archaeal community in natural and man-made environments, such as fluid and sediment at a shallow marine hydrothermal site (Lentini et al 2014), biogas-producing and phenol-degrading bioreactor (Ju and Zhang 2014), and reservoir sediment (Zhang and Huang 2013).…”

The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy

“…Illumina/Solexa represents the NGS sequencing system most widely used for amplicon-based metagenomic studies (Luo et al 2012), providing optimal performances in terms of time, costs and coverage (Caporaso et al 2012;Kozich et al 2013;Liu et al 2012;Loman et al 2012;Quail et al 2012). In particular, the Illumina MiSeq benchtop sequencer is very suitable for amplicon-based metagenomic studies, considering its overall features including the obtainable read length up to 300 m. Nevertheless, few available experimental protocols for the ampliconbased metagenomic approach on the MiSeq platform are available involving the application of the TruSeq (Caporaso et al 2012;Gilbert et al 2010;Rubin et al 2013) or a custom designed approach (Kozich et al 2013).…”

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

“…Other biases inherent in molecular approaches to community profiling include the DNA extraction protocol (8) and sample storage conditions (9). For example, frozen samples better maintain alpha diversity and differ least in beta diversity (10). Importantly, low template concentrations may be particularly susceptible to bias due to the increased impact of stochastic processes during PCR (11).…”