Assessment of two whole genome amplification techniques in terms of soil community profiles

Abstract

Whole genome amplification (WGA) facilitates the metagenomics study of low biomass environments, with the risks of introducing biases and community skewing. The objective of this study was therefore to compare two common WGA methods in terms of community distortion. Multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) were evaluated with three contrasting soils and by 16S rRNA genes amplicon and whole genome shotgun sequencing. Both WGA technologies yielded stable amplification from nanogram quantities of soil DNA. The MiSeq sequencing of 16S rRNA genes demonstrated considerable loss of species richness and highly skewed community profiles for MDA-derived templates compared to the actual communities. Bacillales of low GC genome were consistently enriched in all MDA libraries. In contrast, MALBAC captured the community differences between the three soils as revealed by a hierarchical clustering analysis, and the community distortion was moderate in terms of bacterial richness. Unlike MDA, MALBAC may enrich bacteria of high GC genomes. Prokaryotic community analysis of the shotgun data confirmed the findings obtained by the 16S rRNA amplicon sequencing. Despite the wide use of MDA, these findings implicate MALBAC as promising in characterizing microbial communities in low biomass soils and highlights the potential of community profile as a quality control for WGA of environmental samples.