Berkeley Lab

Differences in diversity between extraction techniques

(A) NDMS of weighted UniFrac distances (stress: 0.23). Colors =extraction type and shape =sampling location. PERMANOVA was used to identify if differences in community structure between extraction types were statistically significant (R2 value = 0.59873; p = 0.001).
(B) The relative abundance of each order was plotted for each sample. Sequences from each replicate extraction were merged and taxon plot was drawn. Taxa whose relative abundance was less than 1% were merged into the ‘Other’ category. The most dominant taxa are shown in the figure legend

ENIGMA researchers at University of Tennessee Knoxville examined differences in diversity between extraction techniques.

  • Lipid/DNA co-extraction from one sample is attractive in limiting biases associated with microbial community analysis from separate extractions. We sought to enhance established co-extraction methods and use high-throughput 16S rRNA sequencing to identify preferentially extracted taxa from co-extracted DNA.
  • Co-extraction results in low DNA yields and distinct community structure changes.
  • Anecdotally, many people (including our researchers) have tried this technique and failed over the past decade though nothing has ever been published about using co-extraction. This study documents the method, in order to set the context for future work in the area.

Co-extraction of DNA and PLFA from soil samples. Brewer, S; S.M. Techtmann, N. Mahmoudi, D. Niang, S. Pfiffner, T.C. Hazen. (2015)  Journal of Microbiological Methods 115:64-66 http://dx.doi.org/10.1016/j.mimet.2015.05.018