Bacterial DNA Extraction and Sequencing Protocol

Samples for DNA analysis were kept at −80°C until DNA extraction was performed (in 2012). DNA was extracted from the samples using FastDNA® SPIN Kits for Soil and a FastPrep-24 bead-beading machine (MP Biomedicals, Santa Ana, USA), according to the manufacturer's instructions. Bacterial DNA was amplified using the barcoded primers 338F and 926R according to the protocol described in Torondel et al. (2016 (link)). PCR products were cleaned using the Wizard PCR product purification kit (Promega, Fitchburg, Wisconsin, USA) and were then pyrosequenced at the Wellcome Sanger Institute in 2012 using the Lib-L kit on the 454 GS FLX Titanium System (Roche, Branford, Connecticut, USA). Further details on the protocols used to generate 16S rRNA gene sequence data are as described in Torondel et al. (2016 (link)).