title: phenanthrene_day7_rep2
design: "Soils microcosms (50 g) were set up using soil from a disused wood treatment facility. Half of the microcosms were amended with the PAH phenanthrene and the other half was the unameded control. The microcosms were destructively sampled at 0, 2, 7 and 17 days. DNA was extracted for bacterial 16S rRNA community analysis by 454-sequencing. DNA was extracted from 0.25 grams of soil from triplicate microcosms using a phenol-chloroform combined with bead-beating method. For sequencing, the V1-V3 regions of the 16S rRNA gene were amplified using the 8F-518R (Muyzer et al. 1993; Lane et al. 1985) primers containing the Roche-454 Titanium adapter sequences and unique barcodes for each sample. PCR reactions were quality controlled using GENETOOLS software; the amplicons from each PCR reaction were pooled in equal amounts, gel purified and quantified using picogreen and Qubit fluorimeter. Pyrosequencing was performed using the Roche-454 Titanium platform at the University of Nebraska-Lincoln Core for Applied Genomics and Ecology. Sequences were processed using mothur v.1.31.0. Briefly, after removing sequence noise, sequences smaller than 200 bp, with 1 or more nucleotide ambiguities or > 8 bp long homopolymers were removed from the dataset. "
identifiers.namespace: University of Salford
identifiers.id: phenanthrene_day7_rep2