RNA was extracted from P. putida replicates using the RNeasy mini kit (Qiagen), with rRNA removal performed using the QIAseq FastSelect-5S/16S/23S kit (Qiagen). RNA-Seq libraries were constructed using the KAPA RNA HyperPrep kit (Roche) and barcoded with TruSeq indexes (Illumina). Amplification was monitored in real-time using SYBR-Green and halted upon reaching the amplification plateau.