Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions

Bacteria respond to iron limitation by activating distinct uptake and siderophore-biosynthesis pathways, and comparative transcriptomics under varying iron availability provide insights into these diverse adaptive mechanisms. Here we describe RNA-seq datasets generated from four freshwater bacterial isolates— Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738—cultured under FeCl 3 -treated and untreated conditions. For each strain–condition combination, three biological replicate cultures were prepared, their RNA was pooled, and a single sequencing library was constructed. : The dataset comprises eight paired-end libraries (16 FASTQ files) generated in 2024 and 2025, totaling 349,853,404 processed reads. Raw sequence data are openly available in the NCBI Sequence Read Archive under SRA study accession SRP695241 (BioProject PRJNA1456794; SRR38280322–SRR38280329; BioSamples SAMN57450602–SAMN57450609). Read alignment rates were 78.59% and 71.98% for Pseudomonas sp. FBCC-B13192, 92.30% and 89.11% for Herbaspirillum sp. B12834, 89.29% and 89.23% for Pantoea sp. FBCC-B5559, and 34.75% and 21.39% for Micrococcus sp. FBCC-B5738 under FeCl 3 -treated and untreated conditions, respectively. Quality-control summaries, sample metadata, and figure files are listed in Table 1; these will be released through figshare. The dataset enables comparative analyses of bacterial iron-acquisition responses and supports reanalysis with future transcriptome workflows.