Clonal microbial populations feature cell-to-cell differences in gene expression, growth rate and resistance to stress. Accounting for such heterogeneity is paramount for understanding the mechanisms underlying microbial responses to environmental changes. Membrane transport regulation is crucial, allowing for optimised uptake of nutrients and exclusion of harmful compounds. Nevertheless, we know little about the heterogeneity in membrane transporter regulation across a clonal microbial population. We are currently using RNA sequencing and single-cell analysis based on microfluidics and microscopy to understand how changes in the environmental pH, temperature and nutrient content correlate with the heterogeneity in membrane transporter regulation and the appearance of phenotypic variants.