Colorimetric Aptasensor for Detecting Bacillus carboniphilus Using Aptamer Isolated with a Non-SELEX-Based Method

B. carboniphilus is a naphtha-degradative strain (NDS) that uses hydrocarbons for its growth and causes microbiologically influenced corrosion (MIC) in naphtha pipelines. To date, there have been no studies on receptors or sensors for the detection of B. carboniphilus. We isolate B. carboniphilus-specific aptamers with a non-SELEX-based method, which employs repetitive cycles of centrifugation-based partitioning. The binding affinities of three aptamers are evaluated by obtaining their dissociation constants (Kd), which range from 13.2 to 26.3 nM. The BCA-05 aptamer with the lowest Kd value is employed for a two-stage label-free aptasensing platform to verify the aptamer selectivity using colorimetric detection of B. carboniphilus. This platform starts with the aptamer-bacteria binding step, and the concentration of residual aptamer after binding depends on the amount of the target bacteria. Then, the amount of separated residual aptamer determines the degree of salt-induced aggregation of gold nanoparticles (AuNPs), which results in a color change from red to blue. The AuNP color change is expressed as the ratio of absorbances at 630 and 520 nm (A630/A520). Under optimized conditions, this aptasensor shows reliable performance with a linear correlation in the range 104–107 CFU mL−1 and a limit of detection of 5 × 103 CFU mL−1.