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The quantitative and qualitative effect of water immiscible and miscible carbon-rich substrates on the production of biosurfactants, surfactin and rhamnolipids, by  Bacillus amyloliquefaciens  ST34 and  Pseudomonas aeruginosa  ST5, respectively, was analysed. A small-scale high throughput 96 deep-well micro-culture method was utilised to cultivate the two strains in mineral salt medium (MSM) supplemented with the water miscible (glucose, glycerol, fructose and sucrose) and water immiscible carbon sources (diesel, kerosene and sunflower oil) under the same growth conditions. The biosurfactants produced by the two strains were isolated by acid precipitation followed by an organic solvent extraction. Ultra-performance liquid chromatography coupled to electrospray ionisation mass spectrometry was utilised to analyse yields and characterise the biosurfactant variants. For  B. amyloliquefaciens  ST34, maximum surfactin production was observed in the MSM supplemented with fructose (28 mg L −1 ). In addition, four surfactin analogues were produced by ST34 using the different substrates, however, the C 13 –C 15  surfactins were dominant in all extracts. For  P. aeruginosa  ST5, maximum rhamnolipid production was observed in the MSM supplemented with glucose (307 mg L −1 ). In addition, six rhamnolipid congeners were produced by ST5 using different substrates, however, Rha–Rha–C 10 –C 10  and Rha–C 10 –C 10  were the most abundant in all extracts. This study highlights that the carbon sources utilised influences the yield and analogues/congeners of surfactin and rhamnolipids produced by  B. amyloliquefaciens  and  P. aeruginosa , respectively. Additionally, glucose and fructose were suitable substrates for rhamnolipid and surfactin, produced by  P. aeruginosa  ST5 and  B. amyloliquefaciens  ST34, which can be exploited for bioremediation or as antimicrobial agents.   Electronic supplementary material  The online version of this article (doi:10.1186/s13568-017-0367-4) contains supplementary material, which is available to authorized users.

Variants of lipopeptides and glycolipids produced by Bacillus amyloliquefaciens and Pseudomonas aeruginosa cultured in different carbon substrates