Quantification of polyketide synthase genes in tropical urban soils using real-time PCR

Abstract

Polyketide synthases (PKSs) catalyze the biosynthesis of polyketides and may contribute to the natural production of antibiotics and pose selective pressure for the development of antibiotic resistant bacteria in the environment. Although conventional PCR have been developed to detect the presence of PKS genes, no previous studies have been done to quantify the abundance of PKS genes in environmental samples. In this study, two sets of degenerate real-time PCR (qPCR) primers (PKS1-F/PKS1-R, PKS2-F/PKS2-R) with high specificity and sensitivity were developed to quantify PKS type I and type II genes. These primers were subsequently used to quantify PKS genes in tropical urban soils, and both PKS genes were widely detected in all soil samples. The absolute abundance of PKS type I ranged from 1.7×106 to 4.7×106 copies per gram of soil and the absolute abundance of PKS type II genes ranged from 2.4×105 to 1.5×106 per gram of soil, and the abundance of PKS type I gene was consistently higher than that of PKS type II gene. The relative abundance of PKS type I gene was positively correlated with that of PKS type II gene (p<0.01). Regression analyses indicate that PKS gene abundance was negatively correlated with environmental factors, such as selected antibiotics, sulfate, and metals (p<0.05), but was not correlated with land use type. The studies on the correlation between environmental factors and PKS genes could provide useful information to understand natural production of antibiotics and its associated environmental risks.