Coupling magnetic-nanoparticle mediated isolation (MMI) and stable isotope probing (SIP) for identifying and isolating the active microbes involved in phenanthrene degradation in wastewater with higher resolution and accuracy

Stable isotope probing (SIP) is a cultivation-independent approach identifying the functional microbes in their natural habitats, possibly linking their identities to functions. DNA-SIP is well-established but suffers from the shift of C-12-DNA into the heavy DNA (C-13-DNA) fraction, which significantly reduces the resolution and accuracy. In this study, we coupled magnetic-nanoparticle mediated isolation (MMI) and DNA-SIP, namely MMI-SIP, to identify the active microbes involved in phenanthrene degradation from PAH-contaminated wastewater. Microbes affiliated to Pseudomonas and Sphingobium were responsible for in situ phenanthrene metabolism from the SIP results, and Pigmentiphaga was only unraveled for phenanthrene degradation in the MMI and MMI-SIP microcosms. MMI-SIP also significantly increased the enrichment of the above microbes and genes encoding the alpha subunit of the PAH-ring hydroxylating dioxygenase (PAH-RHD alpha) in the heavy DNA fractions. Our findings suggest that MMI-SIP is a powerful tool, with higher resolution and accuracy, to distinguish the active microbes involved in phenanthrene metabolism in the wastewater, provide a more precise map of functional microbial communities, and offer suggestions for effective management for wastewater treatment plants. (C) 2018 Elsevier Ltd. All rights reserved