Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

Abstract

Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community.

Keywords:

• biofouling
• biofilm sample preparation
• confocal microscopy
• extracellular polymeric substances
• Miseq sequencing

Acknowledgements

This study was supported by King Abdullah University of Science and Technology (KAUST, Thuwal, Saudi Arabia). The authors would like to thank Chris Wright at the University of Illinois at Urbana-Champaign Roy J. Carver Biotechnology Center for performing the Illumina MiSeq sequencing. The flow cells were kindly provided by Dr Peiying Hong and Moustapha Harb at the KAUST Water Desalination Reuse Center.