Comparison of methods for preservation of activated sludge samples for high-throughput nucleic acid sequencing and bacterial diversity analysis

Abstract

Preservation of environmental samples is an important step in maintaining the original microbial community until the nucleic acid extraction in the laboratory. Here, we collected activated sludge samples to both immediately extract nucleic acids (control) and submit to different storage/preservation methods for 48 h before nucleic acids extraction: room temperature storage, storage on ice, direct storage at −20 °C, rapid freezing in liquid nitrogen followed by storage at −20 °C, and preservation with TRIzol®, RNAlater®, and Nucleic Acid Preservation (NAP) buffers. Bacterial community was compared by high-throughput 16S rRNA gene sequencing from total DNA and RNA. Among the evaluated methods, TRIzol® and rapid freezing with liquid nitrogen were the least indicated, since they led to significant changes in the microbial community structure and abundance of functional groups involved in ammonia metabolism. Compared to control, storage on ice and NAP preserved more than 80% and 75% of genera at the DNA and RNA level respectively, indicating that these methods are the most suitable for storage/preservation of activated sludge samples intended for nucleic acids sequencing.