Differences Between DNA- and RNA-Based Bacterial Communities in Marine Sediments

Abstract

Microorganisms in marine sediments play crucial roles in biogeochemical processes. Currently, 16S rRNA gene-based sequencing is popular for studying bacterial communities; however, the DNA used in analysis can include not only that from active microorganisms but also that from inactive microorganisms, while the RNA can represent active microorganisms and more recent activity in the environment; therefore, a study of the difference between the total bacterial community based on the 16S rRNA gene and the active bacterial community based on 16S rRNA will support a better understanding of bacterial community structure and function in marine sediments. In this study, the total and active bacterial community structures in surface sediments from the Bohai Sea and South Yellow Sea were investigated at DNA and RNA level using quantitative real-time polymerase chain reaction and Illumina high-throughput sequencing, respectively. The results show that the 16S rRNA gene abundances of bacterial communities are 1-2 orders of magnitude higher than the transcript abundances. The total bacterial community is more diverse compared to the active bacterial community, and there are distinct differences between them. The bacteria in the sediments take part in active chemoheterotrophy, sulfate reduction, and nitrification. Moreover, 16S rRNA gene-based sequencing misestimates some important functional microbiota when exploring bacterial community functions. The 'rare biosphere' in the total bacterial communities consists of actively transcriptional players, which could play key roles in biogeochemistry cycles. Overall, in the analysis of bacterial communities in marine sediments from a stable sedimentary environment, it is beneficial to use the 16S rRNA sequencing to reflect the true ecological status.