Investigation of the protein synthesis potential in bacterial communities from Landsort Deep sediment

Numerous investigations of microbial communities using sequencing of total DNA have revealed an extensive diversity of microbial taxa in an array of different environments. Community analysis based on total DNA solely, however, does not reveal whether community members are alive (i.e. in a growing, active, dormant state) or dead. This dilemma is of particular concern at the seafloor of the Baltic Sea’s deepest point, the Landsort Deep, where the anoxic bottom sediment is below half a kilometer of highly stratified water column with distinct differences in community structure and functions at different depths. Our previous metagenomics results showed that these anoxic sediments hold a taxonomically diverse community rich in functional capacities, but whether the diversity reflected living organisms was not evident. In this study, we sought to provide improved insight into the physiological state of the Landsort Deep sediment bacterial community members through complementary sequencing of 16S rDNA amplicons, total DNA and total RNA. Ratios of 16S rRNA OTUs in total RNA and rDNA amplicons were used to estimate protein synthesis potential among the sediment community members. Results show surprisingly high protein synthesis potential for sediment Cyanobacteria that are abundant seasonally in surface water. Furthermore, Mycobacteria, which are comparatively abundant in the Landsort Deep sediment metagenome to that of other marine sediment metagenomes, show levels of protein synthesis potential indicating they are alive and contribute to the sediment community functioning. In conclusion, our approach provides a new window of insight into the complexities of sediment microbial communities, and highlights both expected and unexpected members of the living community in the anoxic sediment of Landsort Deep.