Snot1
Chasing shadows in the deep - exploring hydrothermal vent microbial communities using RNA and DNA
Hidden deep beneath the ocean surface, hydrothermal vents are but one of the fascinating ecosystems that DNA sequencing technology has helped shed light on. Using a combination of amplicon- and shotgun sequencing of the small-subunit ribosomal RNA and its gene, we examined the composition and diversity of a microbial mat community from the recently discovered Jan Mayen vent field, located on Mohn’s Ridge in the Norwegian-Greenland Sea. The community was dominated by the Epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are microaerobic mesophiles that mainly derive energy from the oxidation of sulphur compounds typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon sequencing and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels between taxa. Further, predicted diversity from RNA samples was consistently lower than from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.