Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives

Abstract

Lake sediments accumulate information on biological communities thus acting asnatural archives. Traditionally paleolimnology has focussed on fossilized remains oforganisms, however, many organisms do not leave fossil evidence, meaning major eco-system components are missing from environmental reconstructions. Many paleolim-nology studies now incorporate molecular methods, including investigating microbialcommunities using environmental DNA (eDNA), but there is uncertainty about thecontribution of living organisms to molecular inventories. In the present study, weobtained DNA and RNA inventories from sediment spanning 700 years to investigatethe contribution of past and active communities to the molecular signal from sedimen-tary archives. Additionally, a droplet digital PCR (ddPCR) targeting the 16S ribosomalRNA (16S rRNA) gene of the photosynthetic cyanobacterial genera Microcystis wasused to explore if RNA signals were from legacy RNA. We posit that the RNA signalis a mixture of legacy RNA, dormant cells, living bacteria and modern-day trace levelcontaminants that were introduced during sampling and preferentially amplified. Thepresence of legacy RNA was confirmed by the detection of Microcystis in sedimentsaged to ~200 years ago. Recent comparisons between 16S rRNA gene metabarcod-ing and traditional paleo proxies showed that past changes in bacterial communitiescan be reconstructed from sedimentary archives. The recovery of RNA in the presentstudy has provided new insights into the origin of these signals. However, caution isrequired during analysis and interpretation of 16S rRNA gene metabarcoding dataespecially in recent sediments were there are potentially active bacteria.