Amplicon sequencing and metagenomics in the Golfo Almirante Montt (GAM), Chile
An interdisciplinary approach combining geological, oceanographic, microbiological and gas-geochemical studies was conducted to characterize the sedimentary and pelagic CH4 sources and to investigate how physical and biological factors are affecting CH4 dynamics and fluxes in the GAM. Sampling in the GAM was conducted during expedition SO296/2 aboard RV SONNE between February 3rd and 8th, 2023, using 5 or 10L free-flow bottles (Hydrobios, Germany attached to a rosette water sampler and equipped with a CTD system (SBE 911plus, Seabird Electronics) for conductivity, temperature and depth recordings.  Nucleic acids were collected on membrane filters of different pore sizes for size fractionation (47 mm, GVWP 04700, Merck Millipore). DNA was extracted from whole filters using the QIAGEN DNA/RNA AllPrep Kit (Qiagen N.V., Venlo, Netherlands). For sequencing of 16S rRNA genes (by LGC Genomics GmbH, Berlin, Germany), the primer set U341F and U806R was used, which amplifies the 16S V3/V4 region and covers Bacteria and Archaea (Sundberg et al., 2013). Metagenome sequences were generated at Fasteris (Geneva, Switzerland) from four depths at station GAM21 and two depths at station NGAM14, together with metatranscriptomic sequences obtained from two depths at station GAM21 and four depths at station NGAM14.