Isolate genomes from REMEI experiments

Six experimental treatments were set up the following day for each season as described in Sanchez et al 2020. Briefly, the treatments consisted on: (i) unfiltered seawater in light/dark cycles (CL) and in the dark (CD), (ii) seawater prefiltered through a 1 um filter to remove large predators while preserving most bacteria in light/dark cycles (PL) and in the dark (PD), (iii) unfiltered seawater diluted 1/4 with 0.2-um-filtered seawater to reduce predators and increase nutrient availability for bacteria in light/dark cycles (DL), and (iv) unfiltered seawater diluted 1/4 with 30 kDa-filtered seawater to reduce predators, viruses and increase nutrient availability, in light/dark cycles (VL). The different treatments were incubated in triplicated 9 L Nalgene bottles for 48 h at in situ temperature in a water bath with circulating seawater. Light treatments were limited to photosynthetically active radiation, and dark treatments were covered with several layers of dark plastic.The genomic DNA of the selected strains was extracted using DNeasy Blood&Tissue Kit (Qiagen) following the manufacturer's recommendations and their integrity and concentration were checked using DNA gel electrophoresis and a Qubit 1 Fluorometer (Invitrogen), respectively. Samples were then sent to the Centre Nacional d'Analisi Genomica (CNAG) for further quality control, library preparation and whole-genome sequencing with a Illumina MiSeq sequencer (2x 300bp, Illumina).To assemble isolate genomes we used the Nextflow pipeline bacass v.2.0.0 from the nf-core framework. The pipeline runs an automated workflow that uses Skewer to quality trim the reads, performs basic sequencing QC using FastQC and assembles the reads with Unicycler. Assembly contamination is checked with Kraken2 and its quality is assessed using QUAST. Additionally, the CDS of the resulting assembly is annotated with Prokka.