Here we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads and assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate.</p><p>200 L of seawater was collected and filtered through 20, 5, and 0.22 micron pore filter polycarbonate filters on board. DNA extraction was performed from the 0.22 micron filter (free-living bacteria) following the phenol:chloroform extraction. Metagenomes were sequenced using Illumina Nextseq (100 bp, paired-end reads), and using Oxford Nanopore (one MinIon flowcell run, chemistry version 9.4R) and PacBio Sequel II (one 8M SMRT Cell Run, 30-hour movie).