Fig. 4

Accessing the population-level dimension of diversity in marine microbes using metagenomics. The figure aims to provide a simple example of the additional information on population structure that the metagenome-based population genomics approach can produce compared to 16S rRNA surveys. Here, I use the MAG G4.480 (uncultured Flavobacteriales, ~ 95% completeness, and < 10% contamination) that we retrieved from the Mediterranean Sea (LTER Blanes Bay Microbial Observatory; http://bbmo.icm.csic.es/). From this MAG, a fragment of the 16S rRNA gene (770 base pairs) was extracted and then used to estimate the MAG abundance in the global ocean and the Mediterranean Sea using the Ocean Barcode Atlas (OBA) [144] (https://oba.mio.osupytheas.fr/ocean-atlas/); results are shown in A. Only two 16S mTag [145] references from the OBA with > 99% sequence similarity with MAG G4.480 were considered (references AACY020490277.719.2228 and EF572435.1.1502; both Flavobacteriales, Flavobacteriaceae, NS5 marine group). Furthermore, only surface samples originating from two size fractions (0.2–1.6 and 0.2–3.0 μm) from the TARA Oceans cruise were included. In sum, in A, we observe the distribution of the MAG G4.480 as one single taxonomic entity. In B, the diversity within this entity is explored using metagenome-based population genomics (Fig. 3), and we notice that additional patterns emerge. In the upper section of B, the Fst values (measuring population differentiation) among the investigated stations were clustered, and different clusters, which may correspond to populations, were colored (Fst ~ 0.2 was used to delineate clusters). Note that some clusters correspond to geographic regions (B, lower section). For example, the clusters in the Mediterranean Sea, Red Sea, and Indian Ocean suggest that they could represent geographically delineated populations. These patterns are missed by the 16S rRNA gene (A). The abundance of the Mediterranean MAG G4.480 across the global ocean and the Mediterranean Sea based on metagenomic read recruitment is shown in the lower section of B. MAG abundances are indicated in RPKG (Reads Per Kilobase of MAG and Gigabase of metagenomic data). To obtain the Fst values and the abundances of the MAG G4.480 (B), we followed the procedure indicated in Fig. 3, which is partially implemented in POGENOM [104]. Only surface metagenomes from TARA Oceans with enough coverage (horizontal and vertical) of MAG G4.480 were used in downstream analyses, which explains the different numbers of stations included in A and B