Figure 1: Partner specificity and variation of UCYN-A lineages with plankton size fraction.

(a–c) Epifluorescence microscopy images with the double-CARD-FISH assay showing the specificity of symbiont–host pairs and (d–f) fragment recruitment of UCYN-A lineages in size-fractionated metagenomes from surface waters collected in station TARA_078. (a–c) Left panels correspond to the 4′,6-diamidino-2-phenylindole signal (blue-labelled DNA); right panels correspond to the combined signal of the prymnesiophyte-specific probes (green-labelled host under blue light excitation) and the UCYN-A probe (red-labelled symbiont under green-light excitation). (a) UCYN-A1 with its prymnesiophyte partner; (b) the two UCYN-A symbiotic pairs, indicating the specific labelling of UCYN-A1 (upper) and B. bigelowii (lower) with their specific partners, the small prymnesiophyte closely related to B. bigelowii and UCYN-A2 respectively; (c) B. bigelowii with UCYN-A2. The inset in c shows the detail of non-associated UCYN-A2 cells within a common symbiotic structure. Prymnesiophyte partners are indicated by arrow heads. Scale bar in a represents 5 μm and this scale is shared in a–c except in the inset of c where it indicates 2 μm. (d–f) On the left side, recruitment of metagenomic reads using UCYN-A1 and UCYN-A2 genomes as reference. Reads are plotted as red (UCYN-A1) or blue (UCYN-A2) dots depending on the closest hit genome, representing the covered genome positions (x axis) and the % of identity with the closest reference (y axis). A horizontal grey line set at 95% indicates the threshold for reads representing members of the same population as the reference genome. On the right side, histograms represent the number of recruited reads, in logarithmic scale, by UCYN-A1 (red) or UCYN-A2 (blue) genomes in intervals of 1% identity, from 100 to 70% identity.