Cell sorting reveals few novel prokaryote and photosynthetic picoeukaryote associations in the oligotrophic ocean

Abstract

Close associations between single-celled marine organisms can have a central role in biogeochemical processes and are of great interest for understanding the evolution of organisms. The global significance of such associations raises the question of whether unidentified associations are yet to be discovered. In this study, fluorescence-activated cell sorted photosynthetic picoeukayote (PPE) populations and single cells were analysed by sequencing of 16S rRNA genes in the oligotrophic North Pacific Subtropical Gyre. Samples were collected during two cruises, spanning depths near the deep chlorophyll maximum, where the abundance of PPEs was highest. The association between the widespread and significant nitrogen (N₂ )-fixing cyanobacterium, UCYN-A and its prymnesiophyte host was prevalent in both population and single-cell sorts. Several bacterial sequences, affiliating with previously described symbiotic taxa were detected but their detection was rare and not well replicated, precluding identification of novel tightly linked species-specific associations. Similarly, no enrichment of dominant seawater taxa such as Prochlorococcus, SAR11 or Synechococcus was observed suggesting that these were not systematically ingested by the PPE in this study. The results indicate that apart from the UCYN-A symbiosis, similar tight species-specific associations with PPEs are unusual in the oligotrophic ocean.

Fig. 1

Bar graphs of the relative abundance (%) of sequences affiliating with A. Pelagibacter, B. Prochlorococcus, C. Synechococcus and D. UCYN‐A (denovo223459) in each sample group according to Table 1 (PPE sorts, Synechococcus sorts, Prochlorococcus sorts, Seawater >10 μm, Seawater >3 μm, Seawater 0.2–10 μm, and Seawater 0.2–3 μm). The mean relative abundance is indicated by horizontal lines and written in colours representing each sample group.

Fig. 2

A. Bray–Curtis similarity dendrogram showing the similarity of the sorted PPE populations based on average triplicate sorts (1000 PPE cells each) from each sample, including all chloroplast sequences. B. Stacked bar graph of the average relative abundance of the top chloroplast OTUs (>1% of total chloroplast sequences) for each sample based on triplicate sorts. C. Maximum likelihood inferred phylogenetic tree of the top chloroplast OTUs and their nearest relatives with GenBank accession numbers and classification according to the PhytoRef database. Bootstrap values (1000 iterations) are indicated next to the branches. Colours next to the OTUs indicate the colour as shown in Fig. 1B, white colour indicates the sum of OTUs of <1% relative abundance.

Fig. 3

Scatter plots showing the relative abundance (%) of B. bigelowii (denovo283683) and UCYN‐A (denovo223459) sequences in A. PPE sorts and B. seawater samples.

Fig. 4

Bar graphs showing the relative abundance (%) of non‐chloroplast OTUs present in sorted PPE populations in triplicate sorts from each sample. A. Hymenobacter. B–F. ZB3. G–J. Coxiellaceae. Sample IDs correspond to PPE sorts ordered according to the composition of the chloroplast sequences in Fig. 1.