Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly

Abstract

A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273^T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273^T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.

Figure 1

GC content versus read depth for each contig over 3 kb after Newbler and CLC assemblies. Green dots show the sequences related to the blooming chlorobi and selected for subsequent analysis. Red dots show the sequences related to the putative infecting phage.

Figure 2

JSpecies hierarchical clustering analysis carried out on the ANI similarity matrix obtained from the available Chlorobi genomes.

Figure 3

Pairwise comparison values of ANI versus 16S rRNA gene identity for the different available Chlorobi genomes.

Figure 4

Circular map of Chl. luteolum CIII genome using DNAplotter. The first two central circles show GC skew and G+C content, respectively. Baseline on the G+C plot represents 56.7% average value. The remaining four circles show tRNA and rRNA (red and blue labels, respectively), all reverse strand ORFs (light green label), all forward strand ORFs (green label) and all the ORFs more closely related to genes in organisms other than Chl. luteolum DSM 273^T (orange label). Special features are highlighted, see main text.

Figure 5

Maximum likelihood phylogeny with RAxML of five concatenated proteins (SDR, CruB, BciD (RSAM), BchF3 and BchQ2) found in all BChl e synthesizing Chlorobi. A combination of distantly related sequences for each of the four concatenated genes were used as outgroup. The genome synteny of the region is shown next to the phylogenetic tree. The bit score of the BLAST alignment is represented with shades of red (same orientation) and blue (inverse orientation).

Figure 6

Syntenic analysis showing the relationship of the putative GSB phage with the Chl. luteolum CIII genome sequence. A blue shade indicates the homology region of the metallophosphoesterase gene. A red circle indicates the region with the 51 nucleotides identity region. The types of genes identified in the putative Chl. luteolum CIII phage are shown in colors according to DNA metabolism (red), structural and packaging (blue), putative host-derived (yellow) and tRNAs (green). Special features on both sequences are highlighted with arrows.