Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
Highlights
A total of 173 putative prophages were identified in these genomes by VIBRANT (5 complete, 17 high quality, 28 medium quality, and 123 low quality, Table S2), with at least one prophage identified in 66 roseobacter genomes
If only high- and mediumquality prophages were taken into account, roseobacters had an average of 0.96 ± 0.14 (Mean ± SE) prophages per genome (Figure S1A)
The diversity of predicted prophages and gene transfer agents identified here in the genomes of roseobacters suggests that prophages and GTAs are a significant source of genomic diversity in this bacterial group
Summary
Prophages (phage genomes integrated into bacterial genomes) represent a major driving force in bacterial evolution due to genomic rearrangements and the diversification of genetic repertoires [1,2,3,4,5]. Half of the fully sequenced bacterial genomes contain at least one prophage and prophage-encoded genes can represent up to 35% of a bacterial species pangenome [2,6,7]. Prophages can lose their ability to induce and become genomic islands domesticated by the bacterial hosts [1]. These defective prophages commonly encode genes that have been coopted by the bacterial hosts for other functions, such as cell communication and warfare [8]. The changes in bacterial metabolism and ecological interactions caused by active and defective prophages have the potential to impact the biogeochemical and ecological roles of globally abundant bacterial groups
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