Prophage Genomics and Ecology in the Family Rhodobacteraceae

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.

Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex

“…We found that prophages tended to be phylotype-specific with the Inoviridae and Myoviridae prophages almost exclusively found in phylotype I and the RSM-RSS intermediate φRS551 and novel prophage Unclassified A primarily found in phylotype IIB. These findings support previous studies which have observed prophage lineage-specificity in other, primarily human, pathogens (87–92), in addition to free living bacteria (93,94), resulting in their investigation as potential molecular markers of bacterial genomic diversity (95–97). Therefore, this may be a widespread phenomenon.…”

The landscape of lysogeny across microbial community density, diversity and energetics

“…This is a conservative number due to the current limitations of bioinformatic approaches to identify prophages in bacterial genomes (Kieft and Anantharaman, 2021). For example, many temperate phages integrate using host recombination machinery without encoding a specific marker gene for integration (Forcone et al ., 2021). The lack of such marker can lead to underestimating lysogeny in communities.…”

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria

“…Within the Alphaproteobacteria , this is the first report of prophages in genomes of the Rhodobacteraceae family, an environmentally significant clade in the marine environment. Microviridae prophages have been recently reported in a few genomes from Rhodobacteraceae (Forcone et al 2021) , however, a closer look revealed that they are phiX174, most likely an unremoved addition from the sequencing process. The many (pro)-phages we found both in Hyphomicrobiales and Rhodobacterales are unrelated with the Amoyvirinae prophage previously found in Caenibius tardaugens (Hyphomicrobiales) (Zheng et al 2018).…”

“…Within the Alphaproteobacteria, this is the first report of prophages in genomes of the Rhodobacteraceae family, an environmentally significant clade in the marine environment. Microviridae prophages have been recently reported in a few genomes from Rhodobacteraceae (Forcone et al 2021), however, a closer look revealed that they are phiX174, most likely an unremoved addition from the sequencing process.…”