Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i>
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 <i>Rhodobacteraceae</i>. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homolog...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/6/1115 |
| _version_ | 1797533111879204864 |
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| author | Kathryn Forcone Felipe H. Coutinho Giselle S. Cavalcanti Cynthia B. Silveira |
| author_facet | Kathryn Forcone Felipe H. Coutinho Giselle S. Cavalcanti Cynthia B. Silveira |
| author_sort | Kathryn Forcone |
| collection | DOAJ |
| description | 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 <i>Rhodobacteraceae</i>. 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 <i>Rhodobacter capsulatus.</i> 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 <i>acpP</i>, 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. |
| first_indexed | 2024-03-10T11:09:56Z |
| format | Article |
| id | doaj.art-0e5ad458d3d04afda39621fb495a6bf3 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T11:09:56Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-0e5ad458d3d04afda39621fb495a6bf32023-11-21T20:48:30ZengMDPI AGMicroorganisms2076-26072021-05-0196111510.3390/microorganisms9061115Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i>Kathryn Forcone0Felipe H. Coutinho1Giselle S. Cavalcanti2Cynthia B. Silveira3Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USAEvolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, SpainDepartment of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USADepartment of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USARoseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of <i>Rhodobacteraceae</i>. 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 <i>Rhodobacter capsulatus.</i> 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 <i>acpP</i>, 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.https://www.mdpi.com/2076-2607/9/6/1115roseophageauxiliary metabolic genesglobal distribution |
| spellingShingle | Kathryn Forcone Felipe H. Coutinho Giselle S. Cavalcanti Cynthia B. Silveira Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> Microorganisms roseophage auxiliary metabolic genes global distribution |
| title | Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> |
| title_full | Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> |
| title_fullStr | Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> |
| title_full_unstemmed | Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> |
| title_short | Prophage Genomics and Ecology in the Family <i>Rhodobacteraceae</i> |
| title_sort | prophage genomics and ecology in the family i rhodobacteraceae i |
| topic | roseophage auxiliary metabolic genes global distribution |
| url | https://www.mdpi.com/2076-2607/9/6/1115 |
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