Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages
Date
2017
Authors
Amgarten, Deyvid
Martins, Layla Farage
Lombardi, Karen Cristina
Antunes, Luciana Principal
de Souza, Ana Paula Silva
Nicastro, Gianlucca Gonçalves
Kitajima, Elliott Watanabe
Quaggio, Ronald Bento
Upton, Chris
Setubal, João Carlos
Journal Title
Journal ISSN
Volume Title
Publisher
BMC Genomics
Abstract
Background
Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the degradation activity is carried out primarily by bacteria and little is known about the presence and role of bacteriophages in this process.
Results
Using Pseudomonas aeruginosa as host, we isolated three new phages from a composting operation at the Sao Paulo Zoo Park (Brazil). One of the isolated phages is similar to Pseudomonas phage Ab18 and belongs to the Siphoviridae YuA-like viral genus. The other two isolated phages are similar to each other and present genomes sharing low similarity with phage genomes in public databases; we therefore hypothesize that they belong to a new genus in the Podoviridae family. Detailed genomic descriptions and comparisons of the three phages are presented, as well as two new clusters of phage genomes in the Viral Orthologous Clusters database of large DNA viruses. We found sequences encoding homing endonucleases that disrupt a putative ribonucleotide reductase gene and an RNA polymerase subunit 2 gene in two of the phages. These findings provide insights about the evolution of two-subunits RNA polymerases and the possible role of homing endonucleases in this process. Infection tests on 30 different strains of bacteria reveal a narrow host range for the three phages, restricted to P. aeruginosa PA14 and three other P. aeruginosa clinical isolates. Biofilm dissolution assays suggest that these phages could be promising antimicrobial agents against P. aeruginosa PA14 infections. Analyses on composting metagenomic and metatranscriptomic data indicate association between abundance variations in both phage and host populations in the environment.
Conclusion
The results about the newly discovered and described phages contribute to the understanding of tailed bacteriophage diversity, evolution, and role in the complex composting environment.
Description
Keywords
bacteriophages, composting, homing endonucleases, tRNA genes, genomics, metagenomics, Pseudomonas aeruginosa, Siphoviridae, Podoviridae
Citation
Amgarten, D.; Martins, L.F.; Lombardi, K.C.; Antunes, L.P.; de Souza, A.P.S.; Nicastro, G.G.; … & da Silva, A.M. (2017). Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics, 18(346). https://doi.org/10.1186/s12864-017-3729-z