Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family

Abstract

In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host–pathogen pairs were derived from the same sampling location—the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4–25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibres, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.

A Novel Aeromonas popoffii Phage AerP_220 Proposed to Be a Member of a New Tolavirus Genus in the Autographiviridae Family

“…This peculiarity leads to divergence of genomes in phages that infect only one or two bacterial strains. The obtained data are in good agreement with the previous results of the global analysis of members of the Autographiviridae family [19].…”

“…Three different tail fiber proteins were annotated-AerP_220_p48, AerP_220_p58, and AerP_220_p59. The greater part of the ORF48 encoding AerP_220_p48 is similar to the gene encoding the tail fiber adaptor protein Tola_p58 (UOW66401) of another Aeromonas phage vB_AspA_Tola described previously [19]. The N-terminal part of the Tola_p58 resembles the gp17 of Escherichia T7 phage, which is responsible for connection with the baseplate [39].…”

“…The AerP_220 genome was compared with other phage genomes available in the NCBI GenBank Database using BLASTN. The highest similarity was with the genome of another Aeromonas phage vB_AspA_Tola (OM913599) [19] with sequence identity of 73.62% and coverage of 55%. Some similarity was found between the AerP_220 genome fragments and those of Pseudomonas phage MR4 (MT104467), Escherichia phage ECBP5 (KJ749827), Pantoea phage Nufs112 (OK570185); however, coverage was < 5%.…”

“…Aeromonas myophage genomics and biology have been described previously in comprehensive reviews [17,20]. Recently, a number of new Aeromonas phages with podovirus morphotype were described and their genomes appeared in the NCBI GenBank database [19,38,40,[42][43][44]. To evaluate the relations between the studied AerP_220 phage and other Aeromonas phages, vConTACT2 analysis was performed for all Aeromonas phage genomes available in the GenBank database (Table S2, Figure 6).…”

“…More than a hundred Aeromonas phages have been isolated and taxonomically characterized; most of their complete genomes are currently available in the GenBank database (https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239&host=bacteria, accessed on 15 August 2022). Previous studies have been predominantly focused on lytic phages and their biological activity against A. hydrophila and A. salmonicida [15][16][17][18][19]; therefore, the majority of studied Aeromonas phages (n = 73) are specific to strains of these two Aeromonas species. The most prevalent taxonomic groups of Aeromonas phages are members of the Straboviridae and Autographiviridae families.…”