Characterization and comparative genomic analysis of virulent and temperate Bacillus megaterium bacteriophages

Isolation, characterization, and comparative genomic analysis of vB_PlaM_Pd22F, a new bacteriophage of the family Myoviridae

The use of phage and phage-based products for the prevention and treatment of bee disease is one of the promising natural alternatives to chemical or antibiotic treatments in beekeeping. A novel lysogenic bacteriophage, phage Pd22F (vB_PlaM_Pd22F), was isolated from Paenibacillus dendritiformis by the prophage induction method. This phage, which is capable of infecting Paenibacillus larvae and P. dendritiformis strains, was characterized by microbiological and comparative genomic analysis. Transmission electron microscopy images showed that phage Pd22F had the morphology of a myovirus. Whole-genome sequencing results showed that vB_Pla M_Pd22F has an 86,388-bp linear dsDNA genome with a GC content of 50.68%. This genome has 124 coding sequences (CDSs), 53% of which encode functionally unknown proteins and 57 of which encode proteins that show similarity to known proteins. In addition, one tRNA gene was found. The phage Pd22F genome does not contain any antimicrobial resistance genes. The similarity between the genome sequence of phage Pd22F and the whole genome sequences of other Paenibacillus phages available in the NCBI Virus Database was found to be below 50% (42%), indicating that phage Pd22F differs greatly from previously characterized phages at the DNA level. The results of comparative genomics and phylogenetic analysis revealed that Pd22F is a new phage belonging to the family Myoviridae, order Caudovirales. This is the first report of genomic and morphological characterization of a Paenibacillus dendritiformis prophage.

Isolation, characterization, and comparative genomic analysis of vB_PlaP_SV21, new bacteriophage of Paenibacillus larvae

Paenibacillus larvae cause an American foulbrood disease (AFB) that is responsible for the extinction of honeybee colonies and is a honeybee bacterial disease that has to be obligatory notified worldwide. Recently, bacteriophage studies targeting Paenibacillus larvae have emerged as a promising alternative treatment method. The inability of bacteria to create resistance against bacteriophages makes this method advantageous. As a consequence, this study was conducted to describe the genome and biological characteristics of a novel phage capable of lysing Paenibacillus larvae samples isolated from honeybee larva samples in Turkey. The Paenibacillus phage SV21 (vB_PlaP_SV21) was isolated by inducing Paenibacillus larvae strain SV21 with Mitomycin-C. Whole-genome sequencing, comparative genomics, and phylogenetic analysis of vB_PlaP_SV21 were performed. Transmission electron microscopy images showed that vB_PlaP_SV21 phage was a Podovirus morphology. The vB_PlaP_SV21 phage specific for Paenibacillus larvae was determined to belong to the Podoviridae family. Host range and specificity, burst size, lytic activity, and morphological characteristics of the phage were determined. Bioinformatic analysis of the Paenibacillus phage SV21 showed 77 coding sequences in its linear 44,949 bp dsDNA genome with a GC content of 39.33%. In this study, we analysed the genomes of all of the currently sequenced P. larvae phage genomes and classified them into five clusters and a singleton. According to molecular, morphological, and bioinformatics results, ıt was observed that API480 (podovirus), which was reported as a singleton in previous studies and public databases, and Paenibacillus phage SV21 phage could form a new cluster together.

Virulent Drexlervirial Bacteriophage MSK, Morphological and Genome Resemblance With Rtp Bacteriophage Inhibits the Multidrug-Resistant Bacteria

Phage-host interactions are likely to have the most critical aspect of phage biology. Phages are the most abundant and ubiquitous infectious acellular entities in the biosphere, where their presence remains elusive. Here, the novel Escherichia coli lytic bacteriophage, named MSK, was isolated from the lysed culture of E. coli C (phix174 host). The genome of phage MSK was sequenced, comprising 45,053 bp with 44.8% G + C composition. In total, 73 open reading frames (ORFs) were predicted, out of which 24 showed a close homology with known functional proteins, including one tRNA-arg; however, the other 49 proteins with no proven function in the genome database were called hypothetical. Electron Microscopy and genome characterization have revealed that MSK phage has a rosette-like tail tip. There were, in total, 46 ORFs which were homologous to the Rtp genome. Among these ORFs, the tail fiber protein with a locus tag of MSK_000019 was homologous to Rtp 43 protein, which determines the host specificity. The other protein, MSK_000046, encodes lipoprotein (cor gene); that protein resembles Rtp 45, responsible for preventing adsorption during cell lysis. Thirteen MSK structural proteins were identified by SDS-PAGE analysis. Out of these, 12 were vital structural proteins, and one was a hypothetical protein. Among these, the protein terminase large (MSK_000072) subunit, which may be involved in DNA packaging and proposed packaging strategy of MSK bacteriophage genome, takes place through headful packaging using the pac-sites. Biosafety assessment of highly stable phage MSK genome analysis has revealed that the phage did not possess virulence genes, which indicates proper phage therapy. MSK phage potentially could be used to inhibit the multidrug-resistant bacteria, including AMP, TCN, and Colistin. Further, a comparative genome and lifestyle study of MSK phage confirmed the highest similarity level (87.18% ANI). These findings suggest it to be a new lytic isolated phage species. Finally, Blast and phylogenetic analysis of the large terminase subunit and tail fiber protein put it in Rtp viruses' genus of family Drexlerviridae.

Draft genome sequence of Bacillus megaterium TRQ8, a plant growth-promoting bacterium isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in the Yaqui Valley, Mexico

Bacillus megaterium TRQ8 was isolated from wheat (Triticum turgidum subsp. durum) rhizosphere in commercial fields in the Yaqui Valley, Mexico. Here, we report the draft genome of strain TRQ8, with a size of ~ 5.6 Mbp and a G + C content of 38%. Based on the cutoff values on species delimitation established for average nucleotide identity (> 95-96%), genome-to-genome distance calculator (> 70%), and the reference sequence alignment-based phylogeny (REALPHY) builder method, TRQ8 was strongly affiliated to Bacillus megaterium. The rapid annotation using subsystem technology server revealed that TRQ8 contains 153 RNA genes, and 6113 coding DNA sequences, including those related to plant growth promotion traits, i.e. auxin biosynthesis, phosphate metabolism, siderophores production, and osmotic and oxidative stress response. The function of those putative annotated genes was validated at metabolic level, observing that strain TRQ8 was able to produce 12.0 ± 1.9 µg/mL indoles, phosphate solubilization of 38.7 ± 4.2%, siderophore production of 8.1 ± 0.2%, and tolerance to saline (80.0 ± 5.3%), and water (110.0 ± 4.2%) stress conditions. This genomic and metabolic background was in vivo corroborated by the inoculation of TRQ8 to wheat plants (30 days, under axenic conditions), observing a significant (p = 0.05) increment (compared to un-inoculated plants) of shoot height (16.4%), root length (68.4%), total plant length (30.9%), stem diameter (26.7%), stem circumference (34.8%), shoot dry weight (60.0%), root dry weight (55.6%). Those results provide insights for future agricultural studies and potential applications of this strain, as a plant growth-promoting bacterium.