Bacteriophage diversity in haloalkaline environments

>Magister Scientiae - MScThere are limited reports on virus population in haloalkaline environments; therefore the aim of this study was to investigate the genetic diversity and biology of bacteriophage communities in these environments. Bacteria were isolated to be used as phage hosts. One bacterium from Lake Magadi and four bacteria from Lake Shala were successfully isolated from sediment samples. A further two Lake Shala bacterial hosts from the IMBM culture collection were also used to isolate bacteriophages. Bacterial isolates were identified to be most closely related to Bacillius halodurans, Halomonas axialensis, Virgibacillus salarius, Bacillus licheniformis, Halomonas venusta, Bacillus pseudofirmus and Paracoccus aminovorans. Bacteriophages were screened using all bacteria against sediment samples from both Lake Shala and Lake Magadi. One phage was identified from Lake Magadi sediments (MGBH1) and two phages from Lake Shala sediments (SHBH1 and SHPA). TEM analysis showed that these phages belong to three different dsDNA phage families; Siphoviridae (MGBH1), Myoviridae (SHBH1) and Podoviridae (SHPA). All phages showed different genome sizes on agarose gel. Due to the small genome size, phage SHPA was chosen for further investigation. Partial, genome sequence analysis showed homology to both bacterial and phage proteins. A further investigation of phage diversity in this environment is essential using metagenomic approaches to understand these unique communities

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

BACKGROUND : Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS : Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages. RESULTS : Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel. CONCLUSION : The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages.Additional file 1: Figure S1. Whole genome alignment of phage Shbh1 with six of its closest relatives. Similarly coloured regions indicate homology or local collinear blocks (LCB) between nucleotide sequences, with the level of similarity indicated by the height of the bars within each LCB. Genome alignments were performed using MAUVE.Additional file 2: Table S1. Predicted open reading frames on Shpa and closest BLASTp hit on the NCBI database.Additional file 3: Table S2. Predicted open reading frames on Mgbh1 and closest BLASTp hit on the NCBI database.Additional file 4: Table S3. Predicted open reading frames on Shbh1 and closest BLASTp hit on the NCBI database.Additional file 5: Figure S2. GC skew analysis of the Shbh1 genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.Additional file 6: Figure S4. GC skew analysis of the Shpa genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.Additional file 7: Figure S3. GC skew analysis of the Mgbh1 genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp.The National Research Foundation (NRF) of South Africahttp://www.virologyj.comam2017Genetic

Additional file 1: Figure S1. of Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Whole genome alignment of phage Shbh1 with six of its closest relatives. Similarly coloured regions indicate homology or local collinear blocks (LCB) between nucleotide sequences, with the level of similarity indicated by the height of the bars within each LCB. Genome alignments were performed using MAUVE. (DOCX 136 kb

Additional file 3: Table S2. of Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Predicted open reading frames on Mgbh1 and closest BLASTp hit on the NCBI database. (DOCX 23 kb

Additional file 5: Figure S2. of Three novel bacteriophages isolated from the East African Rift Valley soda lakes

GC skew analysis of the Shbh1 genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp. (DOCX 23 kb

Additional file 2: Table S1. of Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Predicted open reading frames on Shpa and closest BLASTp hit on the NCBI database. (DOCX 20 kb

Additional file 6: Figure S4. of Three novel bacteriophages isolated from the East African Rift Valley soda lakes

GC skew analysis of the Shpa genome showing putative replication origin (ori) and termination sites (ter) calculated using a window size of 1000 bp and a step size of 100 bp. (DOCX 22 kb