Comparative genomic analysis of eight novel haloalkaliphilic bacteriophages from Lake Elmenteita, Kenya

Abstract

We report complete genome sequences of eight bacteriophages isolated from Haloalkaline Lake Elmenteita found on the floor of Kenyan Rift Valley. The bacteriophages were sequenced, annotated and a comparative genomic analysis using various Bioinformatics tools carried out to determine relatedness of the bacteriophages to each other, and to those in public databases. Basic genome properties like genome size, percentage coding density, number of open reading frames, percentage GC content and gene organizations revealed the bacteriophages had no relationship to each other. Comparison to other nucleotide sequences in GenBank database showed no significant similarities hence novel. At the amino acid level, phages of our study revealed mosaicism to genes with conserved domains to already described phages. Phylogenetic analyses of large terminase gene responsible for DNA packaging and DNA polymerase gene for replication further showed diversity among the bacteriophages. Our results give insight into diversity of bacteriophages in Lake Elmenteita and provide information on their evolution. By providing primary sequence information, this study not only provides novel sequences for biotechnological exploitation, but also sets stage for future studies aimed at better understanding of virus diversity and genomes from haloalkaline lakes in the Rift Valley.

Bacteriophages of Thermophilic ‘Bacillus Group’ Bacteria—A Review

“…All bacteriophages were isolated from Lake Elmenteita [ 66 ], situated at 0°27′ S 36°15′ E on the floor of the Kenyan Rift Valley, at 1776 m above sea level without a direct water outlet. This area has a hot, dry and semi-arid climate, which results in rapid evaporation rates.…”

“…Comparison of genome sizes, coding density, number of ORFs, GC% and gene organizations revealed that the bacteriophages had no relationship with each other as well as no significant similarities in the GenBank ® sequence data. Furthermore, there is evidence of genes mosaicism to described genes with conserved domains [ 66 ]. The bacterial hosts were not described in details.…”

“…No bacteriophages characteristics are available at the time of this review submission, except bacteriophages genomes bioinformatics analysis. The authors cite ongoing publication, which will contain descriptions of the bacteriophages [ 66 ].…”

“…A conserved replication factor was detected in the genome, suggesting that vB_BpsS-36 employs DNA polymerase III subunit alpha for DNA replication. Furthermore, vB_BpsS-36 codes for replication proteins—domains DnaB and DnaG [ 66 ].…”

“…The bacteriophage exhibits weak similarities to Bacillus bacteriophage PM1 and Geobacillus phage GBK2 in cluster coding for structural components. The vB_BpsM-61 genome is also coding for putative proteins: replicative DnaC, helix destabilizing Ssb, dUTPase, Holliday junction resolvase [ 66 ].…”