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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.

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