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

Leonardo Joaquim Van Zyl,Marla Trindade,Shonisani Nemavhulani,Donald Arthur Cowan,James Cass

doi:10.1186/s12985-016-0656-6

Leonardo Joaquim Van Zyl, Marla Trindade + Show 3 more

Open Access

https://doi.org/10.1186/s12985-016-0656-6

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Abstract

BackgroundSoda 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.MethodsBacteria 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.ResultsPhage 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.ConclusionThe 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 materialThe online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.

Highlights

Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour
The best studied lakes are those of the East African Rift Valley (EARV) which have been scientifically documented for many decades, two of which, Lake Shala
The EARV lakes are situated in an environment of active volcanism and differ from other soda lakes as surrounding hot springs supply water to the lake depressions, whereas others are supplied by the leaching of rainfall through the surface into the lake basins [3]

Summary

Introduction

Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Soda lakes are sodium carbonate (Na2CO3)-dominated environments with varying salinity and high pH values, usually between 9 and 11, but occasionally greater than pH 12 [1,2,3]. These lakes are found in arid and semiarid areas where high evaporation rates facilitate the accumulation of salts in local depressions and due to the high buffering capacity of sodium carbonate, soda lakes are the only habitats that maintain stable high alkalinity [4,5,6]. There is a need to better understand the viral composition in these, and other environments

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Conclusion