Genome-Wide Mutation Rate Response to pH Change in the Coral Reef Pathogen Vibrio shilonii AK1.

Chloe Strauss,Ronald Te,Caitlyn E Patterson,Hongan Long,Michael Lynch,Nancy A Moran

doi:10.1128/mbio.01021-17

Abstract

ABSTRACTRecent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation. However, such explorations have rarely been conducted on marine organisms, and it is unclear how marine habitats have influenced genome stability. This report resolves the mutation rate and spectrum of the coral reef pathogen Vibrio shilonii, which causes coral bleaching and endangers the biodiversity maintained by coral reefs. We found that its mutation rate and spectrum are highly similar to those of other studied bacteria from various habitats, despite the saline environment. The mutational properties of this marine bacterium are thus controlled by other general evolutionary forces such as natural selection and genetic drift. We also found that as pH drops, the mutation rate decreases and the mutation spectrum is biased in the direction of generating G/C nucleotides. This implies that evolutionary features of this organism and perhaps other marine microbes might be altered by the increasingly acidic ocean water caused by excess CO2 emission. Nonetheless, further exploration is needed as the pH range tested in this study was rather narrow and many other possible mutation determinants, such as carbonate increase, are associated with ocean acidification.

Highlights

Recent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation
Divisions (G) Ts Tv Ins Del aCI, confidence interval from t distribution; N, number of MA lines used for mutation analysis, after removing lines with low coverage (Ͻ15ϫ) or cross-line contamination; Transfers, average number of transfers for each MA line (ϳ48 h between two consecutive transfers); X, mean depth of coverage of genome sequencing; Divisions (G), mean number of cell divisions for each MA line passed during the experimental span (G, generation time in hours); Ts, total number of transitions pooled from all MA lines in the group; Tv, total number of transversions; Ins, total number of insertions in the group; Del, total number of deletions in the group
In vitro studies have indicated that low pH increases the efficiency of error removal by the exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I: from pH 9.8 to 6.2, frameshift and base-substitution mutation rates are decreased by 40-fold and 50-fold, respectively, possibly by altering the template-binding properties of the DNA polymerase [7]

Summary

Introduction

Recent application of mutation accumulation techniques combined with whole-genome sequencing (MA/WGS) has greatly promoted studies of spontaneous mutation. We found that as pH drops, the mutation rate decreases and the mutation spectrum is biased in the direction of generating G/C nucleotides This implies that evolutionary features of this organism and perhaps other marine microbes might be altered by the increasingly acidic ocean water caused by excess CO2 emission. Despite the high species diversity and abundance of marine microbes (reviewed in reference 1), the association between their spontaneous mutations and environmental factors is rarely studied. This sharply contrasts with recent research progress in the area on bacteria from other habitats [2, 3]. In vitro studies have indicated that low pH increases the efficiency of error removal by the exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I: from pH 9.8 to 6.2, frameshift (insertion or deletion) and base-substitution mutation rates are decreased by 40-fold and 50-fold, respectively, possibly by altering the template-binding properties of the DNA polymerase [7]

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