Phenotypic Diversity Caused by Differential RpoS Activity among Environmental Escherichia coli Isolates

Abstract

Enteric bacteria deposited into the environment by animal hosts are subject to diverse selective pressures. These pressures may act on phenotypic differences in bacterial populations and select adaptive mutations for survival in stress. As a model to study phenotypic diversity in environmental bacteria, we examined mutations of the stress response sigma factor, RpoS, in environmental Escherichia coli isolates. A total of 2,040 isolates from urban beaches and nearby fecal pollution sources on Lake Ontario (Canada) were screened for RpoS function by examining growth on succinate and catalase activity, two RpoS-dependent phenotypes. The rpoS sequence was determined for 45 isolates, including all candidate RpoS mutants, and of these, six isolates were confirmed as mutants with the complete loss of RpoS function. Similarly to laboratory strains, the RpoS expression of these environmental isolates was stationary phase dependent. However, the expression of RpoS regulon members KatE and AppA had differing levels of expression in several environmental isolates compared to those in laboratory strains. Furthermore, after plating rpoS ؉ isolates on succinate, RpoS mutants could be readily selected from environmental E. coli. Naturally isolated and succinate-selected RpoS mutants had lower generation times on poor carbon sources and lower stress resistance than their rpoS ؉ isogenic parental strains. These results show that RpoS mutants are present in the environment (with a frequency of 0.003 among isolates) and that, similarly to laboratory and pathogenic strains, growth on poor carbon sources selects for rpoS mutations in environmental E. coli. RpoS selection may be an important determinant of phenotypic diversification and, hence, the survival of E. coli in the environment.

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

“…A similar phenotype in terms of SPaNC balance can come from mutations in rpoS itself, hfq, spoT, and rssB (198a, 353) and others that indirectly influence RpoS levels (177). The mutational degeneracy of changing RpoS levels reinforces the huge diversity in RpoS across the species E. coli (51,98). The similar effect on SPaNC is accompanied by very different phenotypic changes with, for example, hfq and spoT mutations (353).…”

The rpoS Gene Is Predominantly Inactivated during Laboratory Storage and Undergoes Source-Sink Evolution in Escherichia coli Species

“…In collections of natural E. coli and Salmonella isolates originating from the environment or various hosts, either as commensal bacteria or as pathogens, the frequency of inactivating alleles of rpoS is very variable and ranges from less than 1% to more than 70% of strains (25)(26)(27)(28)(29)(30). However, these data are difficult to interpret, because inactivation can depend on laboratory storage conditions, as discussed above.…”

“…Interestingly, the rpoS gene is located on the lagging strand, where the rate of point mutations is higher than on the leading strand, probably due to conflicts between replication and transcription (3). rpoS is also located close to the MR gene mutS, in a region that has high genomic variability as a result of horizontal gene transfer (23,24).In collections of natural E. coli and Salmonella isolates originating from the environment or various hosts, either as commensal bacteria or as pathogens, the frequency of inactivating alleles of rpoS is very variable and ranges from less than 1% to more than 70% of strains (25)(26)(27)(28)(29)(30). However, these data are difficult to interpret, because inactivation can depend on laboratory storage conditions, as discussed above.…”

Determination of Survival of Wildtype and Mutant Escherichia coli in Soil

“…However, several studies have isolated E. coli from various natural environments such as municipal wastewater, freshwater, beach water, beach sand and soils (Jiménez et al, 1989;Brennan et al, 2010;Chiang et al, 2011;Byappanahalli et al, 2012;Zhi et al, 2016). The capacity of these E. coli strains to survive for long periods of time and grow in the external environment raises questions about the validity of its continued use as indicator of water quality (Brennan et al, 2010).…”