How Archiving by Freezing Affects the Genome-Scale Diversity of Escherichia coli Populations

In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus each sample archived in this way, consists of many unique genotypes and phenotypes. The effect of archiving on such a heterogeneous population is unknown. Here, we identified optimal archiving conditions for E. coli. We also used genome sequencing of archived samples to study the effects that archiving has on genomic population diversity. We observed no allele substitutions and mostly small changes in allele frequency. Nevertheless, principal component analysis of genome-scale allelic diversity shows that archiving affects diversity across many loci. We showed that this change in diversity is due to selection rather than drift. In addition, ∼1% of rare alleles that occurred at low frequencies were lost after treatment. Our observations imply that archived populations may be used to conduct fitness or other phenotypic assays of populations, in which the loss of a rare allele may have negligible effects. However, caution is appropriate when sequencing populations restarted from glycerol stocks, as well as when using glycerol stocks to restart or replay evolution. This is because the loss of rare alleles can alter the future evolutionary trajectory of a population if the lost alleles were strongly beneficial.

Viability and genetic stability of the bacterium Escherichia coli HB101 with the recombinant plasmid during preservation by various methods

The effects of various methods of preservation (freeze-drying and storage at 4 degrees C; low-temperature freezing on desiccated silica gel and storage at -70 and -150 degrees C; cryopreservation and storage at -196 degrees C) on viability and genetic stability of the bacterium Escherichia coli HB101 carrying the recombinant plasmid with the human DNA fragment were studied. Genetic stability was estimated by maintenance of the selective markers of antibiotic resistance and the stability of the restriction sites in recombinant DNA. Freezing on silica gel and cryopreservation were shown to be the optimal preservation methods providing a high level of survival and genetic stability.

Freeze preservation of synchrony in cultures of enterobacteriaceae synchronized by continuous phasing in phosphate-limited media

In order to achieve synchronization of cell division by continuous phasing, the growth of enteric bacteria has been limited by inorganic phosphate. After a short starvation, the culture was automatically diluted twofold so that the limiting nutrient allowed for one doubling exactly. An automatic device was designed to carry out repeated cycles of growth, starvation and dilution with adjustable periodicity. After 12-24 automatic cycles, which were usually achieved largely overnight, synchronous cell divisions could be observed for several generations in nonlimiting culture conditions. When portions of the phased culture were frozen and kept at low temperature for periods up to several months, these freeze-preserved populations exhibited a synchronous growth upon thawing and cultivation. This technique has thus the potential of providing synchronized cultures of a variety of bacterial strains at the desired time.