Sympatric metabolic diversification of experimentally evolved Escherichia coli in a complex environment

Abstract

Sympatric diversification in bacteria has been found to contravene initial evolutionary theories affirming the selection of the fittest type by competition for the same resource. Studies in unstructured (well-mixed) environments have discovered divergence of an ancestor strain into genomically and phenotypically divergent types growing both on single and mixed energy sources. This study addresses the metabolic diversification in an Escherichia coli population that evolved over ~1,000 generations under aerobic conditions in the nutritional complexity offered by Luria-Bertani (LB) broth. The medium lacked glucose but contained a variety of other resources. Two distinct metabolically-diverged types, coinciding with colony morphologies, were found to dominate the populations. One type was an avid carbohydrate consumer, which could quickly utilize the available (alternative) substrates feeding into glycolysis. The second type was a slow grower, which was able to specifically consume acetate. The capacity to utilize acetate might be providing an advantage to this second type, suggesting an increased capability to deal with adverse conditions that occur in the later stages of growth. The diverged metabolic preferences of the two forms suggested differential and interactive ecological roles within the population. We postulate that these types used different alternative metabolic strategies occupying different niches in a sympatric manner as an outcome of adaptation to the complex environment.

Differential stress resistance and metabolic traits underlie coexistence in a sympatrically evolved bacterial population

“…For instance, initially, isogenic populations of Escherichia coli in glucose‐limited continuous culture diversified into distinct metabolic types (Helling et al ., ; Maharjan et al ., ). Such an effect was recently also found for E. coli developing in complex growth medium (Puentes‐Téllez and van Elsas, ). In another experiment, replicate E. coli populations diversified into two coexisting metabolic types due to a diauxic shift in serial‐batch culture fed with a mixture of two substrates, glucose and acetate (Friesen et al ., ; Herron and Doebeli, ).…”

“…Thus, the potentially fast and active metabolism occurring in forms ‘ b ’ and ‘ c ’ may have incited an accumulation of acetate in the medium and a consequent reduction of the pH (Wolfe, ). Form ‘ a ’ has been found to be able to consume and grow on acetate (Puentes‐Téllez and van Elsas ), and hence there may have been evolutionary pressure favouring form ‘ a ’, as it maintained the ancestral capability to cope with acid conditions and could use any released acetate. The former ability was apparently lost by forms ‘ b ’ and ‘ c ’ and so form ‘ a ’ might serve an acetate/acidity vacuum‐cleaner role allowing both ‘ b ’ and ‘ c ’ to survive.…”

“…Two metabolic types among the selected forms ‘ a ’, ‘ b ’ and ‘ c ’ have previously been selected, i.e. ‘metabolic types’ a and c , with c representing both forms ‘ b ’ and ‘ c ’ (Puentes‐Téllez and van Elsas, ). Whereas type c showed a fast carbohydrate consumption ability, type a (a slow grower on major substrates of LB), had developed the ability to consume acetate.…”

“…Assessment of the growth of both types separately in LB broth showed faster exponential growth ( μ = 0.26) of type c and, consequently, an earlier entrance into stationary phase, compared with type a ( μ = 0.22; P < 0.05). Type a thus revealed a longer lag phase, resulting in a later exponential phase and also a later stationary phase (Puentes‐Téllez and van Elsas, ).…”

“…Isolated colonies obtained from an end‐point populations of an experimental evolution setup with E. coli K12 MC1000 were characterized in terms of morphology and metabolic behaviour (Puentes‐Téllez et al ., ; Puentes‐Téllez and van Elsas, ). We sorted the colonies in three different types: (i) small (‘ a ’ form), diameter < 1 mm, pronounced centre (‘fried egg’ shaped), (ii) large/rough/irregular (‘ b ’ form), diameters > 1 mm and (iii) large/smooth/regular (‘ c ’ form) with diameters > 1 mm.…”