Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

Abstract

bIn a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response of Escherichia coli MC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxygen conditions (defined environments), and 19 evolved forms were isolated. The emergence of forms with enhanced fitness was evident in competition experiments of all evolved forms versus the ancestral strain. The evolved forms were then subjected to phenotypic and genomic analyses relative to the ancestor. Profound changes were found in their phenotypes as well as whole-genome sequences. Interestingly, considerable heterogeneity was found at the intrapopulational level. However, consistently occurring parallel adaptive responses were found across all populations. The evolved forms all contained a mutation in galR, a repressor of the galactose operon. Concomitantly, the new forms revealed enhanced growth on galactose as well as galactose-containing disaccharides. This response was likely driven by the LB medium.

Acid-Adapted Strains of Escherichia coli K-12 Obtained by Experimental Evolution

“…Indeed, we observed a fitness improvement much greater than that which has been seen in previous long-term evolution experiments at pH 5.3 (31). Our experiment was performed in a complex medium, LBK mal , which broadened the range of possible metabolic responses and, hence, targets of selection to the acidic conditions (9,27). Evolved populations showed both a significantly higher endpoint culture density ( Fig.…”

“…A protocol based on successful evolution protocols described in the literature (22,25,27) was devised for experimental evolution of E. coli growth at external pH values below 5. Twentyfour populations were established from the same parental freezer stock of strain W3110.…”

“…If the specified environment deviates from the optimal conditions for peak fitness, then there exists strong selective pressure for mutant alleles that enhance fitness in the new environment. E. coli has been the subject of a number of evolution studies involving adaptation to high temperatures (25), high ethanol concentrations (26), growth in complex media (27), and resistance to antibiotics (28).…”

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

“…The occurrence of unexplored (vacant) niches in the aforementioned habitats may thus constitute a key driver of the rapid emergence of novel bacterial types in initially homogeneous populations (Rainey and Travisano, ; MacLean et al ., ; Puentes‐Téllez et al ., ), in which frequency‐dependent selection may be involved (Friesen et al ., ; Tyerman et al ., ). One may consider complex environments with nutrient mixtures to offer spatial ‘structure’ with fine‐scale variation (Kassen, ).…”

“…Two distinct metabolic types were identified after analysis of multiple colonies from the evolved population. Initial studies of these revealed that colony morphology correlated with some distinct genotypes and phenotypes (Puentes‐Téllez et al ., 2013; 2014). Here, we further explore the ecological nature of selected divergent types that apparently maintained a coexisting interaction.…”