Laboratory-Dependent Bacterial Ecology: a Cautionary Tale

Abstract

Although laboratory dependence is an acknowledged problem in microbiology, it is seldom intensively studied or discussed. We demonstrate that laboratory dependence is real and quantifiable even in the popular model Escherichia coli. Here laboratory effects alter the equilibrium composition of a simple community composed of two strains of E. coli. Our data rule out changes in the bacterial strains, chemical batches, and human handling but implicate differences in growth medium, especially the water component.Laboratory dependence, or variable performance of organisms when they are cultured at different locations, is an acknowledged phenomenon in microbiology and has the potential to cause major problems for microbial science (and for laboratory-based biology in general). However, laboratory dependence is rarely studied in detail, or even discussed. Underreporting may stem from the perception that the observed laboratory dependence is uninteresting (detracting from the impact of other results) or unbelievable (blamed on unidentified differences in experimental technique). It is crucial that microbiologists begin to understand which organisms are susceptible to laboratory dependence (perhaps all are), what factors in the laboratory environment commonly underlie this phenomenon, and what types of changes in microbial growth are to be expected. We begin to address these issues with a simple community composed of two genotypes of Escherichia coli. We hope that our study motivates closer investigation of laboratory dependence in other systems and promotes discussion of this important topic within the microbial ecology community.The strains used in this study, REL4397 (Lac ϩ ) and REL4398 (Lac Ϫ ), are previously described recombinant genotypes of E. coli B and E. coli K-12 that differ in lactose utilization (15,18). They evolved as a polymorphism in a single population propagated by 24-h serial culture. Under the conditions in which they evolved, the two strains coexisted stably at an equilibrium ratio of ϳ1:1 (18). The strains were isolated and stored at Ϫ80°C in the laboratory of R. E. Lenski at Michigan State University (lab I) in East Lansing, MI. Samples of the strains were shipped frozen to the laboratory of P. E. Turner at Yale University (lab II) in New Haven, CT.The coexistence of the Lac Ϫ and Lac ϩ strains in lab I was attributed to (i) the higher maximum growth rate (growth in abundant glucose) of the Lac Ϫ strain and (ii) the ability of the Lac ϩ strain to scavenge glucose at the end of the growth cycle and also to increase in cell number and relative fitness late in the growth cycle, long after glucose should have been exhausted from the medium (18). This late-cycle growth occurred only when the Lac ϩ strain was grown in the presence of the Lac Ϫ strain, which suggested a possible "cross-feeding" relationship (8, 14).We cultured the E. coli Lac ϩ and Lac Ϫ strains in lab II, where we observed a shift in the composition of this simple bacterial community in favor of the Lac ϩ strain. Below we describe labo...

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