Subinhibitory antibiotic concentrations mediate nutrient use and competition among soil streptomyces

Abstract

Though traditionally perceived as weapons, antibiotics are also hypothesized to act as microbial signals in natural habitats. However, while subinhibitory concentrations of antibiotics (SICA) are known to shift bacterial gene expression, specific hypotheses as to how SICA influence the ecology of natural populations are scarce. We explored whether antibiotic 'signals', or SICA, have the potential to alter nutrient utilization, niche overlap, and competitive species interactions among Streptomyces populations in soil. For nine diverse Streptomyces isolates, we evaluated nutrient utilization patterns on 95 different nutrient sources in the presence and absence of subinhibitory concentrations of five antibiotics. There were significant changes in nutrient use among Streptomyces isolates, including both increases and decreases in the capacity to use individual nutrients in the presence vs. in the absence of SICA. Isolates varied in their responses to SICA and antibiotics varied in their effects on isolates. Furthermore, for some isolate-isolate-antibiotic combinations, competition-free growth (growth for an isolate on all nutrients that were not utilized by a competing isolate), was increased in the presence of SICA, reducing the potential fitness cost of nutrient competition among those competitors. This suggests that antibiotics may provide a mechanism for bacteria to actively minimize niche overlap among competitors in soil. Thus, in contrast to antagonistic coevolutionary dynamics, antibiotics as signals may mediate coevolutionary displacement among coexisting Streptomyces, thereby hindering the emergence of antibiotic resistant phenotypes. These results contribute to our broad understanding of the ecology and evolutionary biology of antibiotics and microbial signals in nature.

Figure 1. Principal components analysis of nutrient use profiles of Streptomyces isolates.

Principal components analysis of nutrient use profiles for Streptomyces isolates 1232-2 and Mont3-8 in the presence and absence of SICA. Growth was evaluated on Biolog SF-P2 plates; each treatment was replicated three times. The percent variation in nutrient use explained by each axis is shown in parentheses.

Figure 2. Characterizing Escape Ratios (ER) among competing microbes.

The niche of each microbe is denoted by a shaded circle, which represents the cumulative growth of an isolate on the total suite of nutrients used by that isolate. Niche overlap is the area of intersection between the two circles, and quantifies the total growth for each isolate on nutrients used by both isolates. Competition-free growth is the non-intersecting area for each circle, or total growth for an isolate on nutrients that the competing isolate does not use. The escape ratio (ER) is the ratio of competition-free growth in the presence vs. the absence of SICA. When the escape ratio is greater than one, we hypothesize benefits to an isolate from the presence of SICA.

Figure 3. ER>1 and Resistance.

Frequencies of escape ratios greater than one among all possible isolate pair-antibiotic combinations (n = 360) and frequencies of resistance to the same antibiotics among a global collection of naturally-occurring soil Streptomyces (21).