Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment

Abstract

Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism. Bacteria were propagated in serial batch culture in a nutrient-restricted environment either with or without a bacterivorous flagellate. Strains isolated after 26 growth cycles of the predator-prey co-cultures formed as much total biomass as the ancestor at ancestral growth conditions, albeit largely reallocated to cell aggregates. A ~273 kbp genome fragment was lost in three strains that had independently evolved with predators. These strains had significantly higher growth yield on substrate-restricted media than others that were isolated from the same treatment before the excision event. Under predation pressure, the isolates with the deletion outcompeted both, the ancestor and the strains evolved without predators even at rich growth conditions. At the same time, genome reduction led to a growth disadvantage in the presence of benzoate due to the loss of the respective degradation pathway, suggesting that niche constriction might be the price for the bidirectional optimization.

Figure 1

Increase of total growth yield during experimental evolution and reallocation of biomass between planktonic and aggregate associated cells. (a) Cell densities of the ancestor Sphingobium sp. Z007 strain (168 h of growth at oligotrophic conditions) and of three strains evolving without (P−) or with (P+) predators that were isolated after 16 and 26 growth cycles. (b) Biomass of planktonic cells (hatched) and aggregates (white) of the ancestor and of strains with different evolutionary background isolated after 26 growth cycles when grown on the original rich medium.

Figure 2

Location of the genomic excision (marked in grey) on chromosome 2, and distribution of transposable elements (black bars) and genes involved in metabolism of aromatic compounds (yellow bars). The size of the excision was approximately 273 kbp.

Figure 3

Cell densities after 96 h of growth in nutrient-limited medium cultivated either without or with predator of three independently evolved P+ strains that were isolated in the middle of the experiment (16 growth cycles), directly before the excision (24, 20 and 22 growth cycles for strains A, B and C, respectively) and after genome reduction (26 growth cycles). Strains were cultivated either without or with predator.

Figure 4

Competitive performance of strains evolved with predators. (a) Differences in fitness between strains from the P+ and P− treatments (26 growth cycles) cultivated either without or with predators. (b) Differences in fitness between strains from the P+ and the ancestor (Anc) without or with predators.

Figure 5

Comparison of growth of the ancestor and of evolved strains (isolated after 26 growth cycles) in the presence or absence of benzoate.