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Microbes inhabit natural environments that are remarkably dynamic. Therefore, microbes harbor regulated genetic mechanisms to sense shifts in conditions and induce the appropriate responses. Recent studies suggest that the initial evolution of microbes occupying new niches favors mutations in regulatory pathways. However, it is not clear how this evolution is affected by how quickly conditions change (i.e. dynamics), or which mechanisms are commonly used to implement new regulation. Here, we perform experimental evolution on continuous cultures of Escherichia coli carrying the tetracycline resistance tet operon to identify specific mutations that adapt drug responses to different dynamic regimens of drug administration. We find that cultures evolved under gradually increasing tetracycline concentrations show no mutations in the tet operon, but instead a predominance of fine-tuning mutations increasing the affinity of an alternative efflux pump AcrB to tetracycline. When cultures are instead periodically exposed to large drug doses, all populations evolved transposon insertions in repressor TetR, resulting in loss of regulation and constitutive expression of efflux pump TetA. We use a mathematical model of the dynamics of antibiotic responses to show that sudden exposure to large drug concentrations overwhelm regulated responses, which cannot induce resistance fast enough, resulting in selection for constitutive expression of resistance. These results help explain the frequent loss of regulation of antibiotic resistance by pathogens evolved in clinical environments. Our experiment supports the notion that initial evolution in new ecological niches proceeds largely through regulatory mutations and suggests that transposon insertions are the main mechanism driving this process. 

A century of beech bark disease (BBD) in North America has transformed hardwood forests by reducing the canopy biomass of American beech (Fagus grandifolia), even as beech has come to dominate the sapling layer of many forests. We do not understand the extent to which environmental change drivers such as climate, acidic atmospheric deposition (and its legacy of acidified soils), and invasive disease (BBD) may have contributed to this transformation. We investigated how BBD effects and tree community composition varied along a well-documented soil acidity gradient in the northeastern United States. We surveyed overstory and sapling layer tree species composition, BBD effects, and soil chemistry on 30 watersheds in forests codominated by beech and sugar maple (Acer saccharum). We analyzed potential drivers of community composition, BBD, and beech sapling density using linear models and non-metric multidimensional scaling. Predictors accounted for soil chemistry, climate, overstory beech (importance value, IV), mortality, and BBD defect. Overall overstory species composition varied most along the acidity gradient, while beech and BBD severity varied along their own distinct environmental gradient. Species composition of the overstory and sapling layers diverged significantly, with the latter dominated by beech. Beech sapling density was positively related to the proportion of standing dead overstory beech and soil exchangeable aluminum, but was unrelated to the overall proportion of overstory beech or their BBD severity. The dominance of sapling layers by beech may have resulted from a gradual accumulation of canopy-opening events precipitated by BBD and sugar maple decline, the latter driven by stressors such as acidification and climate change. 

Aims: Climate change is expected to shift climatic envelopes of temperate tree species into boreal forests where unsuitable soils may limit range expansion. We studied several edaphic thresholds (mycorrhizae, soil chemistry) that can limit seedling establishment of two major temperate tree species, sugar maple (arbuscular mycorrhizal, AM) and American beech (ectomycorrhizal, EM). Methods: We integrate two field surveys of tree seedling density, mycorrhizal colonization, and soil chemistry in montane forests of the Adirondack and Green Mountains (Mtns) in the northeastern United States. We conducted correlation and linear breakpoint analyses to detect soil abiotic and biotic thresholds in seedling distributions across edaphic gradients. Results: In the Green Mtns, sugar maple seedling importance (an index of species relative density and frequency, IV) declined sharply with low pH (< 3.74 in mineral soil) and low mycorrhizal colonization (< 27.5% root length colonized). Sugar maple importance was highly correlated with multiple aspects of soil chemistry, while beech was somewhat sensitive to pH only; beech mycorrhizal colonization did not differ across elevation. Mycorrhizal colonization of sugar maple was positively correlated with soil pH and conspecific overstory basal area. In the Adirondacks, sugar maple importance, but not beech, plateaued above thresholds in soil calcium (~ 2 meq/100 g) and magnesium (~ 0.3 meq/100 g). Conclusions: The establishment of sugar maple, but not beech, was impeded by both biotic and abiotic soil components in montane conifer forests and by soil acidity in temperate deciduous forests. These differences in species sensitivity to edaphic thresholds will likely affect species success and future shifts in forest composition.