Nutrient-rich spatial refuges buffer against extinction and promote evolutionary rescue in evolving microbial populations

Microbial populations are often exposed to long-term abiotic disturbances,
which can reduce population viability and cause local extinction.
Eco-evolutionary theory suggests that spatial refuges can facilitate
persistence and evolutionary rescue. However, one drawback of spatial
refuges is reduced exposure to nutrients such as carbon and oxygen,
suggesting the protective effect of refuges depends on the interplay
between environmental conditions and the degree of stress. Here, we test
this general idea using mathematical modelling, and experimental evolution
of the model bacterium Pseudomonas fluorescens SBW25 under salinity
stress. As our model predicted, we find that the ability of spatial
refuges to rescue evolving populations from extinction crucially depends
on nutrient availability. Populations evolving under salinity stress where
nutrient-rich spatial refuges were available, harboured clones that
displayed enhanced salt resistance, indicating that nutrient-rich spatial
refuges can facilitate evolutionary rescue. Furthermore, while
control-salinity-evolved populations adapted to spatial structure by
evolving enhanced motility (likely through parallel mutations in
PFLU_4551, a predicted aerotaxis response regulator), this phenotype was
constrained under high salinity, because increased motility negates the
benefits of a spatial refuge. Our results reveal a general interplay
between spatial refuges and nutrient availability that could be leveraged
to reduce extinction risk in natural populations.