Spatial heterogeneity of an ecologically relevant environment accelerates diversification and adaptation

Abstract

17Spatial heterogeneity is a key driver for the evolution of resource specialists and has 18 been shown to both promote and constrain the rate of adaptation. However, direct 19 empirical support for these evolutionary consequences of spatial heterogeneity 20 comes from simplified laboratory environments. Here we address how spatial 21 structure, through its effect on resource heterogeneity, alters diversification and 22 adaptive evolution of the soil bacterium Pseudomonas fluorescens in an ecologically 23 relevant context: soil-based compost. Our data show that environmental 24 heterogeneity can both promote phenotypic diversification and accelerate adaptation. 25These results suggest that environmental disturbance, which can decrease spatial 26 heterogeneity, may limit diversification and adaptation of microbial populations. 27 2 28 Introduction 34While there is strong theoretical and empirical evidence that spatial variation in 35 resources can promote the evolution and maintenance of diverse resource 36 specialists 1-9 , the impact of spatial heterogeneity on adaptive evolution is more 37 ambiguous. Theoretically, the structured populations associated with spatial 38 heterogeneity can constrain adaptive evolution by both slowing the spread of 39 beneficial mutations 10 and increasing the role of genetic drift by reducing effective 40 population sizes 11,12 . However, population structure may promote adaptive evolution 41 by allowing greater exploration of adaptive landscapes 13,14 and spatial heterogeneity 42 can also increase the chance that beneficial mutations will encounter an environment 43 that maximises their fitness effect 15,16 . In vitro experimental studies involving bacteria 44 or viruses evolving in nutrient media provide support for both views 3,12,17,18 . This 45 variation in empirical results demonstrates the nuanced effect of in vitro experimental 46 conditions, making it crucial to know how spatial heterogeneity impacts adaptive 47 evolution (and indeed diversification) under ecologically relevant conditions. Here, we 48 conduct such an experiment in potting compost 19 . We evolved the soil bacterium 49 Pseudomonas fluorescens in compost with its spatial structure intact (representing a 50 heterogeneous environment), or in compost that was mixed with water (representing 51 a homogeneous environment), and measured fitness, phenotypic diversity based on 52 substrate use and population genomic changes. 53 54 Materials and methods 55 Strains 56 Pseudomonas fluorescens strain SBW25 20 was used throughout the study. To57 generate a genetically marked SBW25 strain expressing β-galactosidase (LacZ),58 Tn7-mediated transposition was carried out to insert a lacZ gene into the P.59 fluorescens attTn7 genomic location 21 . 60 61 4 Growth conditions of the evolution experiment in compost 62 Pseudomonas fluorescens SBW25 was grown overnight at 28°C in King's media B 63 (KB) in an orbital shaker (180 rpm) and then centrifuged for 10 min at 3500 rpm to 64 produce a bacterial pellet, which was resuspended i...