Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness

Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media.