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

• DOI: 10.1128/aem.02085-24
• Publication Date: 2025-03-11T13:03:52Z
• Authors: Laura M. Kaminsky; Liana Burghardt; Terrence H. Bell
• Keywords: Experimental Evolution; Soil microbiology

ABSTRACT 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 in-soil fitness, particularly focusing incubation in liquid culture as an unavoidable phase inoculant production and pre-incubation target a potential method performance. We conducted experimental evolution phosphorus-solubilizing bacterial species, Priestia megaterium , (i) soil only, (ii) media (iii) followed by media, using population metagenomic sequencing track mutations over time. Several typical vitro evolutionary phenomena were observed media-incubated populations, including clonal interference, genetic hitchhiking, mutation parallelism between replicate the sporulation transcription factor spo0A . Liquid populations also developed clear fitness reduction compared ancestral isolate. However, soil-incubated grew slowly, experienced far fewer generations despite longer absolute time, accumulated minimal mutational changes. Correspondingly, did not display improved survival isolate their soils, though there appear be minor reductions unfamiliar soil. This work demonstrates that adaptation and/or native impact new more complex real-world habitats does closely resemble media. IMPORTANCE Innovative solutions are needed address emerging challenges agriculture while reducing its footprint. Management microbiomes could contribute this effort, plant growth-promoting microorganisms provide key ecosystem services support crops. Yet, inoculating beneficial farm yields unreliable results. require greater knowledge ecology these taxa functioning sustainable agroecosystems. In report, demonstrate laboratory lingering another negatively species. go further highlight underlying give rise patterns. These insights leveraged our understanding soil-dwelling adapt different pressures.