Genome streamlining in bacteria evolving under high predation pressure. Whole genome sequencing of Sphingobium sp. Z007

Predation is the main mortality source for aquatic bacteria and has a strong impact on bacterial populations and their phenotypic appearance. To avoid ingestion by predators, bacteria have developed different antipredator strategies. One such strategy is to form aggregates to exceed the size ingestible by the predator. However, such mechanisms should be under strong selective pressure, as bacteria have to re-allocate resources which they could invest in proliferation otherwise. We set up a long-term predator-prey experiment with the aggregate forming bacterial freshwater bacterial isolate Sphingobium sp. Z007 and the mixootrophic nanoflagellate Poterioochromonas sp.. A co-culture of bacteria and flagellates and a control treatment with bacteria only were maintained in oligotrophic medium with regular propagations for 200 days. Phenotypically, bacteria showed rapid adaptation to the presence or absence of predation. Strains evolved under continuous predation pressure exhibited an enhanced antipredator phenotype both in the presence and absence of a predator. The control treatment had a reduced ability to form aggregates and biofilms, but showed higher efficiency in growth and substrate usage. We next sequenced the genomes of the ancestor strains and of strains from three replicates of each treatment. All strains evolved under predation had lost a genetic element of the size of a larger plasmid. These strains significantly increased their growth efficiency despite the allegedly resource demanding investment in predator defence. However, the genome reduction appeared to come with a trade-off: The excised genetic region codes for several metabolic pathways for the degradation of complex substrates, such as aromatic compounds. If the genome-reduced strains were challenged with such a compound (benzoate) they showed weaker growth or were even inhibited by the substrate. The opposite was observed for strains without such genomic loss, i.e. evolved without predators, and the ancestor. This suggests that predation does not only have a strong influence on abundance and phenotypes of bacteria but can influence unrelated metabolic traits and, as a consequence, reduce their niche space. The loss of an identical genetic element in strains from three independent biological replicates moreover suggest the action of a dedicated mechanism for such genome reduction.