Species and condition shape the mutational spectrum in experimentally evolved biofilms

Abstract

Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from the Bacillus genus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences of Bacillus thuringiensis are critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Further, the higher degree of genetic diversification observed in biotic selective environments indicates an increased spatial niche heterogeneity and a nutritional source difference created by the plant host that provided a strong strength of selection during the adaptation process. Together, these results provide the first comprehensive mutational landscape of two bacterial species biofilms that is adapted to an abiotic and biotic surface.

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

“…Here, we provide more evidence that IS can increase fitness and play an important role in adaptation, as was already shown across different species ranging from Enterobacteria (Consuegra et al 2021 , Frazão et al 2022 ) to Cyanobacteria (Miller et al 2021 ). A recent study in Bacillus subtilis and Bacillus thuringensis revived end-point populations from four different evolution experiments and showed that, independently of growth in either biotic or abiotic conditions, insertion sequences are critical in adaptation (Hu et al 2023 ). No differences were found across Bacillus species.…”

Enhanced niche colonisation and competition during bacterial adaptation to a fungus

“…To dissect the mutational landscapes of B. subtilis adapted in the presence or absence of A. niger, sequential populations of each lineage at each transfer were subjected to high-coverage metagenome sequencing (except the first three timepoints of four Bac lineages). Singlenucleotide polymorphisms (SNPs) and short insertions and deletions (indels) were determined using the breseq pipeline [29][30][31] which detected 142 and 157 mutations with >5% frequency in CoEvo and Bac populations, respectively (frequencies of each mutated gene in each lineage are shown in Supplementary Fig. 2a and the mutation types are shown in Supplementary Dataset 1).…”