Merged confocal image of cells in a thermophilic mat biofilm. Rod/sausage-shaped cells in green represent Cyanobacteria visualized via their photosynthetic chlorophyll emission; long orange filaments represent Roseiflexus sp.. Image credit: Sample: Devaki Bhaya; Image: Andrey Malkovskiy (CCBY 4.0)
Bacteria are among the most successful organisms on Earth. These small, single-cell microbes inhabit nearly every environment on the planet and play essential roles in health, disease, ecology and industry. Their rapid cell division and ability to take up DNA from the environment allow them to adapt quickly to new challenges. After uptake, bacteria foreign DNA into genomes through a process known as recombination. This enables them to acquire beneficial genetic variants, such as antibiotic resistance genes, and spread them through the population.
Although the molecular mechanisms responsible for bacterial recombination have been extensively studied, its evolutionary consequences remain poorly understood. Unlike sexually reproducing organisms, in which the entire genome is recombined every generation, bacteria exchange only a small fraction – typically less than 1% of their genome. In theory, recombination could reduce genetic differences within a population, making them more similar. Alternatively, if genetic divergence between bacterial strains continued to accumulate despite recombination, those strains could eventually evolve into distinct species.
Previous research on thermophilic cyanobacteria from Yellowstone National Park revealed evidence of frequent DNA exchange between these microbes. This recombination produced genomes essentially containing – even in their conserved core – a random assortment of gene variants from across the population. Building on this work, Birzu et al. investigated whether such recombination affects the cohesiveness of different species or whether DNA exchange occurs primarily within a species. Answering this question is an important step toward developing quantitative models of evolution in natural microbial populations.
Birzu et al. quantified the impact of recombination between species – referred to as hybridization – on genetic diversity within species. To do so, they developed a method to identify hybrid DNA segments transferred from other species. When the donor species is known, hybrid segments can be identified simply by comparing genomes, a method typically used to identify Neanderthal DNA in human genomes. However, this approach may fail when donor genomes are unavailable or extinct.
To overcome this limitation, Birzu et al. exploited the fact that genetic distances between species are typically much larger than those within species. Hybridization would thus generate long sequences of highly correlated mutations within the recipient population. Using this idea, Birzu et al. identified hybrid segments and showed that hybridization accounted for up to 95% of the genetic diversity within one of the species.
These results suggest that – rather than diverging – the Yellowstone cyanobacterial population is being homogenized by recombination, leading to a gradual blending between different species. These results have broader implications for understanding microbial evolution in contexts such as the emergence of new pathogens or the adaptation of marine microbes to climate change. They suggest that microbial species may function less as a small number of cohesive strains, and more as quasi-sexual populations with continual DNA exchange within and between species. Extending the approach from this paper to other microbial populations and developing new methods to quantify the impact of hybridization will help clarify which of these evolutionary scenarios is most common in nature.
