When Kostas Konstantinidis proved that many bacteria - like plants and animals - are organized into species, he upended a long-held scientific belief. Scientists widely believed that bacteria, due to their unique genetic exchange mechanisms and the vast size of their global populations, did not - and could not - form distinct species.
New research from Konstantinidis and collaborators further challenges this notion, suggesting that not only do bacteria form species, but they also maintain cohesive species through a process that is somewhat "sexual."
"The next question for us was how individual microbes in the same species maintain their cohesiveness. In other words, how do bacteria stay similar?" said Konstantinidis, the Richard C. Tucker Professor in Georgia Tech's School of Civil and Environmental Engineering.
Bacterial and other microbes are thought to evolve primarily through binary fission, meaning asexual reproduction, while also engaging in infrequent genetic exchange. Using a novel bioinformatic method for detecting gene transfer, along with a new trove of whole genome data, Konstantinidis and an international team of researchers tested their hypothesis for how species emerge and are maintained. They found that bacteria evolve and form species more "sexually" than previously thought.
Their research was published in the journal Nature Communications.
To investigate how microbial species maintain their distinct identities, the team analyzed the complete genomes of microbes from two natural populations. They collected and sequenced over 100 strains of Salinibacter ruber (a salt-loving microbe) from solar salterns in Spain. Then they analyzed a set of previously published Escherichia coli genomes isolated from livestock farms in the U.K. They compared the genomes of closely related microbes to see how genes were being exchanged.
They found that a process called "homologous recombination" plays a major role in keeping microbial species together. Homologous recombination occurs when microbes exchange DNA with each other and integrate the new DNA into their genome by replacing their own similar DNA. They observed that recombination occurs frequently and randomly across the entire genome of microbes, and not just in a few specific regions.
"This may be fundamentally different from sexual reproduction in animals, plants, fungi, and non-bacterial organisms, where DNA is exchanged during meiosis, but the outcome in terms of species cohesion may be similar," Konstantinidis said. "This constant exchange of genetic material acts as a cohesive force, keeping members of the same species similar."
The researchers also observed that members of the same species are more likely to exchange DNA with one another than with members of different species, further contributing to distinct species boundaries.
"This work addresses a major, long-lasting problem for microbiology that is relevant for many research areas," Konstantinidis said. "That is, how to define species and the underlying mechanisms for species cohesion."
This research has implications for several fields, from environmental science and evolution to medicine and public health, and offers valuable insights for identifying, modeling, and regulating clinically or environmentally important organisms. The methodology developed during the research also provides a molecular toolkit for future epidemiological and micro-diversity studies.
Note: The research was made possible by contributions from the groups of Ramon Rossello-Mora at IMEDEA in Majorca, Spain, and Rudolf Amann at the Max Planck Institute for Marine Microbiology in Bremen, Germany, who obtained data from the natural microbial populations and equally contributed to the data analysis and interpretations.
Citation: Conrad, R.E., Brink, C.E., Viver, T. et al. Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination. Nat Commun 15, 9906 (2024).
DOI: https://doi.org/10.1038/s41467-024-53787-0
Funding: U.S. Department of Energy, U.S. National Science Foundation, European Regional Development Fund
