Lateral gene transfer shapes the distribution of nitrogen fixation within a cosmopolitan clade of marine Thalassolituus

Nitrogen fixation, the process of converting dinitrogen gas into ammonia, plays a crucial role in supplying bioavailable nitrogen to marine ecosystems. However, understanding how this process is distributed among heterotrophic bacteria remains a mystery. Thalassolituus, a genus within the family Oceanospirillaceae, is known for its ability to degrade hydrocarbons, yet nitrogen fixation has only been confirmed in a single cultured isolate.

To investigate the distribution and evolutionary history of the minimal nifHDKENB gene set, researchers analyzed 74 high-quality genomes from Thalassolituus within a larger dataset of 421 Oceanospirillaceae genomes.

The analysis revealed that 25 genomes encoded complete or near-complete nif loci and were found within four well-supported clades. Surprisingly, genomes lacking the nitrogen fixation pathway interspersed among these clades. Statistical topology tests rejected the traditional species-tree topology for concatenated NifHDK and NifHDKENB protein alignments, suggesting a more complex evolutionary history.

Eleven recombination events across nif loci were supported by at least four detection methods, indicating lateral gene transfer played a significant role in shaping the distribution of nitrogen fixation. The core nifHDK gene order remained relatively conserved across clades, but accessory neighborhoods differed, with varying degrees of codon adaptation between biosynthesis and structural genes.

Clade 2 exhibited strong congruence between species and gene trees, conserved gene neighborhoods, and relatively high nifH codon adaptation. In contrast, Clades 1 and 4 showed greater phylogenetic discordance, more recombination events, and weaker codon adaptation. These findings support a reticulate history in Thalassolituus, characterized by lateral gene acquisition introducing nitrogen fixation into distinct lineages, vertical inheritance preserving it within some clades, and homologous recombination continuously reshaping nif loci.

Together, these processes help explain the uneven distribution of nitrogen fixation among closely related marine heterotrophic bacteria. Through lateral gene transfer and homologous recombination, nitrogen fixation has become a distributed and dynamic process within the Thalassolituus clade.