(Pan)genomic analysis of two Rhodococcus isolates and their role in phenolic compound degradation

Introduction: Members of the genus Rhodococcus are known for their ability to degrade a wide range of aromatic compounds such as phenolic exudates from plants. They have a high potential to adapt to different habitats due to their linear plasmids and large genome size.

Goals and Methods: We used comparative genomics to investigate the genomic properties of two newly described Rhodococcus strains (R. pseudokoreensis R79T and R. koreensis R85) isolated from apple rhizosphere and compared their traits to other members of the genus. Of particular interest was their ability to degrade phenolic substances as part of a multidisciplinary approach to mitigate apple replant disease (ARD).

Results: The pan-genome of 109 high-quality Rhodococcus genomes was open with a small core (1.3 %), consisting of genes responsible for basic cell functions. The range of genome sizes was immense (3.7 Mbp to 10.9 Mbp). Genomes of strains associated with hosts were generally smaller than those of environmental isolates, that displayed exceptionally large genome sizes. Due to the large genomic differences, we support taxonomic reclassification of certain rhodococci to new genera. Furthermore, we found several strains to be taxonomically incorrectly assigned or being probably undescribed species. Taxonomic affiliation was the most important factor in predicting the genetic content and clustering of the genomes. In addition, we found genes that differentiated between strains based on habitat. This could potentially be used for targeted isolation and screening for desired traits. All members of the genus Rhodococcus had at least one gene involved in benzoate degradation, whereas biphenyl degradation was mainly restricted to strains closely phylogenetically related to our isolates.

Summary: The genomic features displayed by our isolates suggest a potential application in the reduction of phenolic exudates of plants in soil. The approximately 40% of genes that remain unclassified in larger Rhodococcus genomes, particularly those from environmental isolates, require further investigation to explore the metabolic potential of this genus.