Abstract
The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.
Highlights
Rhodococcus is a gram-positive genus within the Actinobacteria class that is ubiquitously distributed in the environment
The 42 phylogenomic groups (PGs) are in total agreement with the reference partition according to the Modified Rand Index (i.e., MRI = 1) using a distance threshold T between 0.1395 and 0.143, which correspond to a 29.8% and 30.5% digital DNA–DNA hybridization (dDDH), respectively (Figure 2)
Some of the PGs identified in this work are in agreement with a previous study conducted by Creason et al, 2014, which identified seven main clades within the Rhodococcus genus using 59 genomes based on whole-genome comparisons [25]
Summary
Rhodococcus is a gram-positive genus within the Actinobacteria class that is ubiquitously distributed in the environment. Strains from this genus have been isolated from a variety of habitats, including soils, oceans and fresh waters [1,2,3], as well as from the guts of insects or living in association with sea sponges [4,5]. Multiple Rhodococcus species are known to degrade diverse organic compounds, including polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and aliphatic hydrocarbons [10,11,12], making this genus a very promising tool for bioremediation purposes. Examples of the inconsistency in the classification can be found in the report of an illegitimate genus name of Rhodococcus Zopf 1981 which postdates the homonym algal genus
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