The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus

Táncsics, Andräs; Benedek, Tibor; Szoboszlay, Sándor; Veres, Péter G.; Farkas, Milán; Máthé, István; Màrialigeti, Károly; Kukolya, József; Lányi, Szabolcs; Kriszt, Balázs

doi:10.1016/j.syapm.2014.10.010

Cited by 31 publications

(31 citation statements)

References 44 publications

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“…ruber species. These results on BCP1 are in line with previous phylogenetic analyses based on Rhodococcus 16S rDNA genes and 1-alkane monooxygenase (AlkB) protein sequences reported by Táncsics et al, 2015 [ 42 ]. In conclusion, Rhodococcus sp.…”

Section: Resultssupporting

confidence: 91%

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

et al. 2015

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In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

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Section: Resultssupporting

confidence: 91%

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

et al. 2015

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“…litoralis DSM 17657 T and V . rumoiensis FERM P-14531 T were 78.2%, 76.4%, 78.0%, and 78.0%, respectively (Fig 3), much below the species threshold of 95–96% for species circumscription [6,21,25–26]. These values of experimental DDH, in silico DDH, and ANI, along with phylogenic analyses, showed that CA-1004 T should be considered as a new species, indicating less genetic cohesion of CA-1004 T to the other Rumoiensis clade species.…”

Section: Resultsmentioning

confidence: 98%

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

et al. 2017

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A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

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“…Furthermore, a number of gene clusters have been found to vary between major rhodococcal clades, emphasizing extensive variation at the genomic level27. Similarly, phylogenetic groups of rhodococcal species have been detected based on other genes, such as alkB 28 and from the analysis of a limited number of rhodococcal genomes29. Thus, there is a clear need to further unravel taxonomic relationships within the genus Rhodococcus , particularly given the importance of R. equi , a facultative intracellular pathogen of animals, especially foals30, Rhodococcus fascians , a phytopathogen of numerous dicotyledonous plants31 and R. erythropolis which is capable of numerous industrially significant bioconversions and biodegradations32.…”

mentioning

confidence: 99%

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

Sci Rep

104

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Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

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The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus

Cited by 31 publications

References 44 publications

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

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