Strain CCM 4446T, with notable biodegradation capabilities, was investigated in this study in order to elucidate its taxonomic position. Chemotaxonomic analyses of quinones, polar lipids, mycolic acids, polyamines and the diamino acid of the cell-wall peptidoglycan corresponded with characteristics of the genus Rhodococcus. Phylogenetic analysis, based on the 16S rRNA gene sequence, assigned strain CCM 4446T to the genus Rhodococcus and placed it in the Rhodococcus erythropolis 16S rRNA gene clade. Further analysis of catA and gyrB gene sequences, automated ribotyping with EcoRI restriction endonuclease, whole-cell protein profiling, DNA–DNA hybridization and extensive biotyping enabled differentiation of strain CCM 4446T from all phylogenetically closely related species, i.e., Rhodococcus baikonurensis, Rhodococcus qingshengii, Rhodococcus erythropolis and Rhodococcus globerulus. The results obtained show that the strain investigated represents a novel species within the genus Rhodococcus, for which the name Rhodococcus degradans sp. nov., is proposed. The type strain is CCM 4446T ( = LMG 28633T).
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Funding
This study was supported by the:
Ministry of Education, Youth and Sports of the Czech Republic
(Award CZ.1.07/2.3.00/20.0183)
CleenwerckI.,
VandemeulebroeckeK.,
JanssensD.,
SwingsJ.
( 2002;). Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microbiol521551–1558[PubMed].
DamborskýJ.,
KočaJ.
( 1999;). Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons. Protein Eng12989–998 [View Article][PubMed]
.
DamborskýJ.,
NyandorohM. G.,
Ne˘mecM.,
HoloubekI.,
BullA. T.,
HardmanD. J.
( 1997;). Some biochemical properties and the classification of a range of bacterial haloalkane dehalogenases. Biotechnol Appl Biochem2619–25[PubMed].
de CarvalhoC. C.,
CostaS. S.,
FernandesP.,
CoutoI.,
ViveirosM.
( 2014;). Membrane transport systems and the biodegradation potential and pathogenicity of genus Rhodococcus
. Front Physiol5133 [View Article][PubMed]
.
EzakiT.,
HashimotoY.,
YabuuchiE.
( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol39224–229 [View Article].
GorisJ.,
SuzukiK.,
De VosP.,
NakaseT.,
KerstersK.
( 1998;). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol441148–1153 [View Article].
JanákováI.,
VojtkováH.
( 2012;). Application of flotation and biodegradation to eliminate persistent organic pollutants in the influent stream of Cerny Prikop. . In Microbes in Applied Research, pp. 28–32. Edited by
Mendez-VilasA.
Singapore:
World Scientific Publishing;
[View Article].
JonesA. L.,
GoodfellowM.
( 2012;). Genus IV. Rhodococcus (Zopf 1891) emend. Goodfellow, Alderson and Chun 1998a. . In Bergey's Manual of Systematic Bacteriology, The Actinobacteria, Part Avol. 5, pp. 437–464. Edited by
WhitmanW.,
GoodfellowM.,
KämpferP.,
BusseH.-J.,
TrujilloM. E.,
LudwigW.,
SuzukiK.-i.,
ParteA.
New York:
Springer;.
KämpferP.,
DottW.,
MartinK.,
GlaeserS. P.
( 2014;). Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol64755–761 [View Article][PubMed]
.
MartínkováL.,
UhnákováB.,
PátekM.,
NešveraJ.,
KřenV.
( 2009;). Biodegradation potential of the genus Rhodococcus
. Environ Int35162–177 [View Article][PubMed]
.
MesbahM.,
WhitmanW. B.
( 1989;). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J Chromatogr A479297–306 [View Article][PubMed]
.
RoachP.C.J.,
RamsdenD. K.,
HughesJ.,
WilliamsP.
( 2003;). Development of a conductimetric biosensor using immobilised Rhodococcus ruber whole cells for the detection and quantification of acrylonitrile. Biosens Bioelectron1973–78 [View Article][PubMed]
.
ScholtzR.,
LeisingerT.,
SuterF.,
CookA. M.
( 1987a;). Characterization of 1-chlorohexane halidohydrolase, a dehalogenase of wide substrate range from an Arthrobacter sp. J Bacteriol1695016–5021[PubMed].
ScholtzR.,
SchmuckleA.,
CookA. M.,
LeisingerT.
( 1987b;). Degradation of eighteen 1-monohaloalkanes by Arthrobacter sp. strain HA1. J Gen Microbiol133267–274.
ScholtzR.,
MessiF.,
LeisingerT.,
CookA. M.
( 1988;). Three dehalogenases and physiological restraints in the biodegradation of haloalkanes by Arthrobacter sp. strain HA1. Appl Environ Microbiol543034–3038[PubMed].
SchumannP.
( 2011;). Peptidoglycan structure. . In Taxonomy of Prokaryotes, Methods in Microbiologyvol. 38, pp. 101–129. Edited by
RaineyF.,
OrenA.
London:
Academic Press;
[View Article].
TáncsicsA.,
BenedekT.,
FarkasM.,
MáthéI.,
MárialigetiK.,
SzoboszlayS.,
KukolyaJ.,
KrisztB.
( 2014;). Sequence analysis of 16S rRNA, gyrB and catA genes and DNA-DNA hybridization reveal that Rhodococcus jialingiae is a later synonym of Rhodococcus qingshengii
. Int J Syst Evol Microbiol64298–301 [View Article][PubMed]
.
TindallB. J.
( 1990b;). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol13128–130 [View Article].
VojtkováH.,
MašlaňováI.,
SedláčekI.,
ŠvanováP.,
JanulkováR.
( 2012;). Removal of heavy metals from wastewater by a Rhodococcus sp. bacterial strain. . In 12th International Multidisciplinary Scientific GeoConference SGEM
SGEM Conference Proceedings, vol. 5. Sofia STEF92 Technology. pp. 685–691. Albena, Bulgaria .