Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water

The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA-DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography-mass spectrometry (GC-MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution.

Biodegradation of di-n-butyl phthalate by an isolated Gordonia sp. strain QH-11: Genetic identification and degradation kinetics

Di-n-butyl phthalate (DBP) is one of the most widely used phthalic acid esters (PAEs), which have shown increasing environmental concerns worldwide. A bacterial strain designated as QH-11, was isolated from activated sludge and found to be capable of utilizing DBP as carbon and energy sources for growth. 16S rRNA and gyrb gene sequence analysis revealed that strain QH-11 was most closely related to Gordonia sp. Kinetics studies of DBP degradation by the strain QH-11 revealed that DBP depletion curves fit with the modified Gompertz model (R(2)>0.98). Meanwhile, substrate utilization tests showed that strain QH-11 could utilize other common PAEs and also the main intermediate product phthalic acid (PA). A gene encoding the large subunit of the phthalate dioxygenase, which is responsible for PA degradation, was successfully detected in strain QH-11. Furthermore, the results of reverse transcription quantitative PCR demonstrate that mRNA expression level of phthalate dioxygenase increased significantly after strain QH-11 was induced by DBP and PA.

[Identification and degradation capability of three pyrene-degrading Gordonia sp. strains]

Three pyrene-degrading bacterial strains named D44, D82S and D82Q were isolated from PAHs-contaminated soil in Shenfu Irrigation Area of Shenyang, Northeast China. The strains were identified as Gordonia sp., based on the morphological observation, physiological and biochemical identification, and phylogenetical analysis of 16S rDNA sequences. For all the three stains, their optimal pH was 7, and their growth was obviously inhibited when the pH was lower than 5 or higher than 9. The three strains were capable of utilizing pyrene, benzo[a] pyrene, anthracene, naphthalene, phenanthrene, and fluoranthene as the sole source of carbon and energy. After seven days incubation, the three strains could degrade more than 65% of pyrene with an initial concentration 100 mg x L(-1), and the D44, D82S, and D82Q could degrade 79.6%, 91.3%, and 62.8% of benzo[a] pyrene with an initial concentration 50 mg x L(-1), respectively. PCR amplification indicated that the strains D82Q and D82S possessed alkane monooxygenase gene alkB.

[Isolation and identification of a hydrocarbon-degrading bacterium Gordonia sp. S14-10 from the surface water of Atlantic Ocean and analysis on its related characteristics]

OBJECTIVE

The aim of this study is to isolate novel and efficient hydrocarbon-degrading bacteria (HDBs) from pelagic ocean.

METHODS

The surface water sample from Atlantic Ocean was enriched in NH medium with crude oil:diesel oil (in a ratio of 1:1) as the sole carbon source. HDBs were isolated and their degradation ability was tested in MMC medium, and further subjected to genotypic and phenotypic analysis. Polymerase chain reaction with degenerate primers was performed to detect the genes encoding integral-membrane non-heme iron monooxygenase (AlkB) and cytochrome P450 CYP153 family. Meanwhile, the production of biosurfactant was examined by surface tension measurement, then extracted and purified for component characterization.

RESULTS

A hydrocarbon-degrading bacterium named S14-10 was obtained,which can utilize C10 - C36 as the sole carbon source. Analysis of 16S rRNA sequence showed that it belonged to Gordonia genus showing the highest similarity (99.86%) with type strain of Gordonia terraeT, while secA1 sequence showed a low identity only 93.69%. Furthermore, two genes alkB and CYP153 P450 were obtained with PCR, which had highest similarities 88.76% and 99.61% to that of Gordonia sp. TF6, respectively. In addition, strain S14-10 was found to produce glycolipid biosurfactant,which lowered the surface tension of water to 31.6 mN/m.

CONCLUSION

Strain S14-10 is possibly a novel species of Gordonia, and the first hydrocarbon-degrading bacterium isolated from open sea. It has potential in bioremediation of oil contaminated environment.

Oil spill remediation by using the remediation agent JE1058BS that contains a biosurfactant produced by Gordonia sp. strain JE-1058

A remediation agent containing a biosurfactant was prepared by spray drying the sterilized culture broth of Gordonia sp. strain JE-1058, and the agent was designated as JE1058BS. On subjection to the baffled flask test developed by the United States Environmental Protection Agency, JE1058BS showed a strong potential to be applied as an oil spill dispersant even in the absence of a solvent. It also proved to be an effective bioremediation agent for the remediation of oil spills at sea. The addition of JE1058BS to seawater stimulated the degradation of weathered crude oil (ANS 521) via the activity of the indigenous marine bacteria. Its addition also stimulated the removal of crude oil from the surface of contaminated sea sand. These results indicate that biosurfactant-containing JE1058BS has a strong potential to be applied as a remediation agent for the clean-up of oil spills at sea and on shorelines.

Biocatalytic Desulfurization of Diesel Oil in an Air-Lift Reactor with Immobilized Gordonia nitida CYKS1 Cells

A new type of air-lift reactor with immobilized Gordonia nitida CYKS1 cells on a fibrous support was designed and used for the biocatalytic desulfurization (BDS) of diesel oil. Its performance was evaluated at different phase ratios of the oil to the aqueous medium (or oil phase fractions) and different sucrose concentrations. When the reaction mixture contained 10% diesel oil (v/v), 61-67% of sulfur was removed as the sulfur content decreased from 202-250 to 76-90 mg L(-1) in 72 h. The sulfur content did not decrease any further because the remaining sulfur compounds were recalcitrant to BDS. During the desulfurization, the strain CYKS1 consumed hydrocarbons in the diesel oil, mainly n-alkanes with 10-26 carbons, as carbon source even though an easily available carbon source, sucrose, was supplied.

Detection of filamentous genus Gordonia in foam samples using genus-specific primers combined with PCR – denaturing gradient gel electrophoresis analysis

A nested-PCR amplification combined with denaturing gradient gel electrophoresis (PCR–DGGE) approach was used to detect and identify Gordonia populations from wastewater treatment plant foam samples. The PCR-amplified region (position 722–1119) by specifically designed primers G699F and G1096R covered the hypervariable region of the Gordonia 16S rRNA gene sequence. This approach successfully distinguished Gordonia species to the interspecies level. The differential ability of PCR–DGGE analysis was effectively used to separate 12 Gordonia species belonging to different 16S rRNA gene-based phylogenetic lineages into 8 groups. Based on this method, the minimum limit of Gordonia detection was 5 × 104CFU·g–1in the seeded soil samples. The PCR–DGGE bands obtained were excised and identified by sequence analysis. Gordonia polyisoprenivorans , Gordonia amicalis , DGGE type II Gordonia species, and an uncertain Gordonia species dominated the activated sludge foam samples. Results of this study indicate that the detection and analyses of genus Gordonia within a complex microbial community could be accomplished using the PCR–DGGE approach to a larger extent, with certain limitations. Detection of diverse Gordonia populations in foam samples from wastewater treatment plants revealed the significant role of Gordonia in biological foaming during wastewater treatment. The nested-PCR amplification and DGGE can be used as a diagnostic tool for the early detection of foaming incidents in wastewater treatment plants using Gordonia as indicator organism.

Gordonia shandongensis sp. nov., isolated from soil in China

The taxonomic position of strain SD29T, isolated from soil, was clarified using a polyphasic taxonomic approach. The organism produced an elementary branching mycelium which fragmented into rod/coccus-shaped elements and it possessed meso-diaminopimelic acid, arabinose, galactose as diagnostic diamino acid and sugars, MK-9(H2) as predominant menaquinone, phospholipids of type PII and mycolic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SD29T was most closely related to Gordonia hydrophobica DSM 44015T and Gordonia sihwensis DSM 44576T, forming a distinct but loosely related branch in the phylogenetic tree. A number of physiological properties readily separated the isolate from its nearest neighbours. It is evident from genotypic and phenotypic data that strain SD29T represents a novel species of the genus Gordonia, for which the name Gordonia shandongensis sp. nov. is proposed. The type strain is SD29T (=CGMCC 4.3492T=JCM 13907T).

Gordonia soli sp. nov., a novel actinomycete isolated from soil

A soil isolate, strain CC-AB07T, was characterized using a polyphasic approach. This organism had chemotaxonomic and morphological properties consistent with its classification in the genusGordonia. 16S rRNA gene sequence analysis showed that the novel strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genusGordonia, its closest neighbours being the type strains ofGordonia alkanivorans,Gordonia amicalis,Gordonia bronchialis,Gordonia desulfuricans,Gordonia polyisoprenivoransandGordonia rhizosphera. The novel isolate was distinguished from all of these type strains using a range of phenotypic properties and bygyrBgene sequence analysis. It was evident from the genotypic and phenotypic data that strain CC-AB07Tshould be classified as representing a novel species in the genusGordonia, for which the nameGordonia solisp. nov. is proposed. The type strain is CC-AB07T(=BCRC 16810T=DSM 44995T).

Etiological misidentification by routine biochemical tests of bacteremia caused by Gordonia terrae infection in the course of an episode of acute cholecystitis

Gordonia terrae has been reported to be a rare cause of bacteremia. We report the first case of bacteremia associated with acute cholecystitis. Commercial biochemical testing was not able to identify the strain at the genus level, classifying it instead as Rhodococcus sp. Definitive identification was obtained by sequencing of the 16S rRNA gene.

Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam

Three strains of non-motile, Gram-positive, filamentous actinomycetes, isolates J4T, J5 and J59, initially recognized microscopically in activated sludge foam by their distinctive branching patterns, were isolated by micromanipulation. The taxonomic positions of the isolates were determined using a polyphasic approach. Almost-complete 16S rRNA gene sequences of the isolates were aligned with corresponding sequences of representatives of the suborder Corynebacterineae and phylogenetic trees were inferred using three tree-making algorithms. The organisms formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. The three isolates showed 16S rRNA gene sequence similarities within the range 96.9–97.2 % with their nearest phylogenetic neighbours, namely Gordonia bronchialis DSM 43247T and Gordonia terrae DSM 43249T. Strain J4T was shown to have a chemotaxonomic profile typical of the genus Gordonia and was readily distinguished from representatives of the genus on the basis of Curie-point pyrolysis mass spectrometric data. The isolates shared nearly identical phenotypic profiles that distinguished them from representatives of the most closely related Gordonia species. It is evident from the genotypic and phenotypic data that the three isolates belong to a novel Gordonia species. The name proposed for this taxon is Gordonia defluvii sp. nov.; the type strain is J4T (=DSM 44981T=NCIMB 14149T).

Native valve endocarditis due to Gordonia polyisoprenivorans: case report and review of literature of bloodstream infections caused by Gordonia species

We report the first case of endocarditis caused by Gordonia polyisoprenivorans and concisely review the English literature regarding bloodstream infections caused by Gordonia species.

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC-mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen compounds as the sole sulfur or nitrogen sources. Resting-cell studies indicated that desulfurization occurs either in cell-associated or in cell-free extracts of F.5.25.8. The biological responses of F.5.25.8 to a series of mutagens and environmental agents were also characterized. The results revealed that this strain is highly tolerant to DNA damage and also refractory to induced mutagenesis. Strain F.5.25.8 was also characterized genetically. Results showed that genes involved in desulfurization (dsz) are located in the chromosome, and PCR amplification was observed with primers dszA and dszB designed based on Rhodococcus genes. However, no amplification product was observed with the primer based on dszC.

[Isolation and characterization of a benzothiophene-desulfurizing bacterium]

A benzothiophene-desulfurizing strain was isolated and identified as Gordonia sp. C-6, which could degrade benzothiophene (BT) in a way analogous to the 4S pathway. It was found strain C-6 had the ability to grow in KT-BT medium whose sole source of sulfur was BT or its derivatives, whereas it couldn't grow well in a medium with DBT and its derivatives as the sole source of sulfur, the desulfurized product was identified as 2-(2'-hydroxyphenyl) ethan-1-al or its isomer benzofuran by GC-MS analysis. Desulfurization activity of strain C-6 was investigated. About 0.15mmol/L(50%) BT was desulfurized by strain C-6 after it was incubated in KT-BT medium at 30 degrees C for 48h, the residual BT has volatilized during aerobic fermentation. The quantitative detection of the benzothiophene-desulfurizing products was established with o-hydroxyphenylacetic acid as standard compound, the standard curve was fitted by Matlab.

Mineralization of the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia and Williamsia spp

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a cyclic nitroamine explosive that is a major component in many military high-explosive formulations. In this study, two aerobic bacteria that are capable of using RDX as the sole source of carbon and nitrogen to support their growth were isolated from surface soil. These bacterial strains were identified by their fatty acid profiles and 16S ribosomal gene sequences as Williamsia sp. KTR4 and Gordonia sp. KTR9. The physiology of each strain was characterized with respect to the rates of RDX degradation and [U-14C]RDX mineralization when RDX was supplied as a sole carbon and nitrogen source in the presence and absence of competing carbon and nitrogen sources. Strains KTR4 and KTR9 degraded 180 microM RDX within 72 h when RDX served as the only added carbon and nitrogen source while growing to total protein concentrations of 18.6 and 16.5 microg/ml, respectively. Mineralization of [U-14C]RDX to 14CO2 was 30% by strain KTR4 and 27% by KTR9 when RDX was the only added source of carbon and nitrogen. The addition of (NH4)2SO4- greatly inhibited KTR9's degradation of RDX but had little effect on that of KTR4. These are the first two pure bacterial cultures isolated that are able to use RDX as a sole carbon and nitrogen source. These two genera possess different physiologies with respect to RDX mineralization, and each can serve as a useful microbiological model for the study of RDX biodegradation with regard to physiology, biochemistry, and genetics.

Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene

Members of the metabolically diverse genus Gordonia were isolated from various biotopes including pristine and polluted sites around Taiwan. Identification, comparison and diversity assessment based on the gyrB gene were carried out using a newly developed primer pair for gyrB. The 16S rRNA gene was also sequenced for comparison. A 1.2-kb fragment of the gyrB gene of 17 Gordonia strains including type strains was determined by direct sequencing of PCR amplified fragments. A total of 25 strains (8 of which were retrieved from a public database) of the genus Gordonia form a distinct phyletic line in the GyrB-based tree and are separated from other closely related species of genera of the suborder Corynebacterineae. Sequence similarity of the gyrB sequence from twelve Gordonia type strains ranged from 79.3 to 97.2%, corresponding to between 270 and 41 nucleotide differences, while there was only a 0.3-3.8% difference in 16S rRNA gene sequence similarity at the interspecies level. Phylogenetic analysis based on the GyrB sequence deduced from the gyrB gene is consistent with that of DNA-DNA hybridization results and provides a better discrimination within the species of Gordonia compared to the 16S rRNA gene. The present study demonstrates that gyrB gene analysis will aid in describing novel species belonging to the genus Gordonia.

Gordonia otitidis sp. nov., isolated from a patient with external otitis

The taxonomic positions of two clinically isolated actinomycetes were established using a polyphasic approach. The two strains, IFM 10032T, isolated from ear discharge of a 28-year-old Japanese female patient with external otitis, and IFM 10148, isolated from pleural fluid of a 60-year-old Japanese male patient with bronchitis, possessed meso-diaminopimelic acid as the diagnostic amino acid, MK-9(H2) as the predominant menaquinone and mycolic acids ranging from 58 to 64 carbons. The 16S rRNA gene sequences of the two strains were most closely related to those of Gordonia aichiensis, Gordonia sputi and ‘Gordonia jacobaea’. Differences in several phenotypic characteristics together with genotypic distinctiveness distinguish strains IFM 10032T and IFM 10148 from these three species. DNA–DNA hybridization results and the combination of genotypic and phenotypic data showed that the two strains belong to a single species, and merit recognition of a novel species within the genus Gordonia. The name proposed for this taxon is Gordonia otitidis sp. nov.; the type strain is IFM 10032T (=DSM 44809T=JCM 12355T=NBRC 100426T).

Recurrent breast abscess caused by Gordonia bronchialis in an immunocompetent patient

We present the first reported case of a recurrent breast infection caused by Gordonia bronchialis. The infection occurred in a 43-year-old immunocompetent female, and species level identification was obtained with 16S rRNA sequencing.

Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999

The name of the species Gordonia nitida is validly published but its type strain DSM 44499T shares high similarity based on 16S rRNA gene sequences with Gordonia alkanivorans DSM 44369T and Gordonia westfalica DSM 44215T. These three species obviously build up a distinct cluster within the genus Gordonia. In the present paper, data from the literature concerning the three Gordonia species were reviewed and the genetic similarity of G. nitida DSM 44499T and G. alkanivorans DSM 44369T was further investigated by DNA–DNA-hybridization experiments, revealing approximately 80 % DNA–DNA relatedness. Even though the two type strains could be differentiated by automated ribotyping, it is proposed that, according to the rules of priority, G. nitida is a later synonym of G. alkanivorans.

Novel actinobacteria from marine sponges

Actinobacteria exclusively within the sub-class Acidimicrobidae were shown by 16S rDNA community analysis to be major components of the bacterial community associated with two sponge species in the genus Xestospongia. Four groups of Actinobacteria were identified in Xestospongia spp., with three of these four groups being found in both Xestospongia muta from Key Largo, Florida and Xestospongia testudinaria from Manado, Indonesia. This suggests that these groups are true symbionts in these sponges and may play a common role in both the Pacific and Atlantic sponge species. The fourth group was found only in X. testudinaria and was a novel assemblage distantly related to any previously sequenced actinobacterial clones. The only actinobacteria that were obtained in initial culturing attempts were Gordonia, Micrococcus and Brachybacterium spp., none of which were represented in the clone libraries. The closest cultured actinobacteria to all the Acidimicrobidae clones from Xestospongia spp. are 'Microthrix parvicella' and Acidimicrobium spp. Xestospongia spp. can now be targeted as source material from which to culture novel Acidimicrobidae to investigate their potential as producers of bioactive compounds. Isolation of sponge-associated Acidimicrobidae will also make it possible to elucidate their role as sponge symbionts.

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Biodegradation of Maya crude oil fractions by bacterial strains and a defined mixed culture isolated from Cyperus laxus rhizosphere soil in a contaminated site

Ten bacterial strains were isolated by enrichment culture, using as carbon sources either aliphatics or an aromatic-polar mixture. Oxygen uptake rate was used as a criterion to determine culture transfer timing at each enrichment stage. Biodegradation of aliphatics (10,000 mg L(-1)) and an aromatic-polar mixture (5000 mg L(-1), 2:1) was evaluated for each of the bacterial strains and for a defined culture made up with a standardized mixture of the isolated strains. Degradation of total hydrocarbons (10,000 mg L(-1)) was also determined for the defined mixed culture. Five bacterial strains were able to degrade more than 50% of the aliphatic fraction. The most extensive biodegradation (74%) was obtained with strain Bs 9A, while strains Ps 2AP and UAM 10AP were able to degrade up to 15% of the aromatic-polar mixture. The defined mixed culture degraded 47% of the aliphatics and 6% of the aromatic-polar mixture. The defined mixed culture was able to degrade about 40% of the aliphatic fraction and 26% of the aromatic fraction when grown in the presence of total hydrocarbons, while these microorganisms did not consume the polar hydrocarbons fraction. The proposed strategy that combines enrichment culture together with oxygen uptake rate allowed the isolation of bacterial strains that are able to degrade specific hydrocarbons fractions at high consumption rates.

Isolation of carotenoid-deficient mutant from alkylated dibenzothiophene desulfurizing nocardioform bacteria, Gordonia sp. TM414

The dibenzothiophene-desulfurizing nocardioform bacteria, Gordonia sp. TM414, was isolated from oil-contaminated soil. To avoid coloration of the oil layer after the desulfurization reaction, which could decrease the quality of the oil, two colorless knock-out mutants, TPc and TPd, were isolated by using a broad-host-range transposon complex. Genomic sequence analysis revealed that the same gene was disrupted in these mutants and that the transposon-inserted gene was assigned as the gene for phytoene desaturase, crt I. The crt I mutants also showed desulfurization activity comparable to that of the parent strain in a model-oil/aqueous bi-phasic reaction, suggesting that the carotenoid production is not responsible for the bi-phasic desulfurization reaction that requires hydrophobic substrate incorporation from the organic phase.

Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well

The taxonomic position of an actinomycete, strain HD321(T), isolated from an oil-producing well of Daqing oilfield, was clarified using a polyphasic taxonomic approach. The strain possessed cell-wall chemotype IV, MK-9(H(2)) as the predominant menaquinone, relatively long-chain mycolic acids (52-62 carbon atoms) of the Gordonia type, straight-chain saturated and monounsaturated fatty acids and tuberculostearic acid. The G+C content of the DNA was 66 mol%. 16S rDNA analyses as well as chemotaxonomic and physiological properties indicated that strain HD321(T) represents a novel species within the genus Gordonia, for which the name Gordonia paraffinivorans sp. nov. is proposed; the type strain is HD321(T) (=AS 4.1730(T)=DSM 44604(T)).

Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor

A nitrate-reducing bacterium, strain SPR2(T), was isolated from a sulphur-oxidizing, autotrophic denitrification reactor used for advanced treatment of wastewater from the lake of Sihwa, Korea. The strain was aerobic but could grow under anaerobic conditions. It was Gram-positive, exhibited rough white colonies on complex nutrient agar, produced elementary branching hyphae that fragmented into rod/coccus-like elements and showed chemotaxonomic markers that were consistent with classification in the genus Gordonia, i.e. meso-diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates, N-glycolylmuramic acid in the peptidoglycan wall, unbranched saturated and monounsaturated fatty acids plus tuberculostearic acid (TBSA), mycolic acids that comprised 48-56 carbon atoms and MK-9(H(2)) as the predominant menaquinone. The 16S rDNA sequence of strain SPR2(T) showed highest similarity to Gordonia amicalis DSM 44461(T) and Gordonia hydrophobica DSM 44015(T), with values of 98.2 and 97.9 %, respectively. These values were far below 99.5 % (usually found at the intraspecies level) and they were in the range that separates species at the intrageneric level. The separate phylogenetic position of SPR2(T) was supported by differences in fatty acid and mycolic acid compositions and in carbon utilization tests that distinguished strain SPR2(T) from all known Gordonia species. Combined genotypic and phenotypic data show that strain SPR2(T) merits recognition as a novel species within the genus Gordonia, for which the name Gordonia sihwensis sp. nov. is proposed; the type strain is SPR2(T) (=DSM 44576(T)=NRRL B-24155(T)).

Gordonia sinesedis sp. nov., a novel soil isolate

The taxonomic position of an actinomycete isolated from soil was evaluated using a polyphasic approach. The organism, strain J72, was found to have chemical and morphological properties consistent with its assignment to the genus Gordonia. A nearly complete 16S rDNA sequence of the strain was determined by direct sequencing of the amplified gene. The tested strain formed a distinct phylogenetic line within the evolutionary radiation occupied by the genus Gordonia and was most closely related to G. polyisoprenivorans DSM 44302T. The phenotypic profile of strain 372 readily distinguishes it from representatives of the validly described species of Gordonia. The combined genotypic and phenotypic data show that strain J72 merits recognition as a new species of Gordonia. The name proposed for the new species is Gordonia sinesedis; the type strain is J72T (= DSM 44455T = NCIMB 13802T).

Degradation of car engine base oil by Rhodococcus sp. NDKK48 and Gordonia sp. NDKY76A

Two microorganisms (NDKK48 and NDKY76A) that degrade long-chain cyclic alkanes (c-alkanes) were isolated from soil samples. Strains NDKK48 and NDKY76A were identified as Rhodococcus sp. and Gordonia sp., respectively. Both strains used not only normal alkane (n-alkane) but also c-alkane as a sole carbon and energy source, and the strains degraded more than 27% of car engine base oil (1% addition).

Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete

A cis-1,4-polyisoprene-degrading bacterium (strain Kb2T) was isolated from foul water taken from the inside of a deteriorated automobile tyre found on a farmer's field in Westfalia, Germany. The strain was aerobic, Gram-positive, exhibited orange smooth and rough colonies on complex nutrient agar, produced elementary branching hyphae that fragmented into rod/coccus-like elements and showed chemotaxonomic markers which were consistent with its classification within the genus Gordonia, i.e. the presence of mesodiaminopimelic acid, arabinose and galactose in whole-cell hydrolysates (cell-wall chemotype IV), N-glycolylmuramic acid in the peptidoglycan wall, a fatty-acid pattern composed of unbranched saturated and monounsaturated fatty acids plus tuberculostearic acid, mycolic acids comprising 56-60 carbon atoms and MK-9(H2) as the only menaquinone. The 16S rDNA sequence of strain Kb2T was found to be most similar to the 16S rDNA sequences of the type strains of Gordonia alkanivorans (DSM 44369T) and Gordonia nitida (KCTC 0605BPT). However, DNA-DNA relatedness data showed that strain Kb2T ( =DSM 44215T NRRL B-24152T) could be distinguished from these two species and represented a new species within the genus Gordonia, for which the name Gordonia westfalica is proposed.