Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine

Gordonia metallireducens sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream

A polyphasic taxonomic study was carried out on strain TSed Te1T, isolated from sediment of a stream contaminated with acid drainage from a coal mine. The bacterium forms pink-pigmented colonies and has a rod-coccus growth cycle, which also includes some coryneform arrangements. This bacterium is capable of growing in the presence of up to 750 μg ml-1 tellurite and 5000 μg ml-1 selenite, reducing each to elemental form. Nearly complete 16S rRNA gene sequence analysis associated the strain with Gordonia, with 99.5 and 99.3 % similarity to Gordonia namibiensis and Gordonia rubripertincta, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization comparisons with the closest phylogenetic neighbour of TSed Te1T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids were C16 : 0, C18 : 1, C16 : 1 and tuberculostearic acid. The DNA G+C content was 67.6 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside, while MK-9(H2) was the only menaquinone found. Mycolic acids of C56-C60 were present. Whole-cell hydrolysates contained meso-diaminopimelic acid along with arabinose and galactose as the major cell-wall sugars. On the basis of the results obtained in this study, the bacterium was assigned to the genus Gordonia and represents a new species with the name Gordonia metallireducens sp. nov. The type strain is TSed Te1T (=NRRL B-65678T=DSM 114093T).

Characterization of pyridine biodegradation by two Enterobacter sp. strains immobilized on Solidago canadensis L. stem derived biochar

In this study, two pyridine-degrading strains namely Enterobacter cloacae complex sp. BD17 and Enterobacter sp.BD19 were isolated from the aerobic tank of a pesticide wastewater treatment plant. The mixed bacteria H4 composed of BD17 and BD19 at a ratio of 1:1 was immobilized by Solidago canadensis L. stem biochar with a dosage of 2 g·L^-1. The highest pyridine removal rate of 91.70% was achieved by the immobilized H4 at an initial pyridine concentration of 200 mg·L^-1, pH of 7.0, temperature of 28 °C and salinity of 3.0% within 36 h. The main intermediates of pyridine degradation by BD17 were pyridine-2-carboxamide, 2-aminopropanediamide, and 2-aminoacetamide, while 2-picolinic acid, isopropyl acetate, isopropyl alcohol, and acetaldehyde were identified with BD19 by adopting GC-MS technique. Interestingly, there was a possibility of totally mineralization of pyridine and the corresponding degradation pathways of BD17 and BD19 were revealed for the first time.

Microbial Degradation of Pyridine: a Complete Pathway in Arthrobacter sp. Strain 68b Deciphered

Pyridine and its derivatives constitute the majority of heterocyclic aromatic compounds that occur largely as a result of human activities and contribute to environmental pollution. It is known that they can be degraded by various bacteria in the environment; however, the degradation of unsubstituted pyridine has not yet been completely resolved. In this study, we present data on the pyridine catabolic pathway in Arthrobacter sp. strain 68b at the level of genes, enzymes, and metabolites. The pyr gene cluster, responsible for the degradation of pyridine, was identified in a catabolic plasmid, p2MP. The pathway of pyridine metabolism consisted of four enzymatic steps and ended by the formation of succinic acid. The first step in the degradation of pyridine proceeds through a direct ring cleavage catalyzed by a two-component flavin-dependent monooxygenase system, encoded by pyrA (pyridine monooxygenase) and pyrE genes. The genes pyrB, pyrC, and pyrD were found to encode (Z)-N-(4-oxobut-1-enyl)formamide dehydrogenase, amidohydrolase, and succinate semialdehyde dehydrogenase, respectively. These enzymes participate in the subsequent steps of pyridine degradation. The metabolites of these enzymatic reactions were identified, and this allowed us to reconstruct the entire pyridine catabolism pathway in Arthrobacter sp. 68b.IMPORTANCE The biodegradation pathway of pyridine, a notorious toxicant, is relatively unexplored, as no genetic data related to this process have ever been presented. In this paper, we describe the plasmid-borne pyr gene cluster, which includes the complete set of genes responsible for the degradation of pyridine. A key enzyme, the monooxygenase PyrA, which is responsible for the first step of the catabolic pathway, performs an oxidative cleavage of the pyridine ring without typical activation steps such as reduction or hydroxylation of the heterocycle. This work provides new insights into the metabolism of N-heterocyclic compounds in nature.

Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant

Two novel actinobacteria, designated NBRC 107696^T and NBRC 107697^T, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and meso-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H₂) and the major fatty acids were C_{16  :  0}, C_18 : 1ω9c and C_16 : 1ω7c. The DNA G+C contents of NBRC 107696^T and NBRC 107697^T were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696^T and NBRC 107697^T were a clade with members of the genus Gordonia. The highest 16S rRNA gene sequence similarity values were obtained with Gordonia araii IFM 10211^T (98.9 %) for NBRC 107697^T, and Gordonia malaquae IMMIB WWCC-22^T, Gordonia neofelifaecis AD-6^T and Gordonia humi CC-12301^T (98.1 %) for NBRC 107696^T, respectively. The digital DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are Gordonia spumicola sp. nov. and Gordonia crocea sp. nov., and the type strains are NBRC 107696^T (=IFM 10067^T=TBRC 11239^T) and NBRC 107697^T (=IFM 10881^T=TBRC 11240^T), respectively.

An insight into the ecology, diversity and adaptations of Gordonia species

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

Gordonia iterans sp. nov., isolated from a patient with pneumonia

A second novel clinical actinobacterial strain, designated IFM 10348T, was isolated from the sputum of the same Japanese patient with bacterial pneumonia from whom the type strain of Gordonia araii had been isolated. The strains differed in phylogenetic position and drug-resistance profiles. The taxonomic position of strain IFM 10348T was clarified by phenotypic, chemotaxonomic and phylogenetic studies. Phylogenetic analyses based on 16S rRNA gene sequences clearly demonstrated that strain IFM 10348T occupied a distinct clade within the genus Gordonia and was related closely to Gordonia malaquae DSM 45064T and Gordonia hirsuta DSM 44140T (97.3 and 97.1 % similarities, respectively). Strain IFM 10348T was also clearly differentiated from G. malaquae DSM 45064T and G. hirsuta DSM 44140T based on gyrB and secA1 gene sequence similarity values. Strain IFM 10348T had MK-9(H2) as the predominant menaquonine, contained meso-diaminopimelic acid, arabinose, galactose and glucosamine as cell-wall components, and contained C18 : 1ω9c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major cellular fatty acids. Mycolic acids were present. The DNA G+C content of strain IFM 10348T was 68.0 mol%. DNA–DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that strain IFM 10348T represents a novel species of the genus Gordonia , for which the name Gordonia iterans sp. nov. is proposed. The type strain is IFM 10348T ( = CCTCC M2011245T = NCCB 100436T).

Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment

A Gram-stain-positive, non-motile, aerobic actinobacterium, designated strain CJ10T, was isolated from tidal flat sediment from the Yellow Sea in South Korea. Strain CJ10T grew on tryptic soy agar in the presence of 0–4 % (w/v) NaCl (optimum growth in the absence of NaCl) and at pH 6–11 (optimum pH 9). On the basis of 16S rRNA gene sequence analysis, strain CJ10T belonged to the genus Gordonia and showed the highest sequence similarity to Gordonia hirsuta DSM 44140T (97.9 %) and Gordonia hydrophobica DSM 44015T (97.6 %). DNA–DNA relatedness levels of strain CJ10T were 47.4 % (CJ10T as probe) and 42.2 % ( G. hirsuta DSM 44140T as probe) to G. hirsuta DSM 44140T and 8.6 % (CJ10T as probe) and 9.3 % ( G. hydrophobica DSM 44015T as probe) to G. hydrophobica DSM 44015T. The major isoprenoid quinone was MK-9(H2). The polar lipid profile of strain CJ10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were C18 : 1ω9c (38.0 %), C16 : 0 (30.1 %) and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 17.4 %). The DNA G+C content was 67.7 mol%. Therefore, the results from our polyphasic taxonomic study suggest that strain CJ10T represents a novel species in the genus Gordonia , for which the name Gordonia alkaliphila sp. nov. is proposed; the type strain is CJ10T ( = KACC 16561T  = JCM 18077T).

Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal

Two Gram-stain-positive, non-endospore-forming actinobacteria (Ca8Tand Ca14) were isolated from a bioreactor with extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strains Ca8T and Ca14 were shown to belong to the genus Gordonia and were most closely related to Gordonia hirsuta DSM 44140T (98.0 % sequence similarity) and Gordonia hydrophobica DSM 44015T (97.2 %). In comparison with the sequences of the type strains of all other species of the genus Gordonia tested, similarities were below 97 %. The quinone systems of the strains were determined to consist predominantly of MK-9H2. The polar lipid profile for both organisms consisted of diphosphatidylglycerol, phosphatidylglycerol, phospatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Whole-organism hydrolysates contained meso-diaminopimelic acid as the diamino acid of the peptidoglycan; mycolic acids were detected as well. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis-9, C16 : 0 and C18 : 1 and tuberculostearic acid strongly supported the grouping of strains Ca8T and Ca14 into the genus Gordonia . The two strains showed a DNA–DNA similarity of 96 %. DNA–DNA hybridizations of strain Ca8T with G. hirsuta DSM 44140T and G. hydrophobica DSM 44015T resulted in values of 26.3 and 25.0 %, respectively. These results and those of the physiological and biochemical tests allowed a clear phenotypic differentiation of strains Ca8T and Ca14 from the most closely related species of the genus Gordonia . It is concluded that strains Ca8T and Ca14 represent a novel species, for which the name Gordonia phosphorivorans sp. nov. is proposed, with the type strain Ca8T ( = DSM 45630T = CCUG 61533T = CCM 7957T = LMG 26648T).

The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential

This review about the genus Gordonia provides a current overview of recent research on a young genus that was introduced in the year 1997 ( Stackebrandt et al., 1997 ). This emerging genus has attracted increasing environmental, industrial, biotechnological and medical interest during the last few years, in particular due to the capabilities of its members to degrade, transform, and synthesize organic compounds as well as to the pathogenic effects that have been described in many case studies. The number of publications about Gordonia has increased significantly after the year 2004 (the year of the first Gordonia review published by Arenskötter et al.) describing 13 new validly published species (type strains), many newly described physiological and metabolic capabilities, new patent applications and many new case reports of bacterial infections. Members of the genus Gordonia are widely distributed in nature and it is therefore important to unravel the species richness and metabolic potential of gordoniae in future studies to demonstrate their environmental impact especially on the degradation of persistent organic compounds and their ecological participation in the carbon cycle of organic material in soil and water. This review summarizes mainly the current state of importance and potential of the members of this genus for the environmental and biotechnological industry ("the strengthsâ) and briefly its pathogenic impact to humans ("the weaknessesâ).

Gordonia humi sp. nov., isolated from soil

A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301T) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301T was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H2), minor amounts of MK-8(H2) and MK-7(H2). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis9, C16 : 0, C18 : 1 and tuberculostearic acid (10-methyl C18 : 0), supported the affiliation of strain CC-12301T to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301T from the most closely related Gordonia species. Strain CC-12301T therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301T (=DSM 45298T =CCM 7727T).

Complete genome sequence of Gordonia bronchialis type strain (3410)

Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Transfer of megaplasmid pKB1 from the rubber-degrading bacterium Gordonia westfalica strain Kb1 to related bacteria and its modification

Because engineering of the 101.016-bp megaplasmid pKB1 of Gordonia westfalica Kb1 failed due to the absence of an effective transfer system, pKB1 was transferred by conjugation from G. westfalica Kb1 to a kanamycin-resistant mutant of Rhodococcus opacus PD630 at a frequency of about 6.2 x 10(-8) events per recipient cell. Furthermore, pKB1 was transferred to G. polyisoprenivorans strains VH2 and Y2K and to Mycobacterium smegmatis by electroporation at frequencies of 5.5 x 10(3), 1.9 x 10(3), and 8.3 x 10(2) transformants per microgram plasmid DNA. The pKB1-encoded cadmium resistance gene cadA was used for selection in these experiments. Recombinant pKB1-containing G. polyisoprenivorans VH2 and M. smegmatis were then used to engineer pKB1. A kanamycin resistance cassette was inserted into the pKB1-encoded cadA gene, ligated to suicide plasmid pBBR1MCS-5, and the resulting plasmid was electroporated into plasmid-harboring strains. Homologous recombination between cadA on suicide plasmid and the respective sequence in pKB1 led to its integration into pKB1. Thus, two selection markers were accommodated in pKB1 to monitor plasmid transfer into Gordonia and related taxa for analysis of genes essential for rubber degradation and others. In this study, two transfer methods for large plasmids and strategies for engineering of pKB1 were successfully applied, thereby, extending the tool box for Gordonia.

Degradation of pyridine and 4-methylpyridine by Gordonia terrea IIPN1

Gordonia terrea IIPN1 was isolated and characterized from soils collected at petroleum drilling sites. The strain was able to catabolize pyridine and 4-methylpyridine as sole carbon and nitrogen source. The strain failed to catabolize other pyridine derivatives. Growing cells completely degraded 30 mM of pyridine in 120 h with growth yield of 0.29 g g(-1). Resting Cells grown on 5 mM pyridine degraded 4-methylpyridine without a lag time and vice versa. Supplementary carbon and nitrogen source did not significantly change the specific growth rate and degradation rate by the resting cells.

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).

Effect of the synthesized mycolic acid on the biodegradation of diesel oil by Gordonia nitida strain LE31

The dynamics of diesel oil biodegradation were previously investigated at initial substrate concentrations of 1000 to 20,000 ppm using Gordonia nitida isolated from wastewater. Following the gas chromatogram profiles of diesel oil degradation, diesel oil with concentrations of up to 15,000 ppm was efficiently degraded by this strain. At a concentrations of 20,000 ppm, however, the degradation by this strain was not effective. The enhancement of the biodegradation of diesel oi1 (at 15,000 and 20,000 ppm) by a synthetic mycolic acid biosurfactant (at 9, 90 and 900 ppm) was also investigated. In G. nitida inoculated cultures, the degradation of diesel oil was enhanced by the biosurfactant. For comparison, diesel oil degradation in batch incubations was measured after the addition of rhamnolipid and other surfactants. Synthetic mycolic acid enhanced the degradation to a greater extent than any other surfactant tested. Additionally, it was demonstrated that the degradation-enhancing property of synthetic mycolic acid was similar to that of rhamnolipid and Tween 80.

Pathways in the Degradation of Hydrolyzed Alcohols of Butyl Benzyl Phthalate in Metabolically Diverse Gordonia sp.Strain MTCC 4818

In the present study, the metabolic pathways involved in the degradation of benzyl alcohol and 1-butanol, the hydrolyzed products of butyl benzyl phthalate, were investigated by the Gordonia sp. strain MTCC 4818. The strain can utilize both benzyl alcohol and 1-butanol individually as sole carbon sources, where benzyl alcohol was found to be metabolized via benzaldehyde, benzoic acid and catechol, which was further degraded by ortho-cleavage dioxygenase to cis,cis-muconic acid and subsequently to muconolactone leading to tricarboxylic acid cycle. On the other hand, 1-butanol was metabolized via butyraldehyde and butyric acid, which was channeled into the tricarboxylic acid cycle via the beta-oxidation pathway. Numbers of dehydrogenases, both NAD+-dependent and NAD+-independent, were found to be involved in the degradation of benzyl alcohol and 1-butanol, where several dehydrogenases exhibited relaxed substrate specificity. Both 2,3- and 3,4-dihydroxybenzoic acids were utilized by the test organism for growth and metabolized by the ortho-cleavage pathway by the cell-free extract of benzoate-grown cells, similar to catechol, suggesting possible broad substrate specificity of the ring cleavage dioxygenase. Moreover, the test organism can utilize various primary and secondary alcohols, aliphatic aldehydes and acids in the C2-C5 range besides n-hexadecane, 1,4-butanediol and cyclohexanol individually as the sole carbon sources indicating metabolic diversity in the Gordonia sp. strain MTCC 4818.

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).

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.

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.

Characterization of the 101-kilobase-pair megaplasmid pKB1, isolated from the rubber-degrading bacterium Gordonia westfalica Kb1

The complete sequence of the circular 101,016-bp megaplasmid pKB1 from the cis-1,4-polyisoprene-degrading bacterium Gordonia westfalica Kb1, which represents the first described extrachromosomal DNA of a member of this genus, was determined. Plasmid pKB1 harbors 105 open reading frames. The predicted products of 46 of these are significantly related to proteins of known function. Plasmid pKB1 is organized into three functional regions that are flanked by insertion sequence (IS) elements: (i) a replication and putative partitioning region, (ii) a putative metabolic region, and (iii) a large putative conjugative transfer region, which is interrupted by an additional IS element. Southern hybridization experiments revealed the presence of another copy of this conjugational transfer region on the bacterial chromosome. The origin of replication (oriV) of pKB1 was identified and used for construction of Escherichia coli-Gordonia shuttle vectors, which was also suitable for several other Gordonia species and related genera. The metabolic region included the heavy-metal resistance gene cadA, encoding a P-type ATPase. Expression of cadA in E. coli mediated resistance to cadmium, but not to zinc, and decreased the cellular content of cadmium in this host. When G. westfalica strain Kb1 was cured of plasmid pKB1, the resulting derivative strains exhibited slightly decreased cadmium resistance. Furthermore, they had lost the ability to use isoprene rubber as a sole source of carbon and energy, suggesting that genes essential for rubber degradation are encoded by pKB1.

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 namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand

A polyphasic approach was used to establish the taxonomic position of two actinomycetes isolated from a Namibian soil and shown to utilise nitrile compounds as growth substrates. The organisms, strains NAM-BN063AT and NAM-BN063B, had chemical and morphological properties consistent with their assignment to the genus Gordonia. Direct 165 rRNA sequencing studies confirmed the taxonomic position of the strains following the generation of phylogenetic trees using four different algorithms. The strains consistently formed a distinct phylogenetic line within the evolutionary radiation occupied by gordoniae and were most closely related to Gordonia rubropertincta DSM 43197T. DNA:DNA relatedness studies indicated that the two organisms belonged to a genomic species that was readily distinguished from G. rubropertincta. The unique phenotypic profile of the strains sharply separated them from representatives of all of the validly described species of Gordonia. The combination of genotypic and phenotypic data indicates that the two strains should be classified in the genus Gordonia as a new species. The name proposed for this taxon is Gordonia namibiensis, the type strain is NAM-BN063AT (= DSM 44568T = NCIMB 13780T).

Degradation of 3-methylpyridine and 3-ethylpyridine by Gordonia nitida LE31

Cells of Gordonia nitida LE31 grown on 3-methylpyridine degraded 3-ethylpyridine without a lag time and vice versa. Cyclic intermediates were not detected, but formic acid was identified as a metabolite. Degradation of levulinic acid was induced in cells grown on 3-methylpyridine and 3-ethylpyridine. Levulinic aldehyde dehydrogenase and formamidase activities were higher in cells grown on 3-methylpyridine and 3-ethylpyridine than in cells grown on acetate. These data indicate that 3-methylpyridine and 3-ethylpyridine were degraded via a new pathway involving C-2-C-3 ring cleavage.