Steroid degradation gene cluster of Comamonas testosteroni consisting of 18 putative genes from meta-cleavage enzyme gene tesB to regulator gene tesR

Steroid degradation genes of Comamonas testosteroni TA441 are encoded in at least two gene clusters: one containing the meta-cleavage enzyme gene tesB and ORF1, 2, 3; and another consisting of ORF18, 17, tesI, H, A2, and tesA1, D, E, F, G (tesA2 to ORF18 and tesA1 to tesG are encoded in opposite directions). Analysis of transposon mutants with low steroid degradation revealed 13 ORFs and a gene (ORF4, 5, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32, 33, and tesR) involved in steroid degradation in the downstream region of ORF3. TesR, which is almost identical to that of TeiR, a positive regulator of Delta1-dehydrogenase (corresponds to TesH in TA441) and 3alpha-dehydrogenase (currently not identified in TA441), in C. testosteroni ATCC11996 (Pruneda-Paz, 2004), was shown to be necessary for induction of the steroid degradation gene clusters identified in TA441, tesB to tesR, tesA1 to tesG, and tesA2 to ORF18. At least some of the ORFs from ORF3 to ORF33 were suggested to be involved in 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid degradation.     

Isolation and identification of N2-fixing microorganisms from the rhizosphere of Capparis spinosa (L.)

Four bacterial strains, Pseudomonas stutzeri var. mendocina, Comamonas sp., Agrobacterium tumefaciens biovar. 2 and Sphingobacterium sp., isolated from the rhizosphere of wild-grown caper (Capparis spinosa L.) plants were able to fix N₂ as shown by their growth in nitrogen-free medium and by the acetylene reduction test. P. stutzeri var. mendocina and Comamonas sp. contained DNA homologous to the Klebsiella pneumoniae M5a1 nifHDK genes. No hybridization was found with total DNA from either A. tumefaciens biovar. 2 or Sphingobacterium sp. using nifHDK probes from either K. pneumoniae or Rhizobium meliloti.     

Genetics of naphthalene and phenanthrene degradation by Comamonas testosteroni

Naphthalene and phenanthrene have long been used as model compounds to investigate the ability of bacteria to degrade polycyclic aromatic hydrocarbons. The catabolic pathways have been determined, several of the enzymes have been purified to homogeneity, and genes have been cloned and sequenced. However, the majority of this work has been performed with fast growing Pseudomonas strains related to the archetypal naphthalene-degrading P. putida strains G7 and NCIB 9816-4. Recently Comamonas testosteroni strains able to degrade naphthalene and phenanthrene have been isolated and shown to possess genes for polycyclic aromatic hydrocarbon degradation that are different from the canonical genes found in Pseudomonas species. For instance, C. testosteroni GZ39 has genes for naphthalene and phenanthrene degradation which are not only different from those found in Pseudomonas species but are also arranged in a different configuration. C. testosteroni GZ42, on the other hand, has genes for naphthalene and phenanthrene degradation which are arranged almost the same as those found in Pseudomonas species but show significant divergence in their sequences. Received 10 August 1997/ Accepted in revised form 15 August 1997     

Bioconversion of pyrimidine by resting cells of quinoline-degrading bacteria

Nine quinoline-degrading bacterial strains were tested for their ability to hydroxylate pyrimidine. All strains converted pyrimidine to uracil via pyrimidine-4-one in a cometabolic process. Quinoline 2-oxidoreductases (QuinORs) were the catalysts of fortuitous pyrimidine hydroxylation. Whereas in most strains the activity of the QuinOR towards pyrimidine was very low compared to its activity towards quinoline, QuinOR in crude extracts from Comamonas testosteroni 63 showed a specific activity of 64 (mU mg protein)-1 with pyrimidine as substrate, compared to a specific activity of 237 (mU mg protein)-1 towards the intrinsic substrate quinoline. Resting cells of Comamonas testosteroni 63 rapidly converted pyrimidine almost stoichiometrically to uracil, which accumulated in the cell suspension. Using an adsorbent resin, uracil was prepared from the supernatant of Comamonas testosteroni 63 resting cells with a yield of > 98%.     

Purification and some properties of (1R,2S)-1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase from Comamonas testosteroni T-2

Abstract Inducible (1 R ,2 S )-1,2-dihydroxy-3,5-cyclohexadiene-l,4-dicarboxylate (diene-diol) dehydrogenase was found in extracts of Comamonas testosteroni T-2 grown in p -toluate-or terephthalate-salts medium and it was purified using anion exchange, hydrophobic interaction and gel filtration chromatography. The enzyme is a homodimer with subunit M r 39000. It had a specific activity of 500 mkat/kg of protein and was activated by the addition of Fe²⁺. The dehydrogenase converted 1 mol diene-diol and 1 mol NAD⁺ to 1 mol protocatechuic acid, 1 mol NADH and 1 mol CO₂. Apparent K _m-values of 43 μM (NAD⁺) and about 90 μM (diene-diol) were determined. The hydride ion was transferred to the si face of NAD⁺.     

Fe(III)-enhanced anaerobic transformation of 2,4-dichlorophenoxyacetic acid by an iron-reducing bacterium Comamonas koreensis CY01

This work studied the ability of Comamonas koreensis CY01 to reduce Fe(III) (hydr)oxides by coupling the oxidation of electron donors and the enhanced biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the presence of Fe(III) (hydr)oxides. The experimental results suggested that strain CY01 can utilize ferrihydrite, goethite, lepidocrocite or hematite as the terminal electron acceptor and citrate, glycerol, glucose or sucrose as the electron donor. Strain CY01 could transform 2,4-D to 4-chlorophenol through reductive side-chain removal and dechlorination. Under the anaerobic conditions, Fe(III) reduction and 2,4-D biodegradation by strain CY01 occurred simultaneously. The presence of Fe(III) (hydr)oxides would significantly enhance 2,4-D biodegradation, probably due to the fact that the reactive mineral-bound Fe(II) species generated from Fe(III) reduction can abiotically reduce 2,4-D. This is the first report of a strain of C. koreensis capable of reducing Fe(III) (hydr)oxides and 2,4-D, which extends the diversity of iron-reducing bacteria associated with dechlorination.     

一株降解对氯硝基苯的Comamonas sp.CNB1的分离鉴定及其降解特性

从处理某化工厂污水的活性污泥中分离到一株降解对氯硝基苯的细菌CNB1菌株。经过对其形态特征、生理生化、以及16S rDNA序列分析,该菌株初步鉴定为Comamonas sp.,进一步研究表明,该菌株能够以对氯硝基苯为唯一碳源、氮源和能源生长。生长过程中,氯离子释放同步于对氯硝基苯降解,且氯离子的释放量与对氯硝基苯的降解量相当。该细菌利用对氯硝基苯生长的最适生长温度和pH分别为28℃和9.0。测定了降解途径中相关酶的活性,表明初始降解过程是由对氯硝基苯还原酶催化的硝基还原反应,芳环的裂解是由2-氨基苯酚1,6-双加氧酶催化。     

Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant

A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03(T), was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and beta-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005(T) (95.9% sequence similarity), Comamonas nitrativorans DSM 13191(T) (95.7%), and Comamonas odontotermitis LMG 23579(T) (95.7%). Strain Ko03(T) had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C(16:1) omega7c (44.7%), C(16:0) (28.1%), C(18:1) (16.1%), and C(10:0) 3-OH (3.5%). These chemo-taxonomic results supported the affiliation of strain Ko03(T) to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03(T) from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03(T) represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03(T) (= KCTC 12199(T) = NBRC 101663(T)).     

Cobalt Uptake and Resistance to Trace Metals in Comamonas testosteroni Isolated From a Heavy-Metal Contaminated Site in the Zambian Copperbelt

A biogeochemical study of a polluted wetland site in Kitwe, Zambia shows high concentration of trace metals (e.g., > 25 and ≈ 2 fold higher than the Eco-toxic threshold values of copper and cobalt, respectively) with many sequestered with the sediment organic phase. Depth profiles in surface sediments suggest trace metal cycling between porewater and solid phases, including that of cobalt. This study documents a bacterium displaying resistance to, and accumulation of cobalt, and that cobalt has a positive effect on growth. The isolate was enriched from the microbial community and identified using 16S rRNA gene sequence analysis as a strain of Comamonas testosteroni (designated C. testosteroni TDKW). Improved growth of C. testosteroni TDKW was seen with the addition of up to 200 μM cobalt (optimal growth ca. 100 μM), while concentrations above 4 mM completely inhibited growth. C. testosteroni TDKW also exhibited resistance to high concentrations of iron and manganese, but showed limited resistance to copper or nickel. Further analysis revealed cellular cobalt accumulation and the presence of heavy-metal resistance genes, tentatively suggesting that this organism could contribute to in situ biological cycling of cobalt in mineral contaminated aquatic systems.     

High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains

Background

Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.

Results

To understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap’s law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.

Conclusions

This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1314-x) contains supplementary material, which is available to authorized users.