Isolation and characterization of a marine bacterium capable of utilizing 2-methylphenanthrene

A marine bacterium isolated from a coastal hydrocarbon-polluted sediment has been described and attributed on the basis of its phenotypic and genotypic characteristics to the genus Sphingomonas sp. This strain was capable of using an alkylated phenanthrene 2-methylphenanthrene, as sole source of carbon and energy. In experiments, 2-methylphenanthrene (0.2 g/l) was added as crystals to the culture medium. After 5 days of aerobic growth at 30 degrees C, 70% was degraded and the complete dissipation occurred after 20 days. Furthermore, the strain could degrade various kinds of polyaromatic compounds, but failed to grow on aliphatic hydrocarbons.     

Hematocrit values in weight-selected and relaxed lines of White Rock chickens

Hematocrits (PCV) were measured at 29 and 106 d of age (PCV1 and PCV2, respectively) in male and female White Plymouth Rocks. Four lines were used, two of which had undergone 40 generations of divergent selection for 8-wk BW (HWS, LWS), and two respective sublines (HWR, LWR), in which selection had been relaxed for five generations. At both ages, males and females did not differ for PCV in lines HWR, LWR, and LWS. For line HWS there was an age by sex interaction that resulted from an age effect for males but not for females, and from a sex effect at each age. At both ages, PCV was higher for the HW than the LW lines. Initially, there was no difference between the selected and their respective relaxed lines, but by 106 d, HWR chickens had a higher PCV than HWS chickens. In lines HWR and LWR, PCV increased with age. There was a negative correlation in HWS males for PCV1 with 28 and 56 d BW. The HWR males also had a negative correlation for PCV1 with BW at 28 d, but not between PCV2 and BW. The correlation for PCV1 with PCV2 was high and positive for HWR males and females.     

Incidence of subacute thyroiditis recurrences after a prolonged latency: 24-year survey

A bacterium isolated from a polluted stream, capable of metabolizing biphenyl, naphthalene, phenanthrene, and higher-molecular-weight polycyclic aromatic hydrocarbons (D. Gibson, V. Mahadevan, D. Jerina, H. Yagi, and H. Yeh, Science 189:295-297, 1975), was previously identified as Beijerinckia sp. strain B1. In this investigation, 16S rRNA gene sequencing, biochemical tests, fatty acid methyl ester analysis, polyacrylamide gel electrophoresis of protein, and DNA-DNA hybridization were used to determine the taxonomic relationship of Beijerinckia sp. strain B1. The sequence of the 16S rRNA gene of B1 was identical to that of Sphingomonas yanoikuyae ATCC 51230T. The biochemical tests, fatty acid analysis, and sodium dodecyl sulfate-polacrylamide gel electrophoresis profile of soluble proteins of strain B1 showed results similar to those of S. yanoikuyae. DNA-DNA hybridization indicated that B1 and S. yanoikuyae ATCC 51230T are 75% homologous at the DNA level. We propose that Beijerinckia sp. strain B1 be reclassified as S. yanoikuyae.     

Classification of "Pseudomonas azotocolligans" Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov

"Pseudomonas azotocolligans" ATCC 12417T (T = type strain), which was described as a diazotrophic bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this strain clusters phylogenetically with species of the genus Sphingomonas and represents a new species. The results of investigations of the fatty acid patterns, polar lipid profiles, and quinone system supported this placement. The substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of any previously described species of the genus Sphingomonas. The new name Sphingomonas trueperi is proposed on the basis of these results and previously published data for the G + C content of the genomic DNA and the polyamine pattern.     

Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy)propionic acid] in an enantioselective manner by Sphingomonas herbicidovorans sp. nov

Sphingomonas herbicidovorans MH (previously designated Flavobacterium sp. strain MH) was able to utilize the chiral herbicide (RS)-2-(4-chloro-2-methylphenoxy)propionic acid (mecoprop) as the sole carbon and energy source. When strain MH was offered racemic mecoprop as the growth substrate, it could degrade both the (R) and the (S) enantiomer to completion, as shown by biomass formation, substrate consumption, and stoichiometric chloride release. However, the (S) enantiomer disappeared much faster from the culture medium than the (R) enantiomer. These results suggest the involvement of specific enzymes for the degradation of each enantiomer. This view was substantiated by the fact that resting cells of strain MH grown on (S)-mecoprop were able to degrade the (S) but not the (R) enantiomer of mecoprop. Accordingly, resting cells of strain MH grown on (R)-mecoprop preferentially metabolized the (R) enantiomer. Nevertheless, such cells could transform (S)-mecoprop at low rates. Oxygen uptake rates with resting cells confirmed the above view, as oxygen consumption was strongly dependent on the growth substrate. Cells grown on (R)-mecoprop showed oxygen uptake rates more than two times higher upon incubation with the (R) than upon incubation with the (S) enantiomer and vice versa.     

Comparison of [125I]iodomelatonin binding sites in infant cerebellum of sudden infant death syndrome and non-sudden infant death syndrome

A tributyltin chloride (TBTCl)-resistant bacterium, Alteromonas sp. M-1, was isolated from coastal seawater. This bacterium grew in medium containing 125 microM TBTCl. TBTCl added to the medium was taken up by this bacterium, however, the amount of TBTCl in the cellular fraction was low after the logarithmic phase, suggesting the existence of a TBTCl-efflux system. A genetic library was constructed using plasmid vector pUC 19. Three positive clones were obtained, by which E. coli was transformed to TBTCl resistance. Of the three clones, the shortest fragment from HindIII-library was analyzed. This fragment was 1.8 kb long and contained one complete open reading frame. The predicted amino acid sequence of this open reading frame had a homologous domain to transglycosylases of bacteriophage and E. coli. TBTCl-tolerant marine bacteria other than Alteromonas sp. M-1 were obtained from natural seawater to which TBTCl was added. DNA-DNA hybridization was performed between the three cloned fragments from Alteromonas sp. M-1 and chromosomal DNA of the TBTCl-tolerant bacteria. Some strains hybridized with the fragments and some did not, suggesting that several genes are responsible for TBTCl tolerance.     

Isolation of a bacterial strain able to degrade branched nonylphenol

Conventional enrichment of microorganisms on branched nonylphenol (NP) as only carbon and energy source yielded mixed cultures able to grow on the organic compound. However, plating yielded no single colonies capable, alone or in combination with other isolates, of degrading the NP in liquid culture. Therefore, a special approach was used, referred to as "serial dilution-plate resuspension," to reduce culture complexity. In this way, one isolate, TTNP3, tentatively identified as a Sphingomonas sp., was found to be able to grow on NP in liquid culture. Remarkably, this isolate was able to be filtered through a 0.45-micrometer-pore-diameter filter. Moreover, isolate TTNP3 did not form visible colonies on mineral medium with NP, and it formed visible colonies on R2A agar only after a prolonged incubation of 1 week. High-performance liquid chromatography and gas chromatography-mass spectroscopy analysis of the culture media indicated that the strain starts the degradation of NP with a fission of the phenol ring and preferably uses the para isomer of NP and not the ortho isomer. No distinct accumulation of an intermediary product could be observed.     

Biodegradation pathway of 2-chlorodibenzo-p-dioxin and 2-chlorodibenzofuran in the biphenyl-utilising strain JB1

The biphenyl-utilising Burkholderia (previously Alcaligenes) strain JB1 is also able to degrade a number of chlorinated dibenzo-p-dioxins and dibenzofurans. In this study, 4-chlorocatechol and a chlorotrihydroxydiphenyl ether were identified as metabolites of 2-chlorodibenzo-p-dioxin. 5-Chlorosalicylic acid and a chlorotrihydroxybiphenyl were metabolites of 2-chlorodibenzofuran. These results show that degradation of these compounds follows pathways in which the initial reaction is angular dioxygenation, followed by cleavage of an ether bridge. This pathway is similar to that used by dibenzofuran-degrading strains such as Sphingomonas sp. strain RW1.     

An unusual histone H3 specific for early macronuclear development in Euplotes crassus

A bacterial strain (CF06) that mineralized both the carbonyl group and the aromatic ring of the insecticide carbofuran and that is capable of using carbofuran as a sole source of carbon and nitrogen was isolated from a soil in Washington state. Phospholipid fatty acid and 16S rRNA sequencing analysis indicate that CF06 is a Sphingomonas sp. CF06 contains five plasmids, at least some of which are required for metabolism of carbofuran. Loss of the plasmids induced by growth at 42 degrees C resulted in the inability of the cured strain to grow on carbofuran as a sole source of carbon. Introduction of the plasmids confers on Pseudomonas fluorescens M480R the ability to use carbofuran as a sole source of carbon for growth and energy. Of the five plasmids, four are rich in insertion sequence elements and contain large regions of overlap. Rearrangements, deletions, and loss of individual plasmids that resulted in the loss of the carbofuran-degrading phenotype were observed following introduction of Tn5.     

Biochemical and genetic characterization of a gentisate 1, 2-dioxygenase from Sphingomonas sp. strain RW5

A 4,103-bp long DNA fragment containing the structural gene of a gentisate 1,2-dioxygenase (EC 1.13.11.4), gtdA, from Sphingomonas sp. strain RW5 was cloned and sequenced. The gtdA gene encodes a 350-amino-acid polypeptide with a predicted size of 38.85 kDa. Comparison of the gtdA gene product with protein sequences in databases, including those of intradiol or extradiol ring-cleaving dioxygenases, revealed no significant homology except for a low similarity (27%) to the 1-hydroxy-2-naphthoate dioxygenase (phdI) of the phenanthrene degradation in Nocardioides sp. strain KP7 (T. Iwabuchi and S. Harayama, J. Bacteriol. 179:6488-6494, 1997). This gentisate 1,2-dioxygenase is thus a member of a new class of ring-cleaving dioxygenases. The gene was subcloned and hyperexpressed in E. coli. The resulting product was purified to homogeneity and partially characterized. Under denaturing conditions, the polypeptide exhibited an approximate size of 38.5 kDa and migrated on gel filtration as a species with a molecular mass of 177 kDa. The enzyme thus appears to be a homotetrameric protein. The purified enzyme stoichiometrically converted gentisate to maleylpyruvate, which was identified by gas chromatography-mass spectrometry analysis as its methyl ester. Values of affinity constants (Km) and specificity constants (Kcat/Km) of the enzyme were determined to be 15 microM and 511 s-1 M-1 x 10(4) for gentisate and 754 microM and 20 s-1 M-1 x 10(4) for 3, 6-dichlorogentisate. Three further open reading frames (ORFs) were found downstream of gtdA. The deduced amino acid sequence of ORF 2 showed homology to several isomerases and carboxylases, and those of ORFs 3 and 4 exhibited significant homology to enzymes of the glutathione isomerase superfamily and glutathione reductase superfamily, respectively.     

Initial reactions in the oxidation of 1,2-dihydronaphthalene by Sphingomonas yanoikuyae strains

The substrate oxidation profiles of Sphingomonas yanoikuyae B1 biphenyl-2,3-dioxygenase and cis-biphenyl dihydrodiol dehydrogenase activities were examined with 1,2-dihydronaphthalene and various cis-diols as substrates. m-Xylene-induced cells of strain B1 oxidized 1,2-dihydronaphthalene to (-)-(1R,2S)-cis-1,2-dihydroxy-1,2-3,4-tetrahydronaphthalene as the major product (73% relative yield). Small amounts of (+)-(R)-2-hydroxy-1,2-dihydronaphthalene (15%), naphthalene (6%), and alpha-tetralone (6%) were also formed. Strain B8/36, which lacks an active cis-biphenyl dihydrodiol dehydrogenase, formed (+)-(1R,2S)-cis-1,2-dihydroxy-1,2-dihydronaphthalene (51%), in addition to (-)-(1R,2S)-cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene (44%) and (+)-(R)-2-hydroxy-1,2-dihydronaphthalene (5%). The cis-biphenyl dihydrodiol dehydrogenase of strain B1 oxidized both enantiomers of cis-1,2-dihydroxy-1,2-dihydronaphthalene, but only the (+)-(1S,2R)-enantiomers of cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene and cis-1,2-dihydroxy-3-phenylcyclohexa-3,5-diene. The results show that biphenyl dioxygenase expressed by S. yanoikuyae catalyzes dioxygenation, monooxygenation, and desaturation reactions with 1,2-dihydronaphthalene as the substrate, and cis-biphenyl dihydrodiol dehydrogenase catalyzes the enantioselective dehydrogenation of (+)-(1S,2R)-cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene and (+)-(1S,2R)-cis-1,2-dihydroxy-3-phenylcyclohexa-3,5-diene.     

Resistance of Rhizobium strains to phygon, spergon, and thiram

Strains of Rhizobium meliloti, Rhizobium sp. nodulating cowpeas, and R. phaseoli derived from cultures susceptible to tetramethylthiuram disulfide (thiram), 2,3-dichloro-1,4-naphthoquinone (phygon), and 2,3,5,6-tetrachloro-p-benzoquinone (spergon), respectively, grew in the presence of high concentrations of the fungicides and converted them to products not toxic to the sensitive rhizobia. The results of chemical assays demonstrated that the pesticides were destroyed by the resistant bacteria but not by the susceptible parent rhizobia. Resting cells of thiram-metabolizing R. meliloti formed large quantities of dimethyldithiocarbamate, dimethylamine, and CS2 from the pesticide. The products were characterized by gas and thin-layer chromatography, colorimetric reactions, and ultraviolet spectrometry. Dimethylamine and CS2 were formed spontaneously from dimethyldithiocarbamate, but the yield was higher in the presence of R. meliloti. The phygon-resistant bacterium converted the fungicide to five metabolites and thereby rendered the chemical nontoxic to a test fungus. The resistant strain of R. phaseoli generated at least one organic product and released about one-third of the chlorine during its detoxication of spergon.     

Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions

A fastidious, slowly growing, strictly aerobic, gram-negative bacterium was isolated from a culture of blood from a 25-year-old man with common variable immunodeficiency. The man had been admitted to hospital with febrile progressive cerebellar ataxia. The use of standard phenotypic schemes did not lead to identification, but sequence analysis demonstrated that the 16S rRNA gene of the isolate was most similar to those of the environmental bacteria Duganella zoogloeoides (formerly Zoogloea ramigera 115) and Telluria mixta. Further characterization of the bacterium by biochemical analysis, electron microscopy, G+C content estimation, and fatty acid analysis demonstrated significant differences between the bacterium and D. zoogloeoides and Telluria species; thus, we propose it as a new taxon with the name Massilia timonae gen. nov., sp. nov.     

Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate

The L-2-haloacid dehalogenase from the 1,2-dichloroethane degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Its crystal structure was solved by the method of multiple isomorphous replacement with incorporation of anomalous scattering information and solvent flattening, and was refined at 1.95-A resolution to an R factor of 21.3%. The three-dimensional structure is similar to that of the homologous L-2-haloacid dehalogenase from Pseudomonas sp. YL (1), but the X. autotrophicus enzyme has an extra dimerization domain, an active site cavity that is completely shielded from the solvent, and a different orientation of several catalytically important amino acid residues. Moreover, under the conditions used, a formate ion is bound in the active site. The position of this substrate-analogue provides valuable information on the reaction mechanism and explains the limited substrate specificity of the Xanthobacter L-2-haloacid dehalogenase.     

Taxonomy of ticks of the genus Microtimyobia (Acariformes: Myobiidae: Radfordia) and their distribution on voles (Rodentia: Cricetidae: Arvicolinae)

A phylogenetic system of the subgenus Microtimyobia (Myobiidae: Radfordia) elaborated for the first time by means of the software HENNIG-86 is proposed. The subgenus Microtimyobia including three species groups, lemnina, hylandi and zibethicalis, was divided for a cladistic analysis into 6 operation units based mainly on a male genital shield structure. The analysis shows, that the zibethicalis group is a polyphyletic, while the hylandi and lemnina groups are monophyletic. Host-parasite associations of myobiid mite taxa with vole taxa (Arvicolinae) and some peculiarities of mite and host taxa distribution are analysed. The zibethicalis group is represented by two species, associated with the North American rodents of the genera Ondatra and Phenacomys respectively. The hylandi group are most widely distributed among Arvicolinae taxa, both in Eurasia and North America. However, R. hylandi occurs on those vole species of the genera Microtus and Pitymys, which are distributed only in central and southern parts of North America and represent descendants of the earlier migration wave of Microtus from the Eurasia. As far as R. hylandi is also found in the pleistocenus of the Yakutia, that means that its areal was wider than in recent period. The lemnina group lives on hosts of 2 subtribes of the tribe Arvicolini (Arvicolina and Clethrionomyina) and is restricted to Eurasian range, except R. lemnina. This species is also mainly distributed on Eurasian vole species, however it occurs on vole species distributed in Alaska and being decendants of the later wave of Microtus migration. As far as R. lemnina and R. hylandi are associated with representatives of different migration waves of Microtus from the Euroasia, it is suggested that mites of the hylandi group are the original myobiid fauna of the Microtus voles. The species of the lemnina group had apparently originated on voles of the subtribe Clethrionomyina and then migrated onto phylogenetically young hosts of the subtribe Arvicolina (Euroasian species of the Microtus and related genera), where they probably eliminated mites of the hylandi group from these hosts in Euroasia. The recent pattern of myobiid species distribution on vole species is a result of both a mite cospeciation with their hosts and a shift of hosts. Five new myobiid mite species are described and distinguished by characters as follows. R. (M.) abramovi sp. n. from Phodopus roborovskii (Cricetidae) is closely related to R. (M.) triton Fain et Lukoschus, 1977. In both sexes of the new species setae cxI 1, 2 are scale-shaped, while in R. (M.) triton these setae (cxI 1, 2) are hair-like. R. (M.) stekolnikovi sp. n. from Chionomys nivalis (type host) and Ch. gud is similar to R. (M.) lemnina (Koch, 1841). Females of new species have setae ra with 2 apical processes; female tritonymphs with long whip-like setae ic4. R. (M.) lemnina females have setae ra with 3 processes; female tritonymphs with short hair-like setae ic4. R. (M.) stenocrani sp. n. from Microtus gregalis is also closely related to R. (M.) lemnina. Females of the new species have setae ra with 2 processes; female tritonymphs with whip-like setae ic3. R. (M.) lemnina females have seate ra with 3 processes, female tritonymph with short hair-like setae ic3. R. (M.) synaptomysi sp. n. (ABSTRACT TRUNCATED)     

Environment-dependent tight-binding potential model

The yellow-pigmented bacterium isolated from a ditch was a gram negative rod with a G+C content of 63 mol%, and was classified in the genus Sphingomonas. Electron microscopy revealed that the bacterial cell surface was covered with many large plaits. When grown in a medium containing a polysaccharide as an essential nutrient, a pit of 0.02-0.1 micrometers in diameter was formed on the cell surface, and a thin section showed the rearrangement of the plaits and the presence of a region where the cell membrane sinks into the cytosol. The dependence of the pit formation on the presence of macromolecule may predict the existence of a direct uptake mechanism for macromolecules through a mouth-like pit, possibly in endocytosis fashion. The confirmation of the pit structure is the first such finding in the history of microbiology and may provide a new insight into the cell morphology and biochemistry of macromolecule transport in microbial cell system.     

Effects of curdlan and gellan gum on the surface structure of intestinal mucosa in rats

The effects of curdlan and gellan gum on the gastrointestinal function were studied, and the morphological structure of the intestinal mucosal surface was observed by scanning electron microscopy of rats fed curdlan and gellan gum diets for four weeks. The rats fed the curdlan diet showed a significant increase in the weight of the cecum and its contents and a decrease in fecal weight as compared to the rats fed a cellulose diet. On the other hand, the rats fed the gellan gum diet showed a weight loss in cecal contents and weight gain in colonic contents. The transit time of the gastrointestinal tract was extended by curdlan supplementation whereas it was shortened by gellan gum supplementation. The surface structures of the ileal and cecal mucosa were markedly abnormal in the rats fed the curdlan diet: the microvilli were tightly packed and had fallen out at places. In the gellan gum-fed rats, the tops of the ileal and cecal microvilli adhered to one another and were covered with their contents. There was no difference in the surface structure of colonic mucosa among the cellulose, curdlan and gellan gum diet groups.     

Biotreatment of Surfactant Flush Wastewater from Wood Treatment Soil

The high cost of surfactant enhanced aquifer remediation (SEAR) could be reduced if contaminants in the extracted surfactant flushing water could be biodegraded, and the surfactant reinjected. To test this concept, ex situ biotreatment using immobilized bacteria was simulated in laboratory columns. Nonionic surfactant solutions of 1,000–5,000?mg/L Tergitol NP-10 (TNP10) were flushed through contaminated soil collected from a wood-treatment site. The highest TNP10 dose increased the effluent concentrations of tetrachlorophenol (TeCP) and tetrachlorohydroquinone (TCHQ) by about 3 and 16 times, respectively. These wash solutions were then treated by the aerobic bacterium Sphingomonas chlorophenolica RA2 immobilized in polyurethane foam. The immobilized bacteria were capable of degrading pentachlorophenol, TeCP and TCHQ in soil flushing wastewater containing up to 4,900?mg/L TNP10. Surfactant sorption to the biotreatment columns occurred, but these losses decreased over time as the sorption capacity of the foam was exhausted. The results suggest that SEAR wastewater could be biotreated, thus enabling reinjection of the surfactant.     

Doppler sonography in the evaluation of corporovenous competence after penile vein ligation surgery

Pure cultures of Chryseomonas luteola and Sphingomonas paucimobilis isolated from Manitoban soils were able to utilize diclofop-methyl (methyl-2-[4-(2,4-dichlorophenoxy)phenoxy] propanoate) as the sole source of carbon and energy. An actively growing culture of C. luteola completely degraded 1.5 micrograms diclofop-methyl.mL-1 to diclofop acid and 4-(2,4-dichlorophenoxy)phenol within 71 h, as determined by gas chromatographic analysis. The accumulation of these metabolites in the growth medium resulted in the cessation of growth, indicating the organism's inability to degrade phenoxyphenol in the presence of diclofop acid. Sphingomonas paucimobilis mineralized 1.5 micrograms diclofop-methyl.mL-1 to diclofop acid within 54 h. A biphasic growth pattern indicated that this organism was capable of degrading diclofop acid to 4-(2,4-dichlorophenoxy)phenol and 2,4-dichlorophenol and (or) phenol. Neither of the organisms was able to utilize 2,4-dichlorophenol as the sole source of carbon and energy.     

N-type calcium channel blockers from a marine bacterium, Cytophaga sp. SANK 71996

N-(3-Acyloxyacyl)glycines were isolated as N-type calcium channel blockers from a marine bacterium Cytophaga sp. SANK 71996. The identification and fermentation of the producing strain and structure characterization of N-(3-acyloxyacyl)glycines by spectral analyses and chemical syntheses are described together with their antagonistic activities.