Fe(II)EDTA-NO reduction coupled with Fe(II)EDTA oxidation by a nitrate- and Fe(III)-reducing bacterium.

The nitrate- and Fe(III)-reducing bacterium Paracoccus versutus LYM was characterized in terms of its ability to perform Fe(II)EDTA-NO reduction coupled with Fe(II)EDTA oxidation (NO-dependent Fe(II)EDTA oxidation, NDFO). It experienced a single anaerobic FeEDTA redox cycling through NDFO and dissimilatory Fe(III)EDTA reduction in FeEDTA culture. The increase in the Fe(II)EDTA concentration contributed to the ascending Fe(II)EDTA-NO reduction rate. The amount of glucose controlled the rate and extent of Fe(II) oxidation during NDFO. Without glucose addition, Fe(II)EDTA-NO reduction rate was at a rather slow rate even in presence of relatively sufficient Fe(II)EDTA. Unlike aqueous Fe(2+) and solid-phase Fe(II), Fe(II)EDTA could prevent cells from encrustations. These findings suggested the occurrence of NDFO preferred being beneficial via a mixotrophic physiology in the presence of an organic cosubstrate to being out of consideration for metabolic strategy.

Paracoccus oceanense sp. nov., isolated from the West Pacific.

A Gram-negative, short ovoid- to coccus-shaped, aerobic, motile, non-spore-forming bacterium (designated strain JLT1679(T)) was isolated from West Pacific. Cells have subpolar flagella, dividing by binary fission. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to branch of the evolutionary radiation occupied by the genus Paracoccus, family Rhodobacteraceae, order Rhodobacterales, class Alphaproteobacteria. The closest neighbours were Paracoccus stylophorae KTW-16(T) (97.1% similarity), Paracoccus caeni strain MJ17(T) (96.5% similarity), Paracoccus homiensis DD-R11(T) (96.0% similarity) and Paracoccus alcaliphilus JCM 7364(T) (95.8% similarity). The predominant cellular fatty acids of strain JLT1679(T) were summed feature 8 (18:1ω6c) (38.8%), C(18:0) (27.7%), C(16:0) (22.5%), and significant amounts of C(18:1) ω9c (5.1%), C(14:0) (3.8%) and C(18:1) ω7c 11-methyl (2.1%), were present. The predominant respiratory ubiquinone of strain JLT1679(T) was Q-10 and the DNA G + C content of strain JLT1679(T) was 59.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The isolate was distinguishable from members of the genus Paracoccus on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data that strain JLT1679(T) represents a novel species of the genus Paracoccus, for which the name Paracoccus oceanense sp. nov. is proposed. The type strain is JLT1679(T) (= JCM 17768(T) = CGMCC 1.10831(T)).

Microbial degradation and metabolic pathway of pyridine by a Paracoccus sp. strain BW001.

A bacterial strain using pyridine as sole carbon, nitrogen and energy source was isolated from the activated sludge of a coking wastewater treatment plant. By means of morphologic observation, physiological characteristics study and 16S rRNA gene sequence analysis, the strain was identified as the species of Paracoccus. The strain could degrade 2,614 mg l(-1) of pyridine completely within 49.5 h. Experiment designed to track the metabolic pathway showed that pyridine ring was cleaved between the C2 and N, then the mineralization of the carbonous intermediate products may comply with the early proposed pathway and the transformation of the nitrogen may proceed on a new pathway of simultaneous heterotrophic nitrification and aerobic denitrification. During the degradation, NH3-N occurred and increased along with the decrease of pyridine in the solution; but the total nitrogen decreased steadily and equaled to the quantity of NH3-N when pyridine was degraded completely. Adding glucose into the medium as the extra carbon source would expedite the biodegradation of pyridine and the transformation of the nitrogen. The fragments of nirS gene and nosZ gene were amplified which implied that the BW001 had the potential abilities to reduce NO2- to NO and/or N2O, and then to N2.

Characterizations of denitrifying polyphosphate-accumulating bacterium Paracoccus sp. Strain YKP-9.

A denitrifying polyphosphate-accumulating bacterium (YKP-9) was isolated from activated sludge of a 5-stage biological nutrient removal process with step feed system. This organism was a Gram-negative, coccus-shaped, facultative aerobic chemoorganotroph. It had a respiratory type of metabolism with oxygen, nitrate, and nitrite as terminal electron acceptors. The 16S rRNA gene sequence of strain YKP-9 was most similar to the 16S rRNA gene sequence of Paracoccus sp. OL18 (AY312056) (similarity level, 97%). Denitrifying polyphosphate accumulation by strain YKP-9 was examined under anaerobicanoxic and anaerobic-oxic batch conditions. It was able to use external carbon sources for polyhydroxyalkanoates (PHA) synthesis and to release phosphate under anaerobic condition. It accumulated polyphosphate and grew a little on energy provided by external carbon sources under anoxic condition, but did neither accumulate polyphosphate nor grow in the absence of external carbon sources under anoxic condition. Cells with intracellular PHA cannot accumulate polyphosphate in the absence of external carbon sources under anoxic condition. Under oxic condition, it grew but could not accumulate polyphosphate with external carbon sources. Based on the results from this study, strain YKP-9 is a new-type denitrifying polyphosphate-accumulating bacterium that accumulates polyphosphate only under anoxic condition, with nitrate and nitrite as the electron acceptors in the presence of external carbon sources.

Performance of a reactor containing denitrifying immobilized biomass in removing ethanol and aromatic hydrocarbons (BTEX) in a short operating period.

A horizontal-flow anaerobic immobilized biomass reactor (HAIB) containing denitrifying biomass was evaluated with respect to its ability to remove, separately and in a short operating period (30 days), organic matter, nitrate, and the hydrocarbons benzene (41.4 mg L-1), toluene (27.8 mg L-1), ethylbenzene (31.1 mg L-1), o-xylene (28.5 mg L-1), m-xylene (28.4 mg L-1) and p-xylene (32.1 mg L-1). The purified culture, which was grown in the presence of the specific hydrocarbon, was used as the source of cells to be immobilized in the polyurethane foam. After 30 days of operation, the foam was removed and a new immobilized biomass was grown in the presence of another hydrocarbon. The average hydrocarbon removal efficiency attained was 97%. The organic matter, especially ethanol, was removed with an average efficiency of 83% at a mean influent concentration of 1185.0 mg L-1. A concomitant removal of 97% of nitrate was observed for a mean influent concentration of 423.4 mg L-1. The independent removal of each hydrocarbon demonstrated that these contaminants can be biodegraded separately, without the need for a compound to be the primary substrate for the degradation of another. This study proposes the application of the system for treatment of areas contaminated with these compounds, with substitution and formation of a biofilm in a 30-day period.

Nitrate-dependent [Fe(II)EDTA]2- oxidation by Paracoccus ferrooxidans sp. nov., isolated from a denitrifying bioreactor.

Enrichments with [Fe(II)EDTA]2- as electron donor and nitrate or nitrite as electron acceptor were established using an inoculum from a bioreactor performing denitrification. A nitrate-reducing, [Fe(II)EDTA]2- oxidizing strain was isolated and named strain BDN-1. The G + C content of strain BDN-1 was 67%, and the organism was closely affiliated to Paracoccus denitrificans, P. pantotrophus and P. versutus by 16S rRNA sequence comparison. Results from DNA-DNA hybridization, rep-PCR, and whole cell protein analysis gave congruent results confirming the genotypic and phenotypic differences between strain BDN-1 and the other species of Paracoccus. From these results, we considered strain BDN-1 as a novel species for which we propose the name Paracoccus ferrooxidans. Apart from [Fe(II)EDTA]2-, BDN-1 could also use thiosulfate and thiocyanate as inorganic electron donors. Nitrate, nitrite, N2O, [Fe(II)EDTA.NO]2- and oxygen could be used by strain BDN-1 as electron acceptors. Repeated transfer on a culture medium with bicarbonate as the sole carbon source confirmed that strain BDN-1 was a facultative autotroph. [Fe(II)EDTA]2- oxidation dependent denitrification was also performed by other Paracoccus species, that were closely affiliated to P. ferrooxidans.

Paracoccus haeundaensis sp. nov., a Gram-negative, halophilic, astaxanthin-producing bacterium.

An aerobic, non-motile, Gram-negative, orange-pigmented, rod-shaped, astaxanthin-producing marine bacterium was isolated from the Haeundae Coast, Korea. This strain, BC74171T, produced carotenoids, mainly astaxanthin. All the type strains of the genus Paracoccus were compared with strain BC74171T using 16S rRNA gene sequence analysis, fatty acid patterns and physiological reaction profiles. Based on the results of these analyses, it is proposed that strain BC74171T represents a novel species, Paracoccus haeundaensis sp. nov. The type strain is BC74171T (= KCCM 10460T = LMG P-21903T).

Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa.

A novel marine Gram-negative, non-motile, non-spore-forming, aerobic bacterium, associated with the bryozoan Bugula plumosa, was isolated in a screening programme for strains containing enzymes able to convert the amino acid L-serine. Strain MBT-A4T produced L-serine dehydratase and was able to grow on L-serine as the sole carbon and nitrogen source. The nearest phylogenetic neighbour was Paracoccus marcusii, as determined by 16S rDNA sequence analysis (97.8% similarity). The DNA-DNA reassociation value obtained for Paracoccus marcusii DSM11574T and MBT-A4T was 32.6%. The major ubiquinone was 0-10. Based on genotypic, chemotaxonomic and physiological characteristics, a new species of the genus Paracoccus is proposed, Paracoccus seriniphilus sp. nov., the type strain being strain MBT-A4T (=DSM 14827T =CIP 107400T).

Presence of bacterial 16S ribosomal RNA gene segments in human intestinal lymph follicles.

BACKGROUND: There is currently no information regarding microbial agents inside the intestinal lymph follicles. METHODS: Biopsy or resected specimens, mostly from macroscopically normal areas, were sectioned with a cryostat. DNA was extracted from microdissected samples, exclusively from the lymph follicle. Amplification of DNA was performed using universal primers designed from conserved regions of bacterial 16S ribosomal RNA (rRNA). Several clones with inserts of around 400 base pairs were subjected to DNA sequence analysis followed by a database homology search. RESULTS: Bacterial 16S rRNA gene segments were detected in the lymph follicle in 2 of 14 (14%) non-inflammatory bowel disease (IBD) cases, 4 of 14 (28%) Crohn disease cases, and in 2 of 5 (40%) ulcerative colitis cases. Nineteen 16S rRNA gene segments were recognized in the eight positive cases. Five segments showed 100% identity to known bacterial 16S rRNAs, namely staphylococcus species, Streptococcus sanguis, and Paracoccus marcusii. However, the other 14 segments showed below 100% identity, indicating either the presence of unknown bacteria or of bacteria without known DNA data. No single identified or unidentified bacterium, characteristic of IBD, including Mycobacterium paratuberculosis and Listeria monocytogenes, was detected. CONCLUSIONS: The present study confirms the presence of bacterial 16S rRNA gene segments in human intestinal lymph follicles and paves the way for new investigations into the microbiology of the lymph follicle. Whether or not bacteria inside the lymph follicle is a primary stimulus in IBD has yet to be clarified.

Paracoccus marcusii sp. nov., an orange gram-negative coccus.

Phenotypic, chemotaxonomic and 16S rDNA sequence analysis of an orange Gram-negative coccus that appeared as a contaminant on a nutrient agar plate delineated a new species of the genus Paracoccus. Phenotypic features of the strain that differ from all or most of the previously described Paracoccus species include its bright orange colour, caused by the synthesis of large amounts of carotenoids (mainly astaxanthin), and its inability to use nitrate as an electron acceptor in respiration. The name Paracoccus marcusii is proposed for this organism. The type strain is DSM 11574T.

Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus.

A facultatively chemolithotrophic thiocyanate-degrading bacterium, strain THI 011T, which was previously isolated from activated sludge and tentatively named Thiobacillus sp., was studied taxonomically and phylogenetically. This bacterium utilizes thiocyanate as sole energy source and the specific growth rate for chemolithoautotrophic growth with thiocyanate was 0.059 h-1. Molecular phylogenetic relationships of strain THI 011T to Thiobacillus versutus and members of the genus Paracoccus were elucidated by comparing 16S rRNA gene sequences. Binary sequence comparisons showed that strain THI 011T was most related to Paracoccus aminophilus, at a similarity level of 97.0%, and T. versutus was most similar to Paracoccus denitrificans, at a level of 99.1%. A neighbour-joining phylogenetic tree showed that strain THI 011T formed a cluster together with T. versutus and known species of the genus Paracoccus within the alpha-3 subclass of the Proteobacteria. DNA-DNA hybridization assays and phenotypic studies indicated that strain THI 011T differed from T. versutus and known species of the genus Paracoccus. On the basis of these results, we propose to classify strain THI 011T into a new species of the genus Paracoccus with the name Paracoccus thiocyanatus sp. nov. We also propose to transfer T. versutus to the genus Paracoccus and present an emended description of the genus.

Paracoccus kocurii sp. nov., a tetramethylammonium-assimilating bacterium.

A new species of tetramethylammonium-assimilating bacteria was isolated from an activated sludge which was used for the treatment of tetramethylammonium hydroxide contained in the wastewater from semiconductor manufacturing processes. Cells of the bacteria were gram-negative, nonmotile, short rods (0.5 to 0.8 micron by 0.7 to 1.1 microns). The major respiratory quinone component of the bacteria was Q-10. The G + C content was 71 mol%. Isolates are mesophilic and assimilate methylated amines such as tetramethylammonium, trimethylamine, dimethylamine, and methylamine under neutral conditions. The isolates resemble Paracoccus species with respect to morphology but were distinguishable from the known species of the genus. We propose Paracoccus kocurii sp. nov. The type strain is strain B (= JCM 7684).

Increased outer membrane ornithine-containing lipid and lysozyme penetrability of Paracoccus denitrificans grown in a complex medium deficient in divalent cations.

Paracoccus denitrificans grown in a complex medium was highly susceptible to lysozyme, in contrast to cells grown in a complex medium supplemented with Mg2+ and Ca2+ or in a succinate-salts medium. The complex medium was deficient in divalent cations needed for optimum outer membrane stability. The major change in molecular compositions of outer membranes isolated from cells grown under the different conditions was a higher ratio of ornithine-containing lipid to phospholipid in complex-medium-grown cells (0.63) than in cells grown in complex medium with Mg2+ and Ca2+ (0.22) or in succinate-salts medium (0.14). We suggest that the dipolarionic ornithine-containing lipid is less dependent than acidic phospholipids on divalent cations for its incorporation into the outer membrane.

Structural analysis of four strains of Paracoccus denitrificans.

Two out of eleven newly isolated strains of Paracoccus denitrificans were investigated by light and electron microscopic methods and compared with two strains of P. denitrificans already kept in culture collections. Samples were taken from different growth phases revealing short rods and nearly spherical cells in the exponential growth phase, and an increasing ratio of nearly spherical cells in the stationary growth phase. Cell division followed the binary fission mode; higher cell aggregates were not observed. Fine structural analysis revealed extracellular surface material stainable with Ruthenium red, a gram-negative cell wall and different storage material inclusions. Structural properties and variations within the four strains under investigation are discussed and compared with those of related bacteria.

Micromorphology of Gram-negative hydrogen bacteria. II. Cell envelope, membranes, and cytoplasmic inclusions.

The fine structure of the cell envelope, of membrane systems and of cytoplasmic inclusions of Gram-negative aerobic hydrogen bacteria has been studied. The results have been tabulated, and three main groups could be recognized: Group 1: Alcaligenes eutrophus, A.paradoxus, A.ruhlandii, Pseudomonas facilis, P.flava, P.pseudoflava, P.palleronii, and Aquaspirillum autotrophicum; Group 2: "Corynebacterium" autotrophicum and strains MA 2 and SA 35; Group 3: Paracoccus denitrificans. Special structures related to the chemoautotrophic way of life of the hydrogen bacteria were not observed.

Micromorphology of Gram-negative hydrogen bacteria. I. Cell morphology and flagellation.

The cell morphology, the arrangement and fine structure of flagella and the piliation of the following Gram-negative aerobic hydrogen bacteria have been studied: Alcaligenes eutrophus, Alcaligenes paradoxus, Alcaligenes ruhlandii, Pseudomonas flava, Pseudomonas pseudoflava, Pseudomonas palleronii, Pseudomonas facilis, Aquaspirillum autotrophicum, Paracoccus denitrificans, Corynebacterium autotrophicum, and strains MA 2 and SA 35. The identity of the bacteria was examined by their substrate spectra and type of flagellation. Three types of flagellar fine structure were differentiated. The presence of pili was noted in strains of Alcaligenes paradoxus, Pseudomonas flava, P.pseudoflava, P.palleronii, and P.facilis.