Isolation and characterization of a nitrile hydrolysing acidotolerant black yeast—<Emphasis Type="Italic">Exophiala oligosperma</Emphasis> R1

Different nitriles were used as sole sources of nitrogen in a series of enrichments under acidic conditions to isolate acidotolerant nitriles hydrolysing microorganisms. From an enrichment in Na–citrate–phosphate buffer at pH 4 with glucose as carbon source and phenylacetonitrile as sole source of nitrogen, a black yeast (strain R1) was obtained which was identified by subsequent 18S rRNA gene sequencing as Exophiala oligosperma. The growth conditions of the organism were optimized for the production of cell material and the induction of the nitrile converting activity. Resting cell experiments demonstrated that phenylacetonitrile was converted via phenylacetic acid and 2-hydroxyphenylacetic acid. The organism could grow at pH 4 with phenylacetonitrile as sole source of carbon, nitrogen, and energy. The nitriles hydrolysing activity was also detected in cell-free extracts and indications for a nitrilase activity were found. The cell-free extracts converted, in addition to phenylacetonitrile, also different substituted phenylacetonitriles. Whole cells of E. oligosperma R1 converted phenylacetonitrile with almost the same reaction rates in the pH range from pH 1.5–pH 9.     

Isolation and characterization of a new strain of Achromobacter sp. with beta-lactam antibiotic acylase activity

A bacterial strain producing a -lactam antibiotic acylase, able to hydrolyze ampicillin to 6-aminopenicillanic acid more efficiently than penicillin G, was isolated from soil and characterized. The isolate was identified as Achromobacter sp. using the phenotypic characteristics, composition of cellular fatty acids and 16S rRNA gene sequence. The enzyme synthesis was fully induced by phenylacetic acid (PAA) at a concentration of 2 g l^–1. PAA at concentrations up to 12 g l^–1 had no negative effect on the specific activity of acylase and biomass production, but slowed down the specific growth rate. Benzoic or 4-hydroxyphenylacetic acids can also induce synthesis of the enzyme. The inducers were metabolized in all cases. Acylase activity in cell-free extracts was determined with various substrates; ampicillin, cephalexin and amoxicillin were hydrolyzed 1.5- and 2-times faster than penicillin G. A high stability of acylase activity was observed over a wide range of pH (5.0–8.5) and at temperatures above 55°C.     

Metabolism of DL-(+/-)-phenylalanine by Aspergillus niger.

A fungus capable of degrading DL-phenylalanine was isolated from the soil and identified as Aspergillus niger. It was found to metabolize DL-phenylalanine by a new pathway involving 4-hydroxymandelic acid. D-Amino acid oxidase and L-phenylalanine: 2-oxoglutaric acid aminotransferase initiated the degradation of D- and L-phenylalanine, respectively. Both phenylpyruvate oxidase and phenylpyruvate decarboxylase activities could be demonstrated in the cell-free system. Phenylacetate hydroxylase, which required reduced nicotinamide adenine dinucleotide phosphate, converted phenylacetic acid to 2- and 4-hydroxyphenylacetic acid. Although 4-hydroxyphenylacetate was converted to 4-hydroxymandelate, 2-hydroxyphenylacetate was not utilized until the onset of sporulation. During sporulation, it was converted rapidly into homogentisate and oxidized to ring-cleaved products. 4-Hydroxymandelate was degraded to protocatechuate via 4-hydroxybenzoylformate, 4-hydroxybenzaldehyde, and 4-hydroxybenzoate.     

Isolation of new 6-methylnicotinic-acid-degrading bacteria, one of which catalyses the regioselective hydroxylation of nicotinic acid at position C2

2-Hydroxynicotinic acid is an important building block for herbicides and pharmaceuticals. Enrichment strategies to increase the chances of finding microorganisms capable of hydroxylating at the C2 position and to avoid the degradation of nicotinic acid via the usual intermediate, 6-hydroxynicotinic acid, were used. Three bacterial strains (Mena 23/3–3c, Mena 25/4–1, and Mena 25/ 4–3) were isolated from enrichment cultures with 6-methylnicotinic acid as the sole source of carbon and energy. Partial characterization of these strains indicated that they represent new bacterial species. All three strains completely degraded 6-methylnicotinic acid, and evidence is presented that the first step in the degradation pathway of strain Mena 23/3–3c is hydroxylation at the C2 position. Resting cells of this strain grown on 6-methylnicotinic acid also hydroxylated nicotinic acid at the C2 position, but did not further degrade the product. Strain Mena 23/ 3–3c showed the highest degree of 16S rRNA sequence similarity to members of the genera Ralstonia and Burkholderia. Received: 4 April 1997 / Accepted: 10 June 1997     

Catabolism of dl-α-phenylhydracrylic,phenylacetic and 3- and 4-hydroxyphenylacetic acid via homogentisic acid in a Flavobacterium sp.

A degradation pathway for dl--phenylhydracrylic, phenylacetic, 3- and 4-hydroxyphenylacetic acid by a Flavobacterium is presented. Experiments with washed cells and enzyme studies revealed that dl--phenylhydracrylic acid in an initial reaction was oxidatively decarboxylated to phenylacetaldehyde. Whole cells oxidized both stereoisomers of phenylhydracrylic acid at different rates. The product phenylacetaldehyde in turn was oxidized to phenylacetic acid. No hydroxylation of phenylacetic acid was detected in cell extracts, but on the basis of experiments with washed cells it is assumed that phenylacetic acid is mainly metabolized via 3-hydroxyphenylacetic acid. This latter product was subsequently hydroxylated yielding the ring-cleavage substrate homogentisate. 4-Hydroxyphenylacetic acid was also degraded via homogentisate. Ringcleavage of homogentisate gave maleylacetoacetate which was further degraded through a glutathione-dependent pathway. Homoprotocatechuate was not an intermediate in the metabolism of dl-phenylhydracrylic acid, phenylacetic, 3- and 4-hydroxyphenylacetic acid metabolism, but it could be hydroxylated aspecifically to 2,4,5-trihydroxyphenylacetic acid by the action of the 3-hydroxyphenylacetic acid-6-hydroxylase.Abbreviations HPLC high-performance liquid chromatography - PHA phenylhydracrylic acid - PA phenylacetic acid - HPA hyxdroxyphenylacetic acid - PMS phenazine methosulphate - PMA phenylmalonic acid - GSH glutathione     

Degradation of homovanillate by a strain of Variovorax paradoxus via ring hydroxylation

Abstract A newly isolated strain of Variovorax paradoxus could grow on homovanillate and several monohydroxylated phenylacetic acids. During growth on homovanillate, the organism formed separate NAD(P)H-dependent hydroxylases with activity towards 4-hydroxyphenylacetic acid and homovanillate. Homovanillate hydroxylase catalysed a typical monooxygenase reaction and had little activity towards 4-hydroxyphenylacetic acid. GC-MS and TLC analysis suggested that homovanillate was 1-hydroxylated to yield a dihydroxymonomethoxyphenylacetic acid which served as a substrate for homogentisate 1,2-dioxygenase. Methanol, but not formaldehyde, was released either during ring-cleavage or subsequent metabolism of the ring-cleavage product.     

Sequential anaerobic–aerobic degradation of munitions waste

A sequential anaerobic–aerobic biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) was studied. The results demonstrated that: (i) a complete degradation of RDX was achieved within 20 days using a consortium of bacteria from a wastewater activated sludge, (ii) RDX degradation did not occur under aerobic conditions alone, (iii) RDX-degrading bacterial strain that was isolated from the activated sludge completely degraded RDX within 2 days, and (iv) RDX- induced protein expressions were observed in the RDX-degrading bacterial strain. Based on fatty acid composition and a confirmation with a 16S rRNA analysis, the RDX-degrading bacterial strain was identified as a Bacillus pumilus—GC subgroup B.     

Anoxybacillus thermarum sp. nov., a novel thermophilic bacterium isolated from thermal mud in Euganean hot springs, Abano Terme, Italy

A novel aerobe thermophilic endospore-forming bacterium designated strain AF/04^T was isolated from thermal mud located in Euganean hot springs, Abano Terme, Padova, Italy. Strain AF/04^T was Gram-positive, motile, rod-shaped, occurring in pairs, or filamentous. The isolate grew between 55 and 67°C (optimum 65°C) and at pH 6.0–7.5 (optimum pH 7.2). The strain was aerobic and grew on maltose, trehalose, and sodium acetate as sole carbon sources. The G + C content of DNA was 53.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AF/04^T falls within the genus Anoxybacillus. Levels of 16S rRNA gene sequence similarity between strain AF/04^T and the type strains of recognized Anoxybacillus species ranged from 95 to 99%. Chemotaxonomic data (major isoprenoid quinone–menaquinone-7; major fatty acid iso-C15:0 and anteiso-C17:0) supported the affiliation of strain AF/04^T to the genus Anoxybacillus. Based on phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA–DNA hybridization data, it was proposed that strain AF/04^T (=DSM 17141^T = ATCC BAA 1156^T) should be placed in the genus Anoxybacillus as the type strain of a novel species, Anoxybacillus thermarum sp. nov.     

Identification and Antimicrobial Activity of Phenylacetic Acid Produced by <Emphasis Type="Italic">Bacillus licheniformis</Emphasis> Isolated from Fermented Soybean,Chungkook-Jang

A bacterial strain, B65-1, which showed strong antimicrobial activity, was isolated from Chungkook-Jang, a traditional Korean fermented-soybean food with antimicrobial properties. Based on carbon utilization pattern and partial 16S rRNA sequence analysis, the B65-1 strain was identified as Bacillus licheniformis. An antibiotic compound, active against bacteria and yeast such as Staphylococcus aureus, Escherichia coli, and Candida albicans, was isolated by various chromatographic procedures from culture filtrates of B. licheniformis B65-1. The purified antibiotic was identified to be phenylacetic acid, with the molecular formula C₈H₈O₂ by analyses of EI-MS and NMR. The phenylacetic acid was detected in fermented soybean made with the strain B65-1 as a starter, but was not present in extracts of nonfermented soybean. Our results indicated that the phenylacetic acid produced by B. licheniformis during fermentation of soybean is one of the main compounds of antimicrobial activity of Chungkook-Jang.     

Biotransformation of Phenylacetonitrile to 2-Hydroxyphenylacetic Acid by Marine Fungi

Marine fungi belonging to the genera Aspergillus, Penicillium, Cladosporium, and Bionectria catalyzed the biotransformation of phenylacetonitrile to 2-hydroxyphenylacetic acid. Eight marine fungi, selected and cultured with phenylacetonitrile in liquid mineral medium, catalyzed it quantitative biotransformation to 2-hydroxyphenylacetic acid. In this study, the nitrile group was firstly hydrolysed, and then, the aromatic ring was hydroxylated, producing 2-hydroxyphenylacetic acid with 51 % yield isolated. In addition, the 4-fluorophenylacetonitrile was exclusively biotransformed to 4-fluorophenylacetic acid by Aspergillus sydowii Ce19 (yield?=?51 %). The enzymatic biotransformation of nitriles is not trivial, and here, we describe an efficient method for production of phenylacetic acids in mild conditions.     

Phenotypic and Phylogenetic Characterization of Burkholderia (Pseudomonas) sp. Strain LB400

The relevant phenotypic traits and phylogenetic relationships between Burkholderia (Pseudomonas) sp. strain LB400 and B. cepacia ATCC 25416^T were compared to determine the degree to which these two strains might be related. Strain LB400 degrades chlorinated biphenyls and has been a model system for potential use in the bioremediation of polychlorinated biphenyls, while some strains of B. cepacia are plant and human pathogens. The fatty acid methyl ester profile, sole carbon source utilization, and biochemical tests confirmed that strain LB400 was a member of the genus Burkholderia. The 16S rRNA gene sequence showed that this strain was not as closely related to B. cepacia as previously suspected or to other known pathogens of this genus, but is closely related to B. phenazinium, B. caribensis, B. graminis, and three unnamed Burkholderia spp. not known to be pathogenic. Received: 16 August 2000 / Accepted: 27 September 2000     

Isolation of a buprofezin co-metabolizing strain of <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. DFS35-4 and identification of the buprofezin transformation pathway

Buprofezin is a widely used insecticide that has caused environmental pollution in many areas. However, biodegradation of buprofezin by pure cultures has not been extensively studied, and the transformation pathway of buprofezin remains unclear. In this paper, a buprofezin co-metabolizing strain of DFS35-4 was isolated from a buprofezin-polluted soil in China. Strain DFS35-4 was preliminarily identified as Pseudomonas sp. based on its morphological, physiological, and biochemical properties, as well as 16S rRNA gene analysis. In the presence of 2.0 g l⁻¹ sodium citrate, strain DFS35-4 degraded over 70% of 50 mg l⁻¹ buprofezin in 3 days. Strain DFS35-4 efficiently degraded buprofezin in the pH range of 5.0–10.0 and at temperatures between 20 and 30°C. Three metabolites, 2-imino-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one, 2-imino-5-phenyl-1,3,5-thiadiazinan-4-one, and methyl(phenyl) carbamic acid, were identified during the degradation of buprofezin using gas chromatography–mass spectrometry (GC–MS) and tandem mass spectrometry (MS/MS). A partial transformation pathway of buprofezin in Pseudomonas sp. DFS35-4 was proposed based on these metabolites.     

An Escherichia coli mutant defective in the NAD-dependent succinate semialdehyde dehydrogenase

Escherichia coli mutants, unable to grown on 4-hydroxyphenylacetate, have been isolated and found to be defective in the NAD-dependent succinate semialdehyde dehydrogenase. When the mutants are grown with 4-aminobutyrate as sole nitrogen source an NAD-dependent succinate semialdehyde dehydrogenase seen in the parental strain is absent but, as in the parental strain, an NADP-dependent enzyme is induced. Growth of the mutants is inhibited by 4-hydroxyphenylacetate due to the accumulation of succinate semialdehyde. The mutants are more sensitive to inhibition by exogenous succinate semialdehyde than is the parental strain. Secondary mutants able to grow in the presence of 4-hydroxyphenylacetate but still unable to use it as sole carbon source were defective in early steps of 4-hydroxyphenylacetate catabolism and so did not form succinate semialdehyde from 4-hydroxyphenylacetate. The gene encoding the NAD-dependent succinate semialdehyde dehydrogenase of Escherichia coli K-12 was located at min 34.1 on the genetic map.     

Phylogenetic identification of three strains of rhizosphere bacteria based on the results of 16s rRNA gene analysis and genetic typing

The rhizosphere nitrogen-fixing bacteria Herbaspirillum frisingense B416, Burkholderia sp. 418, and Herbaspirillum huttiense B601 (degrader of chlorinated s-triazines) were identified by phylogenetic analysis of the 16S rRNA gene sequences, characterization of the 16S–23S intergenic spacer region, Rep-PCR genotyping, and assessment of differentiating phenotypic characteristics. The results obtained indicate that, for correct taxonomic affiliation by comparative analysis of 16S rRNA gene sequences, the ratio between intra-and interspecies variability of these sequences within the group of bacteria closely related to the identified strain should be taken into consideration. If the interspecies differences between 16S rRNA genes are insufficient for differentiation of closely related species, ribotyping and Rep-PCR analysis of genomic DNA can be used for determination of the species affiliation.     

Molecular identification of filterable bacteria and archaea in the water of acidic lakes of northern Russia

Wetland ecosystems are the natural centers of freshwater formation in northern Russia lowland landscapes. The humic acidic waters formed in bogs feed the numerous lakes of the northern regions. One milliliter of the water in these lakes contains up to 10⁴ ultrasmall microbial cells that pass through “bacterial” filters with a pore size of 0.22 μm. The vast majority of these cells do not grow on nutrient media and cannot be identified by routine cultivation-based approaches. Their identification was performed by analysis of clone libraries obtained by PCR amplification of archaeal and bacterial 16S rRNA genes from the fraction of cells collected from water filtrates of acidic lakes. Most of the obtained bacterial 16S rRNA gene sequences represented the class Betaproteobacteria and exhibited the highest homology of (94–99%) with 16S rRNA genes of representatives of the genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia. The archaeal 16S rRNA gene clone library comprised genes of Euryarchaeota representatives. One-third of these genes exhibited 97–99% homology to the 16S rRNA genes of taxonomically described organisms of the orders Methanobacteriales and Methanosarcinales. The rest of the cloned archaeal 16S rRNA genes were only distantly related (71–74% homology) to those in all earlier characterized archaea.     

Plasma concentrations of p- and m-hydroxyphenylacetic acid and phenylacetic acid in humans : Gas chromatographic—high-resolution mass spectrometric analysis

Conjugated and unconjugated phenylacetic acid and m- and p-hydroxyphenylacetic acid have been determined in the plasma of normal, healthy subjects after fasting, consumption of a meal and ingestion of deuterium-labelled amine precursors, by high-resolution gas chromatography—high-resolution mass spectrometry with selected ion monitoring of their trifluoroethyl-pentafluoropropionyl derivatives.We observed that all three conjugated acids are higher in fasting than in non-fasting subjects, and unconjugated phenylacetic acid was lower. Ingestion of deuterium-labelled amine precursors resulted in the appearance in the blood of the correspondingly labelled acids, a peak in the concentrations being reached about 1 h after consumption. Conjugated and unconjugated acids as expected increased following the consumption of a meal.Unconjugated phenylacetic acid was significantly higher in females than in males. Most values tended to increase with age, with male unconjugated and conjugated m-hydroxyphenylacetic acid and female conjugated phenylacetic and m-hydroxyphenylacetic acids increasing significantly.     

Anaerobic degradation of phenylacetic acid by mixed and pure cultures

Summary A phenylacetic acid-degrading mixed culture was enriched from effluent of an anaerobic reactor for the treatment of waste water from cellulose bleaching. From this consortium a phenylacetic acid-degrading pure culture, strain DSU3, was isolated and, due to its typical morphology and substrate spectrum, tentatively classified as a Desulfosarcina sp. It could grow on and degrade phenylacetic acid, cyclohexane carboxylate, cyclohexylacetate, benzoate, fumaric acid and several volatile fatty acids, while phenol, o-hydroxybenzoate, p-hydroxybenzoate and glucose were not utilized. Production of mandelic acid from phenylacetic acid by the enrichment culture and utilization of benzoate, an intermediate of the mandelic acid pathway, by strain DSU3 may presumably indicate degradation of phenylacetic acid via the mandelic acid pathway.     

Cultural and biochemical diversity of pink-pigmented bacteria isolated from paper mill slimes

A study of 25 paper mill slime deposits and one additive revealed nine pink-pigmented bacterial isolates, eight of which were different from pink-pigmented bacteria identified in the paper industry in the middle 1900s. The pink-pigmented bacteria described previously in pulp and paper included Micrococcus agilis, Bacillus subtilis, Serratia sp. and Alcaligenes viscosus. With the exception of one isolate, Micrococcus sp., these isolates possessed many cultural, biochemical and chemical properties which were different from the ones previously reported for paper mills. Eight of these bacteria were Gram-negative rods or filamentous, aerobic and positive for catalase production. Two isolates were methylotrophic, oxidizing methanol and identified as Methylobacterium zatmanii. Cellular fatty acid analysis and other characteristics showed one isolate to be Roseomonas sp. Using 16S rRNA gene sequencing, one isolate which was a Gram-negative rod was identified as Deionococcus grandis. Four bacteria had cells that were long or filamentous and these were isolated from mills with pink slime problems. The identity of one of the filamentous bacteria was determined by 16S rRNA gene sequencing to be close to Flectobacillus sp. strain MWH38. Most of the isolates were susceptible to 11 industrial biocides. Journal of Industrial Microbiology & Biotechnology (2000) 25, 74–80. Received 28 January 2000/ Accepted in revised form 09 June 2000     

Versatile aromatic compound-degrading capacity and microdiversity of <Emphasis Type="Italic">Thauera</Emphasis> strains isolated from a coking wastewater treatment bioreactor

Bacteria of the Thauera genus have been described as important aromatic compound degraders and have attracted increased attention. In this study, three Thauera strains (Q4, Q20-C, and 3–35) were isolated from a coking wastewater treatment plant (WWTP) with a high abundance of Thauera. The 16S rRNA, nitrite reductase, and phenol hydroxylase (LmPH) genes and pollutant-degrading capacity of these strains were characterized and compared. Their 16S rRNA gene sequences were identical, but the genomic structures differed, as demonstrated by distinct enterobacterial repetitive intergenic consensus sequence PCR profiles with a similarity of less than 0.65. The analysis of degradation of coking wastewater by these strains showed that most of the main organic pollutants—phenol, methylphenol, and indole, but not quinoline—were degraded under aerobic conditions. These strains contained different LmPHs genes and showed different phenol degradation rates (Q4 > 3–35 > Q20-C). The presence of a microdiversity of Thauera spp. implies the existence of various finely differentiated niches in the industrial WWTP. The capacity of the Thauera strains to degrade a wide spectrum of aromatic compounds suggests their potential in bioremediation applications targeting aromatic pollutant-containing wastewater.     

Analysis of changes in congener selectivity during PCB degradation by Burkholderia sp. strain TSN101 with increasing concentrations of PCB and characterization of the bphBCD genes and gene products

We isolated and characterized a gram-negative bacterium, Burkholderia sp. strain TSN101, that can degrade polychlorinated biphenyls (PCBs) at concentrations as high as 150 μg Kaneclor 300/ml, a PCB mixture equivalent to Aroclor 1242. Growing cells of strain TSN101 degraded most of the tri- and tetrachlorobiphenyls in medium containing 25 μg Kaneclor 300/ml. Using PCB concentrations of 50–150 μg of Kaneclor 300/ml, the congener selectivity pattern was different and the pattern of chlorine substitution strongly affected degradation of some congeners. At 25 μg Kaneclor 300/ml, strain TSN101 degraded di- and trichlorinated congeners with chlorine substitutions at both the ortho and the para positions. At higher concentrations of Kaneclor 300, di- and trichlorobiphenyls with ortho substituents in both phenyl rings were not degraded well. Trichlorobiphenyls with para and meta substitutents were degraded equally well at all concentrations studied. The ability of strain TSN101 to degrade ortho and para-substituted congeners was confirmed using a defined PCB mixture with chlorine substituents at 2′- and 4′-positions. A 5-kb DNA fragment containing the bphBCD genes was cloned and sequenced. Comparison of the deduced amino acid sequences of these genes with related proteins indicated 99 and 98% sequence similarity to the BphB and BphD of Comamonas testosteroni strain B-356, respectively. The bphC gene product showed 74% sequence similarity to the BphC of Burkholderia cepacia strain LB400 and exhibited a narrow substrate specificity with strong affinity for 2,3-dihydroxybiphenyl. A bphC-disrupted mutant of Burkholderia sp. strain TSN101, constructed by gene replacement, lost the ability to utilize biphenyl, thus supporting the role of the cloned bph gene in biphenyl metabolism. Received: 18 February 1997 / Accepted: 19 August 1997