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Applied Microbiology and Biotechnology (v.78, #2)

Microbial production of ellagic acid and biodegradation of ellagitannins by Antonio Aguilera-Carbo; Christopher Augur; Lilia A. Prado-Barragan; Ernesto Favela-Torres; Cristóbal N. Aguilar (pp. 189-199).

In the last years, tannin biodegradation has been the subject of a lot of studies due to its commercial importance and scientific relevance. Tannins are molecules of low biodegradation and represent the main chemical group of natural anti-microbials occurring in the plants. Among the different kinds of tannins, ellagitannins represent the group less studied manly due to their diversity and chemical complexity. The general outline of this work includes information on tannins, their classification and properties, biodegradation, ellagic acid production, and potential applications. In addition, it describes molecular, catalytic, and functional information. Special attention has been focused on the biodegradation of ellagitannins describing the possible role of microbial enzymes in the production of ellagic acid.

Keywords: Ellagitannins; Ellagic acid; Biodegradation

A novel approach to microbial breeding—low-energy ion implantation by Shao-bin Gu; Shi-chang Li; Hui-yun Feng; Ying Wu; Zeng-liang Yu (pp. 201-209).

Low-energy ions exist widely in the natural world. People had neglected the interaction between low-energy ions and material; it was even more out of the question to study the relation of low-energy ions and the complicated organism until the biological effects of low-energy ion implantation were discovered in 1989. Nowadays, the value of low-energy ion beam implantation, as a new breeding way, has drawn extensive attention of biologists and breeding experts. In this review, the understanding and utilization of microbial breeding by low-energy ion beam irradiation is summarized, including the characteristics of an ion beam bioengineering facility, present status of the technology of low-energy ions for microbial breeding, and new insights into microbial biotechnology.

Keywords: Microbial breeding; Ion implantation; Mutation; Gene transfer

Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) by Astrid R. Stricker; Robert L. Mach; Leo H. de Graaff (pp. 211-220).

The filamentous fungi Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) have been the subject of many studies investigating the mechanism of transcriptional regulation of hemicellulase- and cellulase-encoding genes. The transcriptional regulator XlnR that was initially identified in A. niger as the transcriptional regulator of xylanase-encoding genes controls the transcription of about 20–30 genes encoding hemicellulases and cellulases. The orthologous xyr1 (xylanase regulator 1-encoding) gene product of H. jecorina has a similar function as XlnR, although at points, the mechanisms seems to be different. Specifically in H. jecorina, the interaction of Xyr1 and the co-regulators Ace1 and Ace2 in the regulation of transcription of xylanases and cellulases has been studied. This paper describes the similarities and differences in the transcriptional regulation of expression of hemicellulases and cellulases in A. niger and H. jecorina.

Keywords: Transcriptional regulation; Gene expression; Xylanase; Cellulase

Efficient production of canine interferon-alpha in silkworm Bombyx mori by use of a BmNPV/Bac-to-Bac expression system by Zhao Na; Yao Huipeng; Lan Lipan; Cao Cuiping; M. L. Umashankar; Lu Xingmeng; Wu Xiaofeng; Wang Bing; Cui Weizheng; J. L. Cenis (pp. 221-226).

We exploited the silkworm Bombyx mori for the production of recombinant canine interferon-alpha (CaIFN-α). The recombinant baculovirus harboring canine interferon gene was rapidly generated by the BmNPV/Bac-to-Bac system that was recently developed. In B. mori-derived cell lines, the expression of the recombinant protein reached maximal levels around 72–96 h post-infection. For the isolation of the expressed recombinant protein from B. mori larvae, the whole bodies of the infected larvae were homogenized, and the expressed protein was purified by affinity chromatography. Based on the fact that the recombinant CaIFN-α showed two bands on the sodium dodecyl sulfate polyacrylamide gel electrophoresis pattern, the expressed protein was thought to be glycosylated. The rCaIFN-α yield was about 528 μg per larva, showing that the expression in silkworm was successful. Furthermore, the recombinant protein was proven to be able to inhibit the infection of Madin–Darby canine kidney cells by the vesicular stomatitis virus, indicating that it is biologically active in vitro. The method established in this study provides an efficient way to produce a large amount of CaIFN-α and paves the way for further utilization of this protein as a therapeutic agent or vaccine adjuvant in dogs.

Keywords: Canine interferon-α; BmNPV/Bac-to-Bac expression system; Silkworm

Poly(3-hydroxybutyrate) production by Halomonas boliviensis in fed-batch culture by Jorge Quillaguamán; Thuoc Doan-Van; Héctor Guzmán; Daniel Guzmán; Javier Martín; Akaraonye Everest; Rajni Hatti-Kaul (pp. 227-232).

High poly(3-hydroxybutyrate) (PHB) content and volumetric productivity were achieved by fed-batch culture of Halomonas boliviensis using a defined medium. Initial shake flask cultivations in a minimal medium revealed that the growth of H. boliviensis was supported only when the medium was supplemented with aspartic acid, glycine, or glutamine. Addition of 0.1% (w/v) glutamine in the medium resulted in the highest cell dry weight (CDW; 3.9 g l⁻¹). Glutamine was replaced by the less expensive monosodium glutamate (MSG) in the medium without any notable change in the final cell density. Effect of initial concentrations of NH₄Cl and K₂HPO₄ on cell growth and PHB accumulation by H. boliviensis was then analyzed using a fed-batch fermentation system. The best conditions for PHB production by H. boliviensis were attained using 0.4% (w/v) NH₄Cl and 0.22% (w/v) K₂HPO₄ and adding MSG intermittently to the fermentor. Poly(3-hydroxybutyrate) content and CDW reached 90 wt.% and 23 g l⁻¹, respectively, after 18 h of cultivation. In order to increase CDW and PHB content, MSG, NH₄Cl, and K₂HPO₄ were initially fed to the fermentor to maintain their concentrations at 2%, 0.4%, and 0.22% (w/v), respectively, and subsequently their feed was suppressed. This resulted in a CDW of 44 g l⁻¹, PHB content of 81 wt.%, and PHB volumetric productivity of 1.1 g l⁻¹ h⁻¹.

Keywords: Halomonas boliviensis ; Moderate halophile; Fed-batch cultivation; PHB production; Glutamate

Production of l-phenylacetylcarbinol by microbial transformation in polyethylene glycol-induced cloud point system by Wenzhi Zhang; Zhilong Wang; Wei Li; Baohua Zhuang; Hanshi Qi (pp. 233-239).

Microbial transformation of benzaldehyde into l-phenylacetylcarbinol by whole cell Saccharomyces cerevisiae has been carried out in a novel polyethylene glycol (PEG)-induced cloud point system. The system is composed of 80 g PEG 20,000, 75 ml Triton X-100, 20 g peptone, 10 g yeast extract, 25 g glucose, 1 g MgSO₄·7H₂O, 0.05 g CaCl₂·2H₂O, 35 g Na₂HPO₄·12H₂O, and 10.7 g citric acid per liter of tap water. The microbial transformation is conducted at 0.6 ml of acetaldehyde (35% volume content), 0.9 ml of benzaldehyde, and 7 g of wet cell per 100 ml of the PEG-induced cloud point system. Under the conditions, a relatively longer-term bioactivity of whole cell microorganism in the PEG-induced cloud point system has been achieved. A fed-batch microbial transformation process with a discrete addition of glucose and substrate gets a high final product concentration of about 8 g/l.

Keywords: Microbial transformation; l-phenylacetylcarbinol; Polyethylene glycol; Nonionic surfactant; Cloud point system

Antimicrobial activity of an endophytic Xylaria sp.YX-28 and identification of its antimicrobial compound 7-amino-4-methylcoumarin by Xiaoli Liu; Mingsheng Dong; Xiaohong Chen; Mei Jiang; Xin Lv; Jianzhong Zhou (pp. 241-247).

An endophytic Xylaria sp., having broad antimicrobial activity, was isolated and characterized from Ginkgo biloba L. From the culture extracts of this fungus, a bioactive compound P3 was isolated by bioactivity-guided fractionation and identified as 7-amino-4-methylcoumarin by nuclear magnetic resonance, infrared, and mass spectrometry spectral data. The compound showed strong antibacterial and antifungal activities in vitro against Staphylococcus aureus [minimal inhibitory concentrations (MIC) 16 μg·ml⁻¹], Escherichia coli (MIC, 10 μg·ml⁻¹), Salmonella typhia (MIC, 20 μg·ml⁻¹), Salmonella typhimurium (MIC, 15 μg·ml⁻¹), Salmonella enteritidis (MIC, 8.5 μg·ml⁻¹), Aeromonas hydrophila (MIC, 4 μg·ml⁻¹), Yersinia sp. (MIC, 12.5 μg·ml⁻¹), Vibrio anguillarum (MIC, 25 μg·ml⁻¹), Shigella sp. (MIC, 6.3 μg·ml⁻¹), Vibrio parahaemolyticus (MIC, 12.5 μg·ml⁻¹), Candida albicans (MIC, 15 μg·ml⁻¹), Penicillium expansum (MIC, 40 μg·ml⁻¹), and Aspergillus niger (MIC, 25 μg·ml⁻¹). This is the first report of 7-amino-4-methylcoumarin in fungus and of the antimicrobial activity of this metabolite. The obtained results provide promising baseline information for the potential use of this unusual endophytic fungus and its components in the control of food spoilage and food-borne diseases.

Keywords: Endophytes; Xylaria ; 7-Amino-4-methylcoumarin; Antimicrobial activity; Ginkgo biloba

Biocalorimetric and respirometric studies on biological treatment of tannery saline wastewater by Sivaprakasam Senthilkumar; Mahadevan Surianarayanan; Gopalraman Swaminathan (pp. 249-255).

This study is focused on the biodegradation of saline tannery effluent by identified halotolerant bacterial consortia in a bench-scale reaction calorimeter. A satisfactory agreement was observed between oxygen uptake rate profiles and heat flux–time curves confirming that, under strict aerobic conditions, calorimetry and respirometry provided the same information. Oxycalorific equivalent determined from our experiments was found to agree well to the theoretical value. A linear relationship was observed between chemical oxygen demand consumption and total metabolic heat production. The study confirmed that the heat release profiles could be used as an indirect parameter for online monitoring of the degradation process. The effect of salt (NaCl) inhibition on acetate and ammonia $$left( {{ ext{NH}}_{ ext{4}}^{ ext{ + }} } ight)$$ uptake by the halobacterial consortia is also reported in this paper.

Keywords: Soak liquor; Halotolerant; Biological treatment; Calorimetry; Oxycaloric equivalent; COD removal

Improving intracellular production of recombinant protein in Pichia pastoris using an optimized preinduction glycerol-feeding scheme by Chun Wei; Xiangshan Zhou; Yuanxing Zhang (pp. 257-264).

High-cell-density production of recombinant growth hormone of Lateolabrax japonicus (rljGH) expressed intracellularly in Pichia pastoris was investigated. In the regular strategy of induction at a cell density of 160 g l⁻¹, short duration of intracellular rljGH accumulation (17 h) resulted in a low final cell density of 226 g l⁻¹. Thus, a novel strategy of induction at a cell density of 320 g l⁻¹ was investigated. In this strategy, the preinduction glycerol-feeding scheme had a significant effect on the post-induction production. Constant glycerol feeding led to a decrease of the specific rljGH production and specific production rate because of low preinduction specific growth rate. This decrease was avoided by exponential glycerol feeding to maintain a preinduction specific growth rate of 0.16 h⁻¹. The results from exponential glycerol feeding indicated that the rljGH production depended on the preinduction specific growth rate. Moreover, mixed feeding of methanol and glycerol during induction improved the specific production rate to 0.07 mg g⁻¹ h⁻¹ from 0.043 mg g⁻¹ h⁻¹. Consequently, both high cell density (428 g l⁻¹) and high rljGH production could be achieved by the novel strategy: growing the cells at the specific growth rate of 0.16 h⁻¹ to the cell density of 320 g l⁻¹ and inducing the expression by mixed feeding.

Keywords: Exponential feeding; High-cell-density fermentation; Intracellular production; Mixed feeding; Pichia pastoris ; Specific growth rate

Purification and characterization of a novel β-agarase, AgaA34, from Agarivorans albus YKW-34 by Xiao Ting Fu; Hong Lin; Sang Moo Kim (pp. 265-273).

An extracellular β-agarase (AgaA34) was purified from a newly isolated marine bacterium, Agarivorans albus YKW-34 from the gut of a turban shell. AgaA34 was purified to homogeneity by ion exchange and gel filtration chromatographies with a recovery of 30% and a fold of ten. AgaA34 was composed of a single polypeptide chain with the molecular mass of 50 kDa. N-terminal amino acid sequencing revealed a sequence of ASLVTSFEEA, which exhibited a high similarity (90%) with those of agarases from glycoside hydrolase family 50. The pH and temperature optima of AgaA34 were pH 8.0 and 40°C, respectively. It was stable over pH 6.0–11.0 and at temperature up to 50°C. Hydrolysis of agarose by AgaA34 produced neoagarobiose (75 mol%) and neoagarotetraose (25 mol%), whose structures were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy and ¹³C NMR. AgaA34 cleaved both neoagarohexaose and neoagarotetraose into neoagarobiose. The k _cat/K _m values for hydrolysis agarose and neoagarotetraose were 4.04 × 10³ and 8.1 × 10² s⁻¹ M⁻¹, respectively. AgaA34 was resistant to denaturing reagents (sodium dodecyl sulfate and urea). Metal ions were not required for its activity, while reducing reagents (β-Me and dithiothreitol, DTT) increased its activity by 30%.

Keywords: β-Agarase; Agarivorans albus ; Purification; Characterization; Neoagarobiose

Generation of a fusion protein of the extracellular domain of BR3 with the Fc fragment of human IgG1 (sBR3-Fc) in Pichia pastoris as an antagonist for BLyS by Peng Cao; Shuangquan Zhang; Zhijun Fang; Houcai Huang; Ping Bai; Qiuhong Zhang; Changliang Luo (pp. 275-282).

Elevated levels of B cell-activating factor of the TNF family (BlyS) have been implicated in the pathogenesis of autoimmune diseases in human. Removal of pathogenic B lymphocytes by decoy receptors has demonstrated clinical benefit in both oncological and immunological diseases. In this report, we have constructed vectors for the convenient and rapid expression of the extracellular domain of BR3(sBR3) fused to the Fc fragment (hinge, CH2, CH3) of human IgG1 in the methylotrophic yeast, Pichia pastoris. SDS-PAGE assays of culture broth from a methanol-induced expression strain demonstrated that the recombinant sBR3-Fc fusion protein is secreted and recovered from the culture medium as a disulfide-linked, glycosylated homodimer. The recombinant protein was purified to >95% using protein A affinity chromatography and size exclusion chromatography steps. Bioactivity of the recombinant sBR3-Fc was confirmed by the ability of the protein to inhibit mouse B lymphocyte proliferation induced by BLyS in vitro. Our results suggest that the P. pastoris expression system can be used to produce large quantities of fully functional sBR3-Fc fusion protein for both research and industrial purposes.

Keywords: BR3; IgG1 Fc; Fusion protein; Pichia pastoris ; Secretion expression; Protein purification

Metabolic engineering of Escherichia coli to enhance phenylalanine production by N. Yakandawala; T. Romeo; A. D. Friesen; S. Madhyastha (pp. 283-291).

The global regulatory system of Escherichia coli, carbon storage regulator (Csr), was engineered to increase the intracellular concentration of phosphoenolpyruvate. We examined the effects of csrA and csrD mutations and csrB overexpression on phenylalanine production in E. coli NST37 (NST). Overexpression of csrB led to significantly greater phenylalanine production than csrA and csrD mutations (2.33 vs 1.67 and 1.61 g l⁻¹, respectively; P < 0.01). Furthermore, the overexpression of csrB was confirmed by the observed increase in csrB transcription level. We also determined the effect of overexpressing transketolase A (TktA) or glucose-6-phosphate dehydrogenase (Zwf) in NST and the csrA mutant of NST (NSTCSRA) on phenylalanine production. The NSTCSRA strain overexpressing TktA (NSTCSRA [pTktA]) produced significantly more phenylalanine than that of Zwf (2.39 vs 1.61 g l⁻¹; P > 0.01). Furthermore, we examined the effect of overexpressing TktA, 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (AroF^FR), and chorismate mutase/prephenate dehydratase (PheA^FR) together in NSTCSRA (NSTCSRA [pTkaFpA]). It is interesting to note that NSTCSRA [pTkaFpA] produced significantly less phenylalanine than both NSTCSRA [pTktA] and NST overexpressing csrB (NST [pCsrB]) (1.84 vs 2.39 and 2.33 g l⁻¹, respectively; P < 0.01). Thus, csrB overexpression or csrA mutation in combination with tktA overexpression was more effective than previous approaches that targeted the glycolytic or aromatic pathway enzymes for enhancing phenylalanine production.

PA2663 (PpyR) increases biofilm formation in Pseudomonas aeruginosa PAO1 through the psl operon and stimulates virulence and quorum-sensing phenotypes by Can Attila; Akihiro Ueda; Thomas K. Wood (pp. 293-307).

Previously, we identified the uncharacterized predicted membrane protein PA2663 of Pseudomonas aeruginosa PAO1 as a virulence factor using a poplar tree model; PA2663 was induced in the poplar rhizosphere and, upon inactivation, it caused 20-fold lower biofilm formation (Attila et al., Microb Biotechnol, 2008). Here, we confirmed that PA2663 is related to biofilm formation by restoring the wild-type phenotype by complementing the PA2663 mutation in trans and investigated the genetic basis of its influence on biofilm formation through whole-transcriptome and -phenotype studies. Upon inactivating PA2663 by transposon insertion, the psl operon that encodes a galactose- and mannose-rich exopolysaccharide was highly repressed (verified by RT-PCR). The inactivation of PA2663 also repressed 13 pyoverdine genes, which eliminated the production of the virulence factor pyoverdine in P. aeruginosa. The inactivation of PA2663 also affected other quorum-sensing-related phenotypes in that it repressed the Pseudomonas quinolone signal (PQS) genes, which abolished PQS production, and repressed lasB, which decreased elastase activity sevenfold. Genes were also induced for motility and attachment (PA0499, PA0993, PA2130, and PA4549) and for small molecule transport (PA0326, PA1541, PA1632, PA1971, PA2214, PA2215, PA2678, and PA3407). Phenotype arrays also showed that PA2663 represses growth on d-gluconic acid, d-mannitol, and N-phthaloyl-l-glutamic acid. Hence, the PA2663 gene product increases biofilm formation by increasing the psl-operon-derived exopolysaccharides and increases pyoverdine synthesis, PQS production, and elastase activity while reducing swarming and swimming motility. We speculate that PA2663 performs these myriad functions as a novel membrane sensor.

Keywords: Biofilm; Pseudomonas aeruginosa ; Pyoverdine; psl operon

Regulation of expression of general components of the phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) by the global regulator SugR in Corynebacterium glutamicum by Yuya Tanaka; Haruhiko Teramoto; Masayuki Inui; Hideaki Yukawa (pp. 309-318).

The phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) catalyzes transport of carbohydrates by coupling carbohydrate translocation and phosphorylation. Enzyme I and HPr, encoded in ptsI and ptsH, respectively, are cytoplasmic proteins commonly used for transport of variety of PTS sugars. In this study, we investigated the role of SugR on the expression of the ptsI and ptsH which increases in the presence of PTS sugars in Corynebacterium glutamicum. Disruption of sugR resulted in the increased expression of ptsI and ptsH in the absence of PTS sugar. Introduction of a plasmid containing sugR gene complemented the effect of sugR disruption. SugR was purified and binding to the promoter regions of ptsI and ptsH was indicated by EMSA. DNase I footprinting analysis indicated the binding sites of SugR on the promoter region of divergently transcribed ptsI gene and fructose-pts operon. The binding sites contain a possible SugR binding motif which is conserved in the promoter regions of general and sugar-specific pts genes. Mutations in this motif resulted in the decrease of SugR binding to the ptsI promoter. These results suggest that SugR represses ptsI and ptsH in the absence of PTS sugar and derepression is the mechanism for the induction of the general components of PTS.

Keywords: PTS; SugR; ptsI; Corynebacterium; Glutamicum

Oleic acid delays and modulates the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae after exposure to glucose excess by David Feria-Gervasio; Jean-Roch Mouret; Nathalie Gorret; Gérard Goma; Stéphane E. Guillouet (pp. 319-331).

This work aimed to study the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae CEN.PK 113-7D and more specifically to evaluate the implication of the acetyl-coenzymeA-derived carbon transport from cytosol to mitochondria in the onset of the metabolic shift. The strategy consisted in introducing, during aerobic glucose-limited chemostat (D = 0.16 h¹), a local perturbation around the step to be studied by the addition of cosubstrate and in analyzing the consequences of such a perturbation on the metabolic transition. Oleic acid and l-carnitine were among the tested cosubstrates because they were known to stimulate enzymes implicated in the acetyl-coenzymeA transport between the different cell compartments, such as the carnitine acetyl transferases. The metabolic transition was then comparatively quantified in sole glucose and in glucose/oleic acid chemostats in presence/absence of l-carnitine after a pulse of glucose. Feeding the culture with oleic acid (D _ole = 0.0041 and 0.0073 h¹) led to a delay in the onset of the metabolic shift (up to 15 min), a 33% decrease in the ethanol production and a redirection of the carbon flux toward biomass production. The data clearly showed a modulation of the carbon distribution among respiration and fermentation, in favor of a decrease in the “short-term” Crabtree effect by the oleic acid.

Keywords: Crabtree effect; Saccharomyces; Ethanolic fermentation; Oleic acid; Carnitine; Carnitine acetyl transferase

The effects of bioprocess parameters on extracellular proteases in a recombinant Aspergillus niger B1-D by Qiang Li; Linda M. Harvey; Brian McNeil (pp. 333-341).

Although host proteases are often considered to have a negative impact upon heterologous protein production by filamentous fungi, relatively little is known about the pattern of their appearance in recombinant fungal bioprocesses. In the present study, we investigated extracellular proteases from a filamentous fungus, Aspergillus niger B1-D, genetically modified to secrete hen egg white lysozyme (HEWL). Our findings indicate that extracellular protease activity is only detected after the carbon source is completely utilised in batch cultures. The proteases are predominantly acid proteases and have optimal temperature for activity at around 45°C. Their activity could be partially inhibited by protease inhibitors, indicating the existence of at least four kinds of proteases in these culture fluids, aspartic-, serine-, cysteine-, and metallo-proteases. Oxygen enrichment does not have any noticeable effects on extracellular protease activity except that the onset of protease activity appears earlier in oxygen enrichment runs. Oxygen enrichment stimulates HEWL production substantially, and we propose that it is related to fungal morphology. Thermal stress imposed by raising process temperature (from 25 to 30 and 35°C) in early exponential phase, led to appearance of protease activity in the medium following the heat shock. Continued cultivation at high temperatures significantly reduced HEWL production, which was associated with increased activity of the extracellular proteases in these cultures.

Keywords: Heterologous protein; Extracellular proteases; Hen egg white lysozyme; Aspergillus niger ; Fermentation

Aspergillus niger metabolism of citrus furanocoumarin inhibitors of human cytochrome P450 3A4 by Kyung Myung; John A. Manthey; Jan A. Narciso (pp. 343-349).

Fungi metabolize polycyclic aromatic hydrocarbons by a number of detoxification processes, including the formation of sulfated and glycosidated conjugates. A class of aromatic compounds in grapefruit is the furanocoumarins (FCs), and their metabolism in humans is centrally involved in the “grapefruit/drug interactions.” Thus far, the metabolism by fungi of the major FCs in grapefruit, including 6′, 7′-epoxybergamottin (EB), 6′, 7′-dihydroxybergamottin (DHB), and bergamottin (BM), has received little attention. In this study, Aspergillus niger was observed to convert EB into DHB and a novel water-soluble metabolite (WSM). Bergaptol (BT) and BM were also metabolized by A. niger to the WSM, which was identified as BT-5-sulfate using mass spectrometry, UV spectroscopy, chemical hydrolysis, and ¹H and ¹³C nuclear magnetic resonance spectroscopy. Similarly, the fungus had a capability of metabolizing xanthotoxol (XT), a structural isomer of BT, to a sulfated analog of BT-5-sulfate, presumably XT-8-sulfate. A possible enzyme-catalyzed pathway for the grapefruit FC metabolism involving the cleavage of the geranyl group and the addition of a sulfate group is proposed.

Keywords: Aspergillus niger ; Furanocoumarins; 6′, 7′-Epoxybergamottin; 6′, 7′-Dihydroxybergamottin; Bergamottin; Bergaptol; Xanthotoxol; Bergaptol-5-sulfate; Xanthotoxol-8-sulfate

Microbial characterisation of polyhydroxyalkanoates storing populations selected under different operating conditions using a cell-sorting RT-PCR approach by Paulo C. Lemos; Caterina Levantesi; Luisa S. Serafim; Simona Rossetti; Maria A. M. Reis; Valter Tandoi (pp. 351-360).

The identity of polyhydroxyalkanoates (PHA) storing bacteria selected under aerobic dynamic feeding conditions, using propionate as carbon source (reactor P), was determined by applying reverse transcriptase–polymerase chain reaction (RT-PCR) on micromanipulated cells and confirmed by fluorescence in situ hybridisation (FISH). Four genera, Amaricoccus, Azoarcus, Thauera and Paraccoccus were detected, the latter only rarely present. All the biomass was involved in PHA storage as shown by Nile Blue staining. By quantitative FISH, their specific amount was determined in this and two other systems using acetate as the carbon substrate (sequencing batch reactor [SBR] A and A1). SBR A and reactor P had the same sludge retention time (SRT, 10 days), while reactor A1 was operated with the SRT of 1 day and the double organic loading rate (OLR). Systems fed with acetate (41.1 ± 2.2 and 49.4 ± 1.4% total Bacteria, for A and A1, respectively) became enriched in Thauera independently on the SRT and OLR, while it was only present in a minor amount when propionate was used as a substrate (1.9 ± 0.2% total Bacteria). Amaricoccus was present in both reactors operated at 10 days SRT, favoured in the one fed with propionate (61.4 ± 1.9% total bacteria), and almost completely removed at the SRT of 1 day. Azoarcus cells were found in all the analysed systems (3.9 ± 0.3, 23.3 ± 1.5 and 45.9 ± 1.5 for P, A and A1, respectively), while Paracoccus was scarcely present.

Keywords: PHA production; Aerobic dynamic feeding; Mixed cultures; RT-PCR; FISH; Micromanipulation

Accelerated decolorization of structurally different azo dyes by newly isolated bacterial strains by Azeem Khalid; Muhammad Arshad; David E. Crowley (pp. 361-369).

Wastewater effluents from the textile and other dye-stuff industries contain significant amounts of synthetic dyes that require treatment to prevent groundwater contamination. In research aimed at biotechnology for treatment of azo dyes, this study examined 288 strains of azo-dye degrading bacteria to identify efficient strains and determine incubation times required for decolorization. Initial enrichment cultures were carried out using a mixture of four structurally different dyes (Acid Red 88, Reactive Black 5, Direct Red 81, and Disperse Orange 3) as the sole source of C and N to isolate the bacteria from soil, activated sludge, and natural asphalt. Six strains were selected for further study based on their prolific growth and ability to rapidly decolorize the dyes individually or in mixtures. Treatment times required by the most efficient strain, AS96 (Shewanella putrefaciens) were as short as 4 h for complete decolorization of 100 mg l⁻¹ of AR-88 and DR-81 dyes under static conditions, and 6 and 8 h, respectively, for complete decolorization of RB-5 and DO-3. To our knowledge, these bacterial strains are the most efficient azo-dye degrading bacteria that have been described and may have practical application for biological treatment of dye-polluted wastewater streams.

Keywords: Wastewater; Azo dye; Biodegradation; Bioaugmentation

Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli by Changsoo Lee; Seungyong Lee; Seung Gu Shin; Seokhwan Hwang (pp. 371-376).

Real-time polymerase chain reaction (PCR)-based methodology for the determination of rRNA gene (rrn) copy number was introduced and demonstrated. Both absolute and relative quantifications were tested with Escherichia coli. The separate detection of rRNA gene and chromosomal DNA was achieved using two primer sets, specific for 16S rRNA gene and for D-1-deoxyxylulose 5-phosphate synthase gene (dxs), respectively. As dxs is a single-copy gene of E. coli chromosomal DNA, the rrn copy number can be determined as the copy ratio of rrn to dxs. This methodology was successfully applied to determine the rrn copy number in E. coli cells. The results from absolute and relative quantifications were identical and highly reproducible with coefficient of variation (CV) values of 1.8–4.6%. The estimated rrn copy numbers also corresponded to the previously reported value in E. coli (i.e., 7), indicating that the results were reliable. The methodology introduced in this study is faster and cost-effective without safety problems compared to the traditionally used Southern blot analysis. The fundamentals in our methodology would be applicable to any microorganism, as long as having the sequence information of the rRNA gene and another chromosomal gene with a known copy number.

Keywords: rRNA gene copy number; Real-time PCR; Absolute quantification; Relative quantification; Escherichia coli

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Applied Microbiology and Biotechnology (v.78, #2)