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Applied Microbiology and Biotechnology (v.96, #2)

Features and applications of bilirubin oxidases by Nicolas Mano (pp. 301-307).

Discovered in 1981 by Tanaka and Murao (Agric Biol Chem 45:2383-2384, 1981), bilirubin oxidase (BOD) is a sub-group of multicopper oxidases (MCOs) also utilizing four Cu^+/2+ ions. It catalyzes the oxidation of bilirubin to biliverdin, hence the classification of bilirubin oxidase, and has been primarily used in the determination of bilirubin in serum and thereby in the diagnostic of jaundice. Unlike laccases, the most studied MCOs, BODs display a high activity and stability at neutral pH, a high tolerance towards chloride anions and other chelators, and for some species, a high thermal tolerance. Therefore, BODs could potentially be an alternative to laccase which are so far mainly restricted to applications in acid media. Because of growing interest in BODs for numerous applications under mild pH conditions, based on the number of patents and publications published in the last 5 years, here I will summarize the available data on the biochemical properties of BODs, their occurrence, and their possible biotechnological use in (1) the field of Healthcare for the elaboration of biofuel cells or bilirubin sensors or (2) the field of environmentally desirable applications such as depollution, decolorization of dyes, and pulp bleaching.

Keywords: Bilirubin oxidases; Oxygen reduction; Biofuel cells; Decolorization of dyes; Bilirubin detection; Mutlicopper oxidases

Biodegradation of sulfamethoxazole: current knowledge and perspectives by Simone Larcher; Viviane Yargeau (pp. 309-318).

Antibiotic compounds, like sulfamethoxazole (SMX), have become a concern in the aquatic environment due to the potential development of antibacterial resistances. Due to extensive consumption, excretion and disposal, SMX has been frequently detected in wastewaters and surface waters. This has led to numerous studies investigating the nature of SMX, with many researchers focusing on the biodegradation and persistence of SMX during wastewater treatment and in the environment. This review provides a summary of recent developments, outlines the discrepancies in observations and results, and demonstrates the need for further research to determine optimal biological removal strategies for SMX and other antibiotics.

Keywords: Sulfamethoxazole (SMX); Biodegradation; Antibiotic; Wastewater; Metabolites; Environment

Review of the specific effects of microwave radiation on bacterial cells by Yury Shamis; Rodney Croft; Alex Taube; Russell J. Crawford; Elena P. Ivanova (pp. 319-325).

The aim of the present review was to evaluate the literature suggesting that consideration be given to the existence of specific microwave (MW) effects on prokaryotic microorganisms; that is, effects on organisms that cannot be explained by virtue of temperature increases alone. This review considered a range of the reported effects on cellular components; including membranes, proteins, enzyme activity as well as cell death. It is concluded that the attribution of such effects to non-thermal mechanisms is not justified due to poor control protocols and because of the possibility that an unmeasurable thermal force, relating to instantaneous temperature (T _i) that occurs during MW processing, has not been taken into account. However, due to this lack of control over T _i, it also follows that it cannot be concluded that these effects are not ‘non-thermal’. Due to this ambiguity, it is proposed that internal ‘micro’-thermal effects may occur that are specific to MW radiation, given its inherent unusual energy deposition patterning.

Keywords: Non-thermal; Microwave radiation; Specific microwave effects; Frequency; Microwave power; Cell membrane; Enzyme kinetics; Proteins; Bactericidal effects

Enzymatic approaches in paper industry for pulp refining and biofilm control by C. E. Torres; C. Negro; E. Fuente; A. Blanco (pp. 327-344).

The use of enzymes has a high potential in the pulp and paper industry to improve the economics of the paper production process and to achieve, at the same time, a reduced environmental impact. Specific enzymes contribute to reduce the amount of chemicals and energy required for the modification of fibers and helps to prevent the formation or development of biofilms. This review is aimed at presenting the latest progresses made in the application of enzymes as refining aids and biofilm control agents.

Keywords: Enzymes; Refining; Biofilm; Paper industry

Anticodon nuclease encoding virus-like elements in yeast by Dhira Satwika; Roland Klassen; Friedhelm Meinhardt (pp. 345-356).

A variety of yeast species are known to host systems of cytoplasmic linear dsDNA molecules that establish replication and transcription independent of the nucleus via self-encoded enzymes that are phylogenetically related to those encoded by true infective viruses. Such yeast virus-like elements (VLE) fall into two categories: autonomous VLEs encode all the essential functions for their inheritance, and additional, dependent VLEs, which may encode a toxin–antitoxin system, generally referred to as killer toxin and immunity. In the two cases studied in depth, killer toxin action relies on chitin binding and hydrophobic domains, together allowing a separate toxic subunit to sneak into the target cell. Mechanistically, the latter sabotages codon–anticodon interaction by endonucleolytic cleavage of specific tRNAs 3′ of the wobble nucleotide. This primary action provokes a number of downstream effects, including DNA damage accumulation, which contribute to the cell-killing efficiency and highlight the importance of proper transcript decoding capacity for other cellular processes than translation itself. Since wobble uridine modifications are crucial for efficient anticodon nuclease (ACNase) action of yeast killer toxins, the latter are valuable tools for the characterization of a surprisingly complex network regulating the addition of wobble base modifications in tRNA.

Keywords: Killer yeast; Linear plasmids; Zymocin; PaT

Generation and characterization of neutralizing human recombinant antibodies against antigenic site II of rabies virus glycoprotein by Lina Sun; Zhe Chen; Li Yu; Jingshuang Wei; Chuan Li; Jing Jin; Xinxin Shen; Xinjun Lv; Qing Tang; Dexin Li; Mifang Liang (pp. 357-366).

The currently recommended treatment for individuals exposed to rabies virus (RV) is post-exposure prophylaxis (PEP) through the combined administration of rabies vaccine and rabies immune globulin (RIG). Human monoclonal antibodies (mAbs) that neutralize RV offer an opportunity to replace RIG for rabies PEP. Here, a combinatorial human Fab library was constructed using antibody genes derived from the blood of RV-vaccinated donors. Selections of this library against purified RV virions resulted in the identification of 11 unique Fab antibodies specific for RV glycoprotein. Of the Fab antibodies, five were converted to full human IgG1 format. The human IgG antibodies revealed high binding affinity and neutralizing activities against RV fixed strains through a rapid fluorescent focus inhibition test in vitro as well as the early stage protective function after exposure to RV infection in vivo. Furthermore, epitope mapping and binding competition analysis showed that all of obtained human neutralizing and protective antibodies were directed to the antigenic site II of RV glycoprotein. Our results provide not only important insight into the protective immune response to RV in humans, but also more candidates eligible for use in a mAb cocktail aimed at replacing RIG for rabies post-exposure prophylaxis.

Keywords: Rabies virus (RV); Monoclonal antibody (mAb); Human Fab library; Glycoprotein (gp); Post-exposure prophylaxis (PEP)

On the influence of overexpression of phosphoenolpyruvate carboxykinase in Streptomyces lividans on growth and production of human tumour necrosis factor-alpha by Ivan Lule; Bárbara Maldonado; Pieter-Jan D’Huys; Lieve Van Mellaert; Jan Van Impe; Kristel Bernaerts; Jozef Anné (pp. 367-372).

Streptomyces lividans has shown potential as an expression system for heterologous proteins. Overexpression of proteic factors important for heterologous protein production is a valuable approach to improve yields of such proteins. Comparative transcriptomic analysis revealed that several genes were differentially expressed in strains involved in heterologous protein production. For instance, the gene-encoding phosphoenolpyruvate carboxykinase (pepck) showed a significant twofold change in recombinant S. lividans producing human tumour necrosis factor-alpha (hTNF-α). The effect of pepck overexpression on S. lividans TK24 and its hTNF-α producing recombinant was thus investigated in bench-top fermenters. Results obtained revealed that pepck overexpression resulted into a twofold increase in specific PEPCK activity during growth. This overexpression is correlated with slower growth rate, reduced excretion of pyruvate and less alkalinisation of the growth medium when compared with the control strain. After 26 h of fermentation, hTNF-α yields were enhanced (up to 1.7-fold) in the pepck-overexpressing S. lividans TK24, demonstrating that this metabolic engineering approach is indeed promising for heterologous protein production.

Keywords: Streptomyces lividans ; Phosphoenolpyruvate carboxykinase (PEPCK); Human tumour necrosis factor-alpha (hTNF-α); Heterologous proteins

Co-production of 3-hydroxypropionic acid and 1,3-propanediol from glycerol using resting cells of recombinant Klebsiella pneumoniae J2B strain overexpressing aldehyde dehydrogenase by Vinod Kumar; Mugesh Sankaranarayanan; Kyeung-eun Jae; Meetu Durgapal; Somasundar Ashok; Yeounjoo Ko; Ritam Sarkar; Sunghoon Park (pp. 373-383).

The co-production of 3-hydroxypropionic acid (3HP) and 1,3-propanediol (PDO) from glycerol was studied using the resting cells of a recombinant Klebsiella pneumoniae J2B strain that overexpresses an aldehyde dehydrogenase (KGSADH). Active biomass was produced in a mineral salt medium containing yeast extract and glycerol under a range of aeration conditions, and shifted to potassium phosphate buffer containing glycerol for bioconversion. The microaerobic or anaerobic conditions were favorable for both the production of active biomass and subsequent bioconversion. At the flask level, the recombinant strain (2.0 g CDW/L) grown under microaerobic conditions produced 43.2 mM 3HP and 59.0 mM PDO from glycerol (117 mM) in 30 min with a cumulative yield of 0.87 (mol/mol). The fed-batch bioconversion, which was performed in a 1.5-L bioreactor with 1.0 g CDW/L at a constant pH 7.0 under anaerobic conditions, resulted in 125.6 mM 3HP and 209.5 mM PDO in 12 h with a cumulative overall productivity, yield, and maximum specific production rate of 27.9 mmol/L/h, 0.71 (mol/mol), and 128.5 mmol/g CDW/h, respectively. Lactate, succinate and 2,3-butanediol were the major by-products, whereas the production of acetate and ethanol was marginal. This is the first report of the simultaneous production of 3HP and PDO from glycerol using a resting cell system.

Keywords: Klebsiella pneumoniae ; Co-production; Bioconversion; Resting cells; 3-Hydroxypropionic acid; 1,3-Propanediol

Recombinant hepatitis B surface antigen production in Aspergillus niger: evaluating the strategy of gene fusion to native glucoamylase by ER James; WH van Zyl; PJ van Zyl; JF Görgens (pp. 385-394).

This study demonstrates the potential of Aspergillus niger as a candidate expression system for virus-like particle production using gene fusion. Hepatitis B surface antigen (HBsAg) production, targeted through the secretory pathway in A. niger, resulted in completely assembled and properly folded HBsAg. This was achieved by implementing a gene fusion strategy using the highly expressed catalytic domain of the native glucoamylase gene (GlaA G2) fused to the HBsAg S gene. The inducible glucoamylase promoter (GlaA p) was used to control transcription in the A. niger D15 host. The gene fusion strategy was designed for cleavage of the fused product by the KEX2-like protease, resulting in intracellular accumulation of HBsAg and extracellular secretion of glucoamylase. Immunodetection using a monoclonal HBsAg antibody could not detect the fused GlaA G2 ::S product in intracellular and extracellular fractions, indicating that full assembly and maturation of HBsAg occurred after cleavage of the fused product in the Golgi complex. Several breakdown products showing an immunoreactive response to the glucoamylase polyclonal antibody indicated a level of intracellular degradation. The choice of carbon source used in cultivation significantly affected HBsAg production levels through induction of the glucoamylase promoter. The highest specific HBsAg production was observed during growth on inducing substrates of starch and its degradation products (maltodextrin and maltose), although residual glucose accumulation in the mid-exponential phase reduced HBsAg production. HBsAg production in starch-based cultures may be improved further by optimization of the rates of starch hydrolysis by glucoamylase and subsequent glucose consumption by the host.

Keywords: Aspergillus niger ; Gene fusion; Inducible GlaA promoter; HBsAg; Glucoamylase; KEX2-like processing; Fermentation

Enzymatic decolorization of spent textile dyeing baths composed by mixtures of synthetic dyes and additives by Ilaria Ciullini; Antonella Gullotto; Silvia Tilli; Giovanni Sannia; Riccardo Basosi; Andrea Scozzafava; Fabrizio Briganti (pp. 395-405).

The effects of different components of real dyeing bath formulations, such as the equalizing and fixing additives—acids, salts, and surfactants—on the decolorization catalyzed by Funalia trogii enzymatic extracts, were investigated to understand their influence on the recalcitrance to biodegradation of this type of wastewater. The decolorization of selected dyes and dye mixtures after tissue dyeing was performed in the presence/absence of auxiliary compounds. All spent dyeing baths were enzymatically decolorized to different extents, by the addition of extracts containing laccase only or laccase plus cellobiose dehydrogenase. Whereas surfactant auxiliaries, in some instances, inhibit the decolorization of spent dyeing baths, in several occurrences the acid/salt additives favor the enzymatic process. In general, the complete spent dyeing formulations are better degraded than those containing the dyes only. The comparison of extracellular extracts obtained from spent straws from the commercial growth of Pleurotus sp. mushrooms with those from F. trogii reveals similar decolorization extents thus allowing to further reduce the costs of bioremediation.

Keywords: Trametes trogii ; Funalia trogii ; Pleurotus ; Laccase; Cellobiose dehydrogenase; Textile dye mixtures; Decolorization; Bioremediation; Additives

Expression and characterization of styrene monooxygenases of Rhodococcus sp. ST-5 and ST-10 for synthesizing enantiopure (S)-epoxides by Hiroshi Toda; Ryouta Imae; Tomoko Komio; Nobuya Itoh (pp. 407-418).

Styrene monooxygenase (StyA, SMOA)- and flavin oxidoreductase (StyB, SMOB)-coding genes of styrene-assimilating bacteria Rhodococcus sp. ST-5 and ST-10 were successfully expressed in Escherichia coli. Determined amino acid sequences of StyAs and StyBs of ST-5 and ST-10 showed more similarity with those of Pseudomonas than with self-sufficient styrene monooxygenase (StyA2B) of Rhodococcus. Recombinant enzymes were purified from E. coli cells as functional proteins, and their properties were characterized in detail. StyBs (flavin oxidoreductase) of strains ST-5 and ST-10 have similar enzymatic properties to those of Pseudomonas, but StyB of strain ST-10 exhibited higher temperature stability than that of strain ST-5. StyAs of strains ST-5 and ST-10 catalyzed the epoxidation of vinyl side-chain of styrene and its derivatives and produced (S)-epoxides from styrene derivatives and showed high stereoselectivity. Both StyAs showed higher specific activity on halogenated styrene derivatives than on styrene itself. Additionally, the enzymes could catalyze the epoxidation of short-chain 1-alkenes to the corresponding (S)-epoxides. Aromatic compounds including styrene, 3-chlorostyrene, styrene oxide, and benzene exhibited marked inhibition of SMO reaction, although linear 1-alkene showed no inhibition of SMO activity at any concentration.

Keywords: Rhodococcus sp.; Styrene monooxygenase; Flavin oxidoreductase; Epoxidation; (S)-epoxides; Biocatalysis

Completing the series of BVMOs involved in camphor metabolism of Pseudomonas putida NCIMB 10007 by identification of the two missing genes, their functional expression in E. coli, and biochemical characterization by Maria Kadow; Kathleen Loschinski; Stefan Saß; Marlen Schmidt; Uwe T. Bornscheuer (pp. 419-429).

The camphor-degrading Baeyer–Villiger monooxygenases (BVMOs) from Pseudomonas putida NCIMB 10007 have been of interest for over 40 years. So far the FMN- and NADH-dependent type II BVMO 3,6-diketocamphane 1,6-monooxygenase (3,6-DKCMO) and the FAD- and NADPH-dependent type I BVMO 2-oxo-∆³-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase (OTEMO) have not been entirely studied, since it was not possible to produce those enzymes in satisfactory amounts and purity. In this study, we were able to clone and recombinantly express both enzymes and subsequently use them as biocatalysts for various mono- and bicyclic ketones. Full conversion could be reached with both enzymes towards (±)-cis-bicyclo[3.2.0]hept-2-en-6-one and with 3,6-DKCMO towards (−)-camphor. Further OTEMO gave full conversion with norcamphor. OTEMO was found to have a pH optimum of 9 and a temperature optimum of 20 °C and converted (±)-cis-bicyclo[3.2.0]hept-2-en-6-one with a k _cat/K _M value of 49.3 mM⁻¹ s⁻¹.

Keywords: Baeyer–Villiger monooxygenase; Camphor; Pseudomonas putida ; Bicyclic ketones

Probiotic features of Lactobacillus plantarum mutant strains by Pasquale Bove; Anna Gallone; Pasquale Russo; Vittorio Capozzi; Marzia Albenzio; Giuseppe Spano; Daniela Fiocco (pp. 431-441).

In this study, the probiotic potential of Lactobacillus plantarum wild-type and derivative mutant strains was investigated. Bacterial survival was evaluated in an in vitro system, simulating the transit along the human oro-gastro-intestinal tract. Interaction with human gut epithelial cells was studied by assessing bacterial adhesive ability to Caco-2 cells and induction of genes involved in innate immunity. L. plantarum strains were resistant to the combined stress at the various steps of the simulated gastrointestinal tract. Major decreases in the viability of L. plantarum cells were observed mainly under drastic acidic conditions (pH ≤ 2.0) of the gastric compartment. Abiotic stresses associated to small intestine poorly affected bacterial viability. All the bacterial strains significantly adhered to Caco-2 cells, with the ΔctsR mutant strain exhibiting the highest adhesion. Induction of immune-related genes resulted higher upon incubation with heat-inactivated bacteria rather than with live ones. For specific genes, a differential transcriptional pattern was observed upon stimulation with different L. plantarum strains, evidencing a possible role of the knocked out bacterial genes in the modulation of host cell response. In particular, cells from Δhsp18.55 and ΔftsH mutants strongly triggered immune defence genes. Our study highlights the relevance of microbial genetic background in host–probiotic interaction and might contribute to identify candidate bacterial genes and molecules involved in probiosis.

Keywords: Bacterial adhesion; Immune modulation; Lactobacillus plantarum mutants; Probiotic; Mucosal barrier

Enhanced activity of Rhizomucor miehei lipase by directed evolution with simultaneous evolution of the propeptide by Jue Wang; Dan Wang; Bo Wang; Zhuo-hang Mei; Ji Liu; Hong-wei Yu (pp. 443-450).

Propeptides are short sequences that facilitate the folding of their associated proteins. The present study found that the propeptide of Rhizomucor miehei lipase (RML) was not proteolytically removed in Escherichia coli. Moreover, RML was not expressed if the propeptide was removed artificially during the cloning process in E. coli. This behavior in E. coli permitted the application of directed evolution to full-length RML, which included both propeptide and catalytic domain, to explore the role played by the propeptide in governing enzyme activity. The catalytic rate constant, k _cat, of the most active mutant RML protein (Q5) was increased from 10.63 ± 0.80 to 71.44 ± 3.20 min⁻¹ after four rounds of screening. Sequence analysis of the mutant displayed three mutations in the propeptide (L57V, S65A, and V67A) and two mutations in the functional region (I111T and S168P). This result showed that improved activity was obtained with essential involvement by mutations in the propeptide, meaning that the majority of mutants with enhanced activity had simultaneous mutations in propeptide and catalytic domains. This observation leads to the hypothesis that directed evolution has simultaneous and synergistic effects on both functional and propeptide domains that arise from the role played by the propeptide in the folding and maturation of the enzyme. We suggest that directed evolution of full-length proteins including their propeptides is a strategy with general validity for extending the range of conformations available to proteins, leading to the enhancement of the catalytic rates of the enzymes.

Keywords: RML; Propeptide; Protein folding; Directed evolution; Activity

Transcriptional regulation and increased production of asukamycin in engineered Streptomyces nodosus subsp. asukaensis strains by Pengfei Xie; Yan Sheng; Takuya Ito; Taifo Mahmud (pp. 451-460).

Asukamycin, a member of the manumycin family of antibiotics, exhibits strong antibacterial, antifungal, and antineoplastic activities. However, its production in the wild-type strain of Streptomyces nodosus subsp. asukaensis ATCC 29757 is relatively low. Recently, the biosynthetic gene cluster for asukamycin was identified in the producing organism, and among the 36 genes reported in the cluster, six (asuR1–asuR6) were proposed to encode proteins that function as transcriptional regulators. In order to investigate their involvement in asukamycin biosynthesis and to engineer mutant strains of S. nodosus that are able to produce large amounts of asukamycin, we carried out in vivo gene inactivation, transcriptional analysis of the biosynthetic genes in the mutants, and gene duplication in the producing strain of S. nodosus. The results show that two of the putative regulatory genes (asuR1 and asuR5) are critical for asukamycin biosynthesis, whereas others regulate the pathway at various levels. Overexpression of a gene cassette harboring asuR1, asuR2, asuR3, and asuR4 in S. nodosus resulted in changes in morphology of the producing strain and an approximately 14-fold increase of asukamycin production. However, overexpression of the individual genes did not give a comparable cumulative level of asukamycin production, suggesting that some, if not all, of the gene products act synergistically to regulate the biosynthesis of this antibiotic.

Keywords: Asukamycin; Transcriptional regulation; Biosynthesis; Genetic engineering

RT-qPCR analysis of putative beer-spoilage gene expression during growth of Lactobacillus brevis BSO 464 and Pediococcus claussenii ATCC BAA-344^T in beer by Jordyn Bergsveinson; Vanessa Pittet; Barry Ziola (pp. 461-470).

Lactic acid bacteria (LAB) contamination of beer presents a continual economic threat to brewers. Interestingly, only certain isolates of LAB can grow in the hostile beer environment (e.g., as studied here, Lactobacillus brevis BSO 464 (Lb464) and a non-ropy isolate of Pediococcus claussenii ATCC BAA-344^T (Pc344NR)), indicating that significant genetic specialization is required. The genes hitA, horA, horB, horC, and bsrA, which have been proposed to confer beer-spoiling ability to an organism, are suspected of counteracting the antimicrobial effects of hops. However, these genes are not present in the same combination (if at all) across beer-spoiling organisms. As such, we sought to investigate the extent to which these genes participate during Lb464 and Pc344NR mid-logarithmic growth in beer through reverse transcription quantitative PCR analysis. We first determined the optimal reference gene set needed for data normalization and, for each bacterium, established that two genes were needed for accurate assessment of gene expression. Following this, we found that horA expression was induced for Pc344NR, but not for Lb464, during growth in beer. Instead, horC expression was dramatically increased in Lb464 when growing in beer, whereas no change was detected for the other putative beer-spoilage-related genes. This indicates that HorC may be one of the principle mediators enabling growth of Lb464 in beer, whereas in Pc344NR, this may be attributable to HorA. These findings not only reveal that Lb464 and Pc344NR are unique in their beer-specific genetic expression profile but also indicate that a range of genetic specialization exists among beer-spoilage bacteria.

Keywords: Beer spoilage; Gene expression; Hop resistance; Lactic acid bacteria; Reference gene normalization; RT-qPCR

Air-drying kinetics affect yeast membrane organization and survival by Guillaume Lemetais; Sébastien Dupont; Laurent Beney; Patrick Gervais (pp. 471-480).

The plasma membrane (PM) is a key structure for the survival of cells during dehydration. In this study, we focused on the concomitant changes in survival and in the lateral organization of the PM in yeast strains during desiccation, a natural or technological environmental perturbation that involves transition from a liquid to a solid medium. To evaluate the role of the PM in survival during air-drying, a wild-type yeast strain and an osmotically fragile mutant (erg6Δ) were used. The lateral organization of the PM (microdomain distribution) was observed using a fluorescent marker related to a specific green fluorescent protein-labeled membrane protein (Sur7-GFP) after progressive or rapid desiccation. We also evaluated yeast behavior during a model dehydration experiment performed in liquid medium (osmotic stress). For both strains, we observed similar behavior after osmotic and desiccation stresses. In particular, the same lethal magnitude of dehydration and the same lethal kinetic effect were found for both dehydration methods. Thus, yeast survival after progressive air-drying was related to PM reorganization, suggesting the positive contribution of passive lateral rearrangements of the membrane components. This study also showed that the use of glycerol solutions is an efficient means to simulate air-drying desiccation.

Keywords: Desiccation; Osmotic dehydration; Cell survival; Plasma membrane; Yeast

The mitogen-activated protein kinase kinase kinase BcOs4 is required for vegetative differentiation and pathogenicity in Botrytis cinerea by Qianqian Yang; Leiyan Yan; Qin Gu; Zhonghua Ma (pp. 481-492).

The high-osmolarity glycerol signal pathway plays an important role in the response of fungi to various environmental stresses. In this study, we characterized a mitogen-activated protein kinase kinase kinase gene BcOS4 in Botrytis cinerea, which is homologous to Saccharomyces cerevisiae SSK2/SSK22. The BcOS4 deletion mutant was significantly impaired in vegetative growth and conidial formation. The mutant exhibited increased sensitivity to the osmotic, oxidative stresses and to the fungicides iprodione and fludioxonil. Western blot analysis showed that BcSak1, a putative downstream component of BcOs4, was not phosphorylated in the mutant. In addition, the BcOS4 mutant was unable to infect leaves of rapeseed and cucumber, and grape fruits, although it can cause disease on apple fruits. All the defects were restored by genetic complementation of the BcOS4 deletion mutant with the wild-type BcOS4 gene. The data of this study indicate that BcOS4 is involved in vegetative differentiation, virulence, adaption to hyperosmotic and oxidative stresses, and to fungicides in B. cinerea.

Keywords: Botrytis cinerea ; Mitogen-activated protein kinase kinase kinase; Vegetative differentiation; Pathogenicity

The effect of sourdough and calcium propionate on the microbial shelf-life of salt reduced bread by Markus C. E. Belz; Regina Mairinger; Emanuele Zannini; Liam A. M. Ryan; Kevin D. Cashman; Elke K. Arendt (pp. 493-501).

The consumption of low-salt bread represents an efficient way to improve public health by decreasing cardiovascular health issues related to increased intakes of sodium chloride (NaCl). The reduction of NaCl influences the bread quality characteristics, in particular the shelf-life. Calcium propionate (CP) is commonly used in bread as an antifungal agent. Alternatively, sourdough can be used as a natural preservative. This work addresses the feasibility of NaCl reduction in wheat bread focussing on shelf-life and the compensation using sourdough as well as chemical preservatives. The impact of NaCl reduction and the addition of preservative agents in conjunction with different NaCl concentrations on the shelf-life of bread were tested under ‘environmental’ conditions in a bakery as well as using challenge tests against selected fungi. The challenge tests were performed using fungi commonly found in the bakery environment such as Penicillium expansum, Fusarium culmorum and Aspergillus niger. NaCl reduction decreased the shelf-life by 1–2 days. The addition of sourdough with antifungal activity prolonged the shelf-life to 12–14 days whereas the addition of 0.3 % calcium propionate prolonged the shelf-life to 10–12 days only. The fungal challenge tests revealed differences in the determined shelf-life between the different fungi based on their resistance. Similar antifungal performance was observed in sourdough breads and calcium propionate breads when tested against the different indicator moulds. The findings of this study indicate that addition of sourdough fermented using a specifically selected antifungal Lactobacillus amylovorus DSM 19280 can replace the chemical preservative calcium propionate addition and compensate for the reduced level and, therefore, guarantee the product safety of low-salt bread.

Keywords: Bread spoilage; Biopreservation; Low-salt bread; Antifungal lactic acid bacteria; Calcium propionate; Fungal contamination

Effect of berberine on Escherichia coli, Bacillus subtilis, and their mixtures as determined by isothermal microcalorimetry by Wei-Jun Kong; Xiao-Yan Xing; Xiao-He Xiao; Yan-Ling Zhao; Jian-He Wei; Jia-Bo Wang; Rui-Chuang Yang; Mei-Hua Yang (pp. 503-510).

The strong toxicity of pathogenic bacteria has resulted in high levels of morbidity and mortality in the general population. Developing effective antibacterial agents with high efficacy and long activity is in great demand. In this study, the microcalorimetric technique based on heat output of bacterial metabolism was applied to evaluate the effect of berberine on Escherichia coli, Bacillus subtilis, individually and in a mixture of both using a multi-channel microcalorimeter. The differences in shape of the power–time fingerprints and thermokinetic parameters of microorganism growth were compared. The results revealed that low concentration (20 μg/mL) of berberine began to inhibit the growth of E. coli and mixed microorganisms, while promoting the growth of B. subtilis; high concentration of berberine (over 100 μg/mL) inhibited B. subtilis. The endurance of E. coli to berberine was obviously lower than B. subtilis, and E. coli could decrease the endurance of B. subtilis to berberine. The sequence of half-inhibitory concentration (IC₅₀) of berberine was: B. subtilis (952.37 μg/mL) > mixed microorganisms (682.47 μg/mL) > E. coli (581.69 μg/mL). Berberine might be a good selection of antibacterial agent used in the future. The microcalorimetric method should be strongly suggested in screening novel antibacterial agents for fighting against pathogenic bacteria.

Keywords: E. coli ; B. subtilis ; Mixed microorganisms; Berberine; Isothermal microcalorimetry

Highly sensitive detection and quantification of the pathogen Yersinia ruckeri in fish tissues by using real-time PCR by Asmine Bastardo; Carmen Ravelo; Jesús L. Romalde (pp. 511-520).

Yersinia ruckeri is the causative agent of enteric redmouth diseases (ERM) and one of the major bacterial pathogens causing losses in salmonid aquaculture. Since recent ERM vaccine breakdowns have been described mostly attributed to emergence of Y. ruckeri biotype 2 strains, rapid, reproducible, and sensitive methods for detection are needed. In this study, a real-time polymerase chain reaction (PCR) primer/probe set based on recombination protein A (recA) gene was designed and optimized to improve the detection of Y. ruckeri. The primer/probe set proved to have a 100 % analytical specificity and a sensitivity of 1.8 ag μl⁻¹, equivalent to 1.7 colony-forming units (CFU) ml⁻¹, for purified DNA, 3.4 CFU g⁻¹ for seeded liver, kidney, and spleen tissues, and 0.34 CFU/100 μl⁻¹ for seeded blood, respectively. The assay was highly reproducible with low variation coefficient values for intra- and inter-run experiments (2.9 % and 9.5 %, respectively). Following optimization, the assay was used to detect changes in the bacterial load during experimental infection. Rainbow trout (Onchorhynchus mykiss) were exposed to two strains of Y. ruckeri (biotype 1 and biotype 2) by intraperitoneal inoculation. Internal organs (liver, kidney, spleen) and blood were biopsied from dead fish daily for 15 days to quantify copies of pathogen DNA per gram of tissue. The findings showed the efficacy of this real-time PCR assay to quantify Y. ruckeri cells in the fish tissues and also confirmed this assay as a non-lethal method for the detection of this pathogen in blood samples.

Keywords: Real-time PCR; Yersinia ruckeri ; Enteric redmouth disease; Oncorhynchus mykiss ; Non-lethal method

Construction of in vitro transcription system for Corynebacterium glutamicum and its use in the recognition of promoters of different classes by Jiří Holátko; Radoslav Šilar; Alžbeta Rabatinová; Hana Šanderová; Petr Halada; Jan Nešvera; Libor Krásný; Miroslav Pátek (pp. 521-529).

To facilitate transcription studies in Corynebacterium glutamicum, we have developed an in vitro transcription system for this bacterium used as an industrial producer of amino acids and a model organism for actinobacteria. This system consists of C. glutamicum RNA polymerase (RNAP) core (α2, β, β′), a sigma factor and a promoter-carrying DNA template, that is specifically recognized by the RNAP holoenzyme formed. The RNAP core was purified from the C. glutamicum strain with the modified rpoC gene, which produced His-tagged β′ subunit. The C. glutamicum sigA and sigH genes were cloned and overexpressed using the Escherichia coli plasmid vector, and the sigma subunits σ^A and σ^H were purified by affinity chromatography. Using the reconstituted C. glutamicum holo-RNAPs, recognition of the σ^A- and σ^H-dependent promoters and synthesis of the specific transcripts was demonstrated. The developed in vitro transcription system is a novel tool that can be used to directly prove the specific recognition of a promoter by the particular σ factor(s) and to analyze transcriptional control by various regulatory proteins in C. glutamicum.

Keywords: Corynebacterium glutamicum ; In vitro transcription; RNA polymerase; Promoter; Sigma factor

Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir by Serge Maurice Mbadinga; Kai-Ping Li; Lei Zhou; Li-Ying Wang; Shi-Zhong Yang; Jin-Feng Liu; Ji-Dong Gu; Bo-Zhong Mu (pp. 531-542).

Microbial assemblage in an n-alkanes-dependent thermophilic methanogenic enrichment cultures derived from production waters of a high-temperature petroleum reservoir was investigated in this study. Substantially higher amounts of methane were generated from the enrichment cultures incubated at 55 °C for 528 days with a mixture of long-chain n-alkanes (C₁₅–C₂₀). Stoichiometric estimation showed that alkanes-dependent methanogenesis accounted for about 19.8% of the total amount of methane expected. Hydrogen was occasionally detected together with methane in the gas phase of the cultures. Chemical analysis of the liquid cultures resulted only in low concentrations of acetate and formate. Phylogenetic analysis of the enrichment revealed the presence of several bacterial taxa related to Firmicutes, Thermodesulfobiaceae, Thermotogaceae, Nitrospiraceae, Dictyoglomaceae, Candidate division OP8 and others without close cultured representatives, and Archaea predominantly related to uncultured members in the order Archaeoglobales and CO₂-reducing methanogens. Screening of genomic DNA retrieved from the alkanes-amended enrichment cultures also suggested the presence of new alkylsuccinate synthase alpha-subunit (assA) homologues. These findings suggest the presence of poorly characterized (putative) anaerobic n-alkanes degraders in the thermophilic methanogenic enrichment cultures. Our results indicate that methanogenesis of alkanes under thermophilic condition is likely to proceed via syntrophic acetate and/or formate oxidation linked with hydrogenotrophic methanogenesis.

Keywords: Alkylsuccinate synthase; High-temperature petroleum reservoir; Hydrogenotrophic methanogenesis; Methanogenic degradation of alkanes; Syntrophic acetate oxidation; Microbial community

Mercury-resistant rhizobial bacteria isolated from nodules of leguminous plants growing in high Hg-contaminated soils by Beatriz Ruiz-Díez; Miguel A. Quiñones; Susana Fajardo; Miguel A. López; Pablo Higueras; Mercedes Fernández-Pascual (pp. 543-554).

A survey of symbiotic bacteria from legumes grown in high mercury-contaminated soils (Almadén, Spain) was performed to produce a collection of rhizobia which could be well adapted to the environmental conditions of this region and be used for restoration practices. Nineteen Hg-tolerant rhizobia were isolated from nodules of 11 legume species (of the genera Medicago, Trifolium, Vicia, Lupinus, Phaseolus, and Retama) and characterized. Based on their growth on Hg-supplemented media, the isolates were classified into three susceptibility groups. The minimum inhibitory concentrations (MICs) and the effective concentrations that produce 50% mortality identified the patterns of mercury tolerance and showed that 15 isolates were tolerant. The dynamics of cell growth during incubation with mercury showed that five isolates were unaffected by exposure to Hg concentrations under the MICs. Genetic analyses of the 16S rRNA gene assigned ten strains to Rhizobium leguminosarum, six to Ensifer medicae, two to Bradyrhizobium canariense, and one to Rhizobium radiobacter. Inoculation of host plants and analysis of the nodC genes revealed that most of them were symbiotically effective. Finally, three isolates were selected for bioremediation processes with restoration purposes on the basis of their levels of Hg tolerance, their response to high concentrations of this heavy metal, and their genetic affiliation and nodulation capacity.

Keywords: Mercury-tolerant rhizobia; Hg-contaminated land; Rhizobia–legume symbiosis; Bioremediation

Bioethanol production from Scenedesmus obliquus sugars: the influence of photobioreactors and culture conditions on biomass production by J. R. Miranda; P. C. Passarinho; L. Gouveia (pp. 555-564).

A closed-loop vertical tubular photobioreactor (PBR), specially designed to operate under conditions of scarce flat land availability and irregular solar irradiance conditions, was used to study the potential of Scenedesmus obliquus biomass/sugar production. The results obtained were compared to those from an open-raceway pond and a closed-bubble column. The influence of the type of light source and the regime (natural vs artificial and continuous vs light/dark cycles) on the growth of the microalga and the extent of the sugar accumulation was studied in both PBRs. The best type of reactor studied was a closed-loop PBR illuminated with natural light/dark cycles. In all the cases, the relationship between the nitrate depletion and the sugar accumulation was observed. The microalga Scenedesmus was cultivated for 53 days in a raceway pond (4,500 L) and accumulated a maximum sugar content of 29 % g/g. It was pre-treated for carrying out ethanol fermentation assays, and the highest ethanol concentration obtained in the hydrolysate fermented by Kluyveromyces marxianus was 11.7 g/L.

Keywords: Scenedesmus obliquus ; Photobioreactors; Light; Sugars; Bioethanol

Temperature increases from 55 to 75 °C in a two-phase biogas reactor result in fundamental alterations within the bacterial and archaeal community structure by Antje Rademacher; Christine Nolte; Mandy Schönberg; Michael Klocke (pp. 565-576).

Agricultural biogas plants were operated in most cases below their optimal performance. An increase in the fermentation temperature and a spatial separation of hydrolysis/acetogenesis and methanogenesis are known strategies in improving and stabilizing biogas production. In this study, the dynamic variability of the bacterial and archaeal community was monitored within a two-phase leach bed biogas reactor supplied with rye silage and straw during a stepwise temperature increase from 55 to 75 °C within the leach bed reactor (LBR), using TRFLP analyses. To identify the terminal restriction fragments that were obtained, bacterial and archaeal 16S rRNA gene libraries were constructed. Above 65 °C, the bacterial community structure changed from being Clostridiales-dominated toward being dominated by members of the Bacteroidales, Clostridiales, and Thermotogales orders. Simultaneously, several changes occurred, including a decrease in the total cell count, degradation rate, and biogas yield along with alterations in the intermediate production. A bioaugmentation with compost at 70 °C led to slight improvements in the reactor performance; these did not persist at 75 °C. However, the archaeal community within the downstream anaerobic filter reactor (AF), operated constantly at 55 °C, altered by the temperature increase in the LBR. At an LBR temperature of 55 °C, members of the Methanobacteriales order were prevalent in the AF, whereas at higher LBR temperatures Methanosarcinales prevailed. Altogether, the best performance of this two-phase reactor was achieved at an LBR temperature of below 65 °C, which indicates that this temperature range has a favorable effect on the microbial community responsible for the production of biogas.

Keywords: Anaerobic digestion; TRFLP; Bioaugmentation; Methanogenesis; Microbial communities; Microbial population dynamics

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Applied Microbiology and Biotechnology (v.96, #2)

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Applied Microbiology and Biotechnology (v.96, #2)