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Applied Microbiology and Biotechnology (v.92, #4)

Influence of adhesion on aerobic biodegradation and bioremediation of liquid hydrocarbons by Hassan Abbasnezhad; Murray Gray; Julia M. Foght (pp. 653-675).

Biodegradation of poorly water-soluble liquid hydrocarbons is often limited by low availability of the substrate to microbes. Adhesion of microorganisms to an oil–water interface can enhance this availability, whereas detaching cells from the interface can reduce the rate of biodegradation. The capability of microbes to adhere to the interface is not limited to hydrocarbon degraders, nor is it the only mechanism to enable rapid uptake of hydrocarbons, but it represents a common strategy. This review of the literature indicates that microbial adhesion can benefit growth on and biodegradation of very poorly water-soluble hydrocarbons such as n-alkanes and large polycyclic aromatic hydrocarbons dissolved in a non-aqueous phase. Adhesion is particularly important when the hydrocarbons are not emulsified, giving limited interfacial area between the two liquid phases. When mixed communities are involved in biodegradation, the ability of cells to adhere to the interface can enable selective growth and enhance bioremediation with time. The critical challenge in understanding the relationship between growth rate and biodegradation rate for adherent bacteria is to accurately measure and observe the population that resides at the interface of the hydrocarbon phase.

Keywords: Adhesion; Attachment; Bioavailability; Hydrophobicity; Uptake

Penicillin: the medicine with the greatest impact on therapeutic outcomes by Nelson Kardos; Arnold L. Demain (pp. 677-687).

The principal point of this paper is that the discovery of penicillin and the development of the supporting technologies in microbiology and chemical engineering leading to its commercial scale production represent it as the medicine with the greatest impact on therapeutic outcomes. Our nomination of penicillin for the top therapeutic molecule rests on two lines of evidence concerning the impact of this event: (1) the magnitude of the therapeutic outcomes resulting from the clinical application of penicillin and the subsequent widespread use of antibiotics and (2) the technologies developed for production of penicillin, including both microbial strain selection and improvement plus chemical engineering methods responsible for successful submerged fermentation production. These became the basis for production of all subsequent antibiotics in use today. These same technologies became the model for the development and production of new types of bioproducts (i.e., anticancer agents, monoclonal antibodies, and industrial enzymes). The clinical impact of penicillin was large and immediate. By ushering in the widespread clinical use of antibiotics, penicillin was responsible for enabling the control of many infectious diseases that had previously burdened mankind, with subsequent impact on global population demographics. Moreover, the large cumulative public effect of the many new antibiotics and new bioproducts that were developed and commercialized on the basis of the science and technology after penicillin demonstrates that penicillin had the greatest therapeutic impact event of all times.

Keywords: Penicillins; Antibiotics; β-Lactams; Cephalosporins; Carbapenems

Overproduction and secretion of α-ketoglutaric acid by microorganisms by Christina Otto; Venelina Yovkova; Gerold Barth (pp. 689-695).

This mini-review presents a summary of research results of biotechnological production of alpha-ketoglutaric acid (KGA) by bacteria and yeasts. KGA is of particular industrial interest due to its broad application scope, e.g., as building block chemical for the chemical synthesis of heterocycles, dietary supplement, component of infusion solutions and wound healing compounds, or as main component of new elastomers with a wide range of interesting mechanical and chemical properties. Currently KGA is produced via different chemical pathways, which have a lot of disadvantages. As an alternative several bacteria and yeasts have already been studied for their ability to produce KGA as well as for conditions of overproduction and secretion of this intermediate of the tricarboxylic acid cycle. The aim of this mini-review was to summarize the known data and to discuss the potentials of biotechnological processes of KGA production.

Keywords: α-Ketoglutaric acid (KGA); Biotechnological production; KGA producing organisms; Yarrowia lipolytica

Exopolysaccharide-producing cyanobacteria in heavy metal removal from water: molecular basis and practical applicability of the biosorption process by Roberto De Philippis; Giovanni Colica; Ernesto Micheletti (pp. 697-708).

Microorganisms can remove metals from the surrounding environment with various mechanisms, either as metabolically mediated processes or as a passive adsorption of metals on the charged macromolecules of the cell envelope. Owing to the presence of a large number of negative charges on the external cell layers, exopolysaccharides (EPS)-producing cyanobacteria have been considered very promising as chelating agents for the removal of positively charged heavy metal ions from water solutions, and an increasing number of studies on their use in metal biosorption have been published in recent years. In this review, the attention was mainly focused on the studies aimed at defining the molecular mechanisms of the metal binding to the polysaccharidic exocellular layers. Moreover, the few attempts done in the use of EPS-producing cyanobacteria for metal biosorption at pilot scale and with real wastewaters are here reviewed, discussing the main positive issues and the drawbacks so far emerging from these experiments.

Keywords: Exopolysaccharide-producing cyanobacteria; Heavy metal removal; Biosorption; Metal sorption mechanisms; Metal containing wastewaters; Electroplating effluents

Biodegradation of Enteromorpha prolifera by mangrove degrading micro-community with physical–chemical pretreatment by Chao Zhao; Lingwei Ruan (pp. 709-716).

The bacteria involved in the biodegradation of Enteromorpha prolifera (EP) are largely unknown, especially in offshore mangrove environments. In order to obtain the bacterial EP-degrading communities, sediments from a typical mangrove forest were sampled on the roots of mangrove in Dongzhai Port (Haikou, China). The sediments were enriched with crude EP powders as the sole carbon source. The bacterial composition of the resulting mangrove-degrading micro-community (MDMC), named D2-1, was analysed. With methods of plate cultivation and polymerase chain reaction–denaturing gradient gel electrophoresis and 16S rRNA library analysis, 18 bacteria belonging to nine genera were detected from this community. Among these detected bacteria, five major bands closely related to Bacillus, Marinobacter, Paenibacillus, Photobacterium, and Zhouia were determined. A novel two-step pretreatment for EP was proposed to lower the severity requirement of biodegraded pretreatment time. It consisted of a mild physical or chemical step (ultrasonic or H₂O₂) and a subsequent biological treatment with community D2-1. The combined treatment led to significant increases in the EP degradation. After combined treatment, the net yields of total soluble sugars and reducing sugars increased. The combined pretreatment of H₂O₂ (2%, 48 h) and MDMC (7 days) was more effective than the treatment of MDMC only for 15 days. It could remarkably shorten the residence time and reduce the losses of carbohydrates.

Keywords: Enteromorpha prolifera ; Mangrove-degrading community; Denaturing gradient gel electrophoresis; Combined treatment

Dynamics of bacterial communities during solid-state fermentation using agro-industrial wastes to produce poly-γ-glutamic acid, revealed by real-time PCR and denaturing gradient gel electrophoresis (DGGE) by Xiaoyu Yong; Yaqing Cui; Lihua Chen; Wei Ran; Qirong Shen; Xingming Yang (pp. 717-725).

The dynamics of bacterial communities play an important role in solid-state fermentation (SSF). Poly-γ-glutamic acid (γ-PGA) was produced by Bacillus amyloliquefaciens C1 in SSF using dairy manure compost and monosodium glutamate production residuals as basic substrates. The production of γ-PGA reached a maximum of 0.6% after 20 days fermentation. Real-time polymerase chain reaction showed the amount of total bacteria reached 3.95 × 10⁹ 16S rDNA copies/g sample after 30 days, which was in good accordance with the 4.80 × 10⁹ CFU/g obtained by plate counting. Denaturing gradient gel electrophoresis profile showed a reduction of microbial diversity during fermentation, while the inoculum, B. amyloliquefaciens C1, was detected as the dominant organism through the whole process. In the mesophilic phase of SSF, Proteobacteria was the dominant microbial, which was replaced by Firmicutes and Actinobacteria in the thermophilic phase. The molecular analysis of the bacterial diversity has significant potential for instructing the maturing process of SSF to produce γ-PGA at a large-scale level, which could be a benefit in the production of high quality and stable SSF products.

Keywords: Poly-γ-glutamic acid (γ-PGA); Solid-state fermentation (SSF); Real-time PCR; Denaturing gradient gel electrophoresis (DGGE); Dynamics of bacterial communities

Transformation of prednisolone to a 20β-hydroxy prednisolone compound by Streptomyces roseochromogenes TS79 by Wenquan Zhang; Li Cui; Mengyao Wu; Rongqing Zhang; Liping Xie; Hongzhong Wang (pp. 727-735).

Prednisolone represents an important compound in pharmaceutical preparations. To obtain more bioactive prednisolone derivatives, the microbial transformation of prednisolone was carried out. The steroid products were assigned by an interpretation of their spectral data using mass spectrometry and proton nuclear magnetic resonance (¹H NMR) analyses. The product was assigned the chemical structure of 11β, 17α, 20β, 21-tetrahydroxypregna-1,4-diene-3-one (named as 20β-hydroxy prednisolone). The conversion of prednisolone to 20β-hydroxy prednisolone by Streptomyces roseochromogenes TS79 was different from a previous study on the microbial transformation of steroid by this organism, which usually generates a 16α-hydroxy steroid product. The different reaction parameters for maximum conversion of prednisolone were optimized. The analysis revealed that the optimum values of the tested variables were 7.5 mg/ml prednisolone dissolved in DMSO and added to the 24-h pre-culture fermentation culture containing 0.05% MgSO₄ and incubated for 24 h. A conversion of 95.1% of prednisolone was observed, which has the potential to be used in industrial production.

Keywords: Streptomyces roseochromogenes TS79; C20β-hydroxy prednisolone; Microbial transformation; Hydroxylation

Substrate promiscuity of secondary metabolite enzymes: prenylation of hydroxynaphthalenes by fungal indole prenyltransferases by Xia Yu; Xiulan Xie; Shu-Ming Li (pp. 737-748).

Fungal prenyltransferases of the dimethylallyltryptophan synthase (DMATS) superfamily share no sequence, but structure similarity with the prenyltransferases of the CloQ/NphB group. The members of the DMATS superfamily have been reported to catalyze different prenylations of diverse indole or tyrosine derivatives, while some members of the CloQ/NphB group used hydroxynaphthalenes as prenylation substrates. In this study, we report for the first time the prenylation of hydroxynaphthalenes by the members of the DMATS superfamily. Three tryptophan-containing cyclic dipeptide prenyltransferases (AnaPT, CdpNPT and CdpC3PT), one tryptophan C7-prenyltransferase and one tyrosine O-prenyltransferase (SirD) were incubated with naphthalene and 11 derivatives. The enzyme activity and preference of the tested prenyltransferases towards hydroxynaphthalenes differed clearly from each other. For an accepted substrate, however, different enzymes produced usually the same major prenylation product, i.e. with a regular C-prenyl moiety at para- or ortho-position to a hydroxyl group. Regularly, O-prenylated and diprenylated derivatives were also identified as enzyme products of substrates with low conversion rates and regioselectivity. This was unequivocally proven by mass spectrometry and nuclear magnetic resonance analyses. The K _M values and turnover numbers (k _cat) of the enzymes towards selected hydroxynaphthalenes were determined to be in the range of 0.064–2.8 mM and 0.038–1.30 s⁻¹, respectively. These data are comparable to those obtained using indole derivatives. The results presented in this study expanded the potential usage of the members of the DMATS superfamily for production of prenylated derivatives including hydroxynaphthalenes.

Keywords: Enzyme promiscuity; Fungal indole prenyltransferase; DMATS superfamily; Prenylated hydroxynaphthalenes

Overexpression and biochemical characterization of DagA from Streptomyces coelicolor A3(2): an endo-type β-agarase producing neoagarotetraose and neoagarohexaose by Uyangaa Temuujin; Won-Jae Chi; Soon-Youl Lee; Yong-Keun Chang; Soon-Kwang Hong (pp. 749-759).

The DagA product of Streptomyces coelicolor is an agarase with a primary translation product (35 kDa) of 309 amino acids, including a 30-amino acid signal peptide. Although dagA expression in Streptomyces lividans under the control of its own set of promoters was previously reported, its enzymatic properties have never been elucidated. To develop an improved expression system for dagA, three types of strong promoters for the Streptomyces host were linked to dagA, and their efficiencies in DagA production were compared in S. lividans TK24. All of the transformants with dagA grew at improved rates and produced larger amounts of DagA in the modified R2YE medium containing 0.5% agar as the sole carbon source. Of the three transformants, the S. lividans TK24/pUWL201-DagA (ermE promoter) produced the highest agarase activity (A ₅₄₀ = 4.24), and even the S. lividans TK24/pHSEV1-DagA (tipA promoter) and S. lividans TK24/pWHM3-DagA (sprT promoter) produced higher agarase activity (A ₅₄₀ = 0.24 and 0.12, respectively) than the control (A ₅₄₀ = 0.01) in the modified R2YE medium. The mature form of DagA protein (32 kDa) was successfully purified by one-step affinity column chromatography by using agarose beads with excellent yield. The purified DagA was found to exhibit maximal agarase activity at 40°C and pH 7.0. The K _m, V _max, and K _cat values for agarose were 2.18 mg/ml (approximately 1.82 × 10⁻⁵ M), 39.06 U/mg of protein, and 9.5 × 10³/s, respectively. Thin layer chromatography (TLC) analysis, matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry, and Fourier transform nuclear magnetic resonance (FT-NMR) spectrometry of the hydrolyzed products of agarose by DagA revealed that DagA is an endo-type β-agarase that degrades agarose into neoagarotetraose and neoagarohexaose.

Keywords: Streptomyces coelicolor ; DagA; β-Agarase; Neoagarotetraose; Neoagarohexaose

A genomic island provides Acidithiobacillus ferrooxidans ATCC 53993 additional copper resistance: a possible competitive advantage by Luis H. Orellana; Carlos A. Jerez (pp. 761-767).

There is great interest in understanding how extremophilic biomining bacteria adapt to exceptionally high copper concentrations in their environment. Acidithiobacillus ferrooxidans ATCC 53993 genome possesses the same copper resistance determinants as strain ATCC 23270. However, the former strain contains in its genome a 160-kb genomic island (GI), which is absent in ATCC 23270. This GI contains, amongst other genes, several genes coding for an additional putative copper ATPase and a Cus system. A. ferrooxidans ATCC 53993 showed a much higher resistance to CuSO₄ (>100 mM) than that of strain ATCC 23270 (<25 mM). When a similar number of bacteria from each strain were mixed and allowed to grow in the absence of copper, their respective final numbers remained approximately equal. However, in the presence of copper, there was a clear overgrowth of strain ATCC 53993 compared to ATCC 23270. This behavior is most likely explained by the presence of the additional copper-resistance genes in the GI of strain ATCC 53993. As determined by qRT-PCR, it was demonstrated that these genes are upregulated when A. ferrooxidans ATCC 53993 is grown in the presence of copper and were shown to be functional when expressed in copper-sensitive Escherichia coli mutants. Thus, the reason for resistance to copper of two strains of the same acidophilic microorganism could be determined by slight differences in their genomes, which may not only lead to changes in their capacities to adapt to their environment, but may also help to select the more fit microorganisms for industrial biomining operations.

Keywords: Genomic islands; Copper resistance; Acidithiobacillus ferrooxidans 23270; Acidithiobacillus ferrooxidans 53993

cDNA cloning of a novel gene codifying for the enzyme lycopene β-cyclase from Ficus carica and its expression in Escherichia coli by José Miguel Araya-Garay; Lucía Feijoo-Siota; Patricia Veiga-Crespo; Tomás González Villa (pp. 769-777).

Lycopene beta-cyclase (β-LCY) is the key enzyme that modifies the linear lycopene molecule into cyclic β-carotene, an indispensable carotenoid of the photosynthetic apparatus and an important source of vitamin A in human and animal nutrition. Owing to its antioxidant activity, it is commercially used in the cosmetic and pharmaceutical industries, as well as an additive in foodstuffs. Therefore, β-carotene has a large share of the carotenoidic market. In this study, we used reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE)-PCR to obtain and clone a cDNA copy of the gene Lyc-β from Ficus carica (Lyc-β Fc), which codes for the enzyme lycopene β-cyclase (β-LCY). Expression of this gene in Escherichia coli produced a single polypeptide of 56 kDa of weight, containing 496 amino acids, that was able to cycle both ends of the lycopene chain. Amino acid analysis revealed that the protein contained several conserved plant cyclase motifs. β-LCY activity was revealed by heterologous complementation analysis, with lycopene being converted to β-carotene as a result of the enzyme’s action. The β-LCY activity of the expressed protein was confirmed by high-performance liquid chromatography (HPLC) identification of the β-carotene. The lycopene to β-carotene conversion rate was 90%. The experiments carried out in this work showed that β-LYC is the enzyme responsible for converting lycopene, an acyclic carotene, to β-carotene, a bicyclic carotene in F. carica. Therefore, by cloning and expressing β-LCY in E. coli, we have obtained a new gene for β-carotene production or as part of the biosynthetic pathway of astaxanthin. So far, this is the first and only gene of the carotenoid pathway identified in F. carica.

Keywords: Ficus carica ; Lycopene β-cyclase; cDNA; β-Carotene

Combinatorial engineering of ldh-a and bcl-2 for reducing lactate production and improving cell growth in dihydrofolate reductase-deficient Chinese hamster ovary cells by Min Kyoung Jeon; Da Young Yu; Gyun Min Lee (pp. 779-790).

In Chinese hamster ovary (CHO) cells, rapid glucose metabolism normally leads to inefficient use of glucose, most of which is converted to lactate during cell cultures. Since lactate accumulation during the culture often exerts a negative effect on cell growth and valuable product formation, several genetic engineering approaches have been developed to suppress lactate dehydrogenase-A (LDH-A), the enzyme converting pyruvate into lactate. However, despite the reduced lactate accumulation, such cell cultures are eventually terminated in the late period of the culture, mainly due to apoptosis. Therefore, we developed an apoptosis-resistant, less lactate-producing dhfr ⁻ CHO cell line (CHO-Bcl2-LDHAsi) by overexpressing Bcl-2, one of the most well-known anti-apoptotic proteins, and by downregulating LDH-A in a dhfr ⁻ CHO cell line. When the dhfr ⁻ CHO-Bcl2-LDHAsi cell line was used as a host cell line for the development of recombinant CHO (rCHO) cells producing an Fc-fusion protein, the culture longevity of the rCHO cells was extended without any detrimental effect of genetic engineering on specific protein productivity. Simultaneously, the specific lactate production rate and apparent yield of lactate from glucose were reduced to 21–65% and 37–78% of the control cells, respectively. Taken together, these results show that the use of an apoptosis-resistant, less lactate-producing dhfr ⁻ CHO cell line as a host cell line saves the time and the effort of establishing an apoptosis-resistant, less lactate-producing rCHO cells for producing therapeutic proteins.

Keywords: CHO cells; Specific lactate production rate; Apoptosis; LDH-A; Bcl-2

Simultaneous production and characterization of medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides by Pseudomonas mendocina NK-01 by Wenbin Guo; Cunjiang Song; Meimei Kong; Weitao Geng; Yuanyuan Wang; Shufang Wang (pp. 791-801).

When Pseudomonas mendocina NK-01 was cultivated in a 200-L fermentor using glucose as carbon source, 0.316 g L⁻¹ medium-chain-length polyhydroxyalkanoate (PHA_MCL) and 0.57 g L⁻¹ alginate oligosaccharides (AO) were obtained at the end of the process. GC/MS was used to characterize the PHA_MCL, which was found to be a polymer mainly consisting of 3HO (3-hydroxyoctanoate) and 3HD (3-hydroxydecanoate). T _m and T _g values for the PHA_MCL were 51.03°C and −41.21°C, respectively, by DSC. Its decomposition temperature was about 300°C. The elongation at break was 700% under 12 MPa stress. MS and GPC were also carried out to characterize the AO which had weight-average molecular weights of 1,546 and 1,029 Da, respectively, for the two main components at the end of the fermentation process. MS analysis revealed that the AO were consisted of β-d-mannuronic acid and/or α-l-guluronic acid, and the β-d-mannuronic acid and/or α-l-guluronic acid residues were partially acetylated at position C2 or C3.

Keywords: Pseudomonas mendocina ; Medium-chain-length polyhydroxyalkanoates; Alginate oligosaccharides; Simultaneous production; Characterization

Production of dihydrodaidzein and dihydrogenistein by a novel oxygen-tolerant bovine rumen bacterium in the presence of atmospheric oxygen by Hui Zhao; Xiu-Ling Wang; Hong-Lei Zhang; Chao-Dong Li; Shi-Ying Wang (pp. 803-813).

The original bovine rumen bacterial strain Niu-O16, capable of anaerobically bioconverting isoflavones daidzein and genistein to dihydrodaidzein (DHD) and dihydrogenistein (DHG), respectively, is a rod-shaped obligate anaerobic bacterium. After a long-term domestication, an oxygen-tolerant bacterium, which we named Aeroto-Niu-O16 was obtained. Strain Aeroto-Niu-O16, which can grow in the presence of atmospheric oxygen, differed from the original obligate anaerobic bacterium Niu-O16 by various characteristics, including a change in bacterial shape (from rod to filament), in biochemical traits (from indole negative to indole positive and from amylohydrolysis positive to negative), and point mutations in 16S rRNA gene (G398A and G438A). We found that strain Aeroto-Niu-O16 not only grew aerobically but also converted isoflavones daidzein and genistein to DHD and DHG in the presence of atmospheric oxygen. The bioconversion rate of daidzein and genistein by strain Aeroto-Niu-O16 was 60.3% and 74.1%, respectively. And the maximum bioconversion capacity for daidzein was 1.2 and 1.6 mM for genistein. Furthermore, when we added ascorbic acid (0.15%, m/v) in the cultural medium, the bioconversion rate of daidzein was increased from 60.3% to 71.7%, and that of genistein from 74.1% to 89.2%. This is the first reported oxygen-tolerant isoflavone biotransforming pure culture capable of both growing and executing the reductive activity under aerobic conditions.

Keywords: Isoflavones; Bioconversion; Oxygen-tolerant bacterium; Dihydrodaidzein (DHD); Dihydrogenistein (DHG)

Characterization of the monoclonal antibody against classical swine fever virus glycoprotein E^rns and its application to an indirect sandwich ELISA by Ching-Wei Wu; Maw-Sheng Chien; Ting-Yu Liu; Guang-Jan Lin; Wei-Cheng Lee; Chienjin Huang (pp. 815-821).

Classical swine fever virus (CSFV) E^rns is an envelope glycoprotein possessing RNase activity. The E^rns-based enzyme-linked immunosorbent assay (ELISA) has been considered a discriminating diagnostic test for differentiating infected from vaccinated animals. The purpose of this study was to produce a specific monoclonal antibody (MAb) to E^rns for further developing an indirect sandwich ELISA. The MAb CW813 was shown to specifically recognize both the monomer and dimer forms of Pichia pastoris yeast-expressed E^rns (yE^rns). The antigenic site recognized by MAb CW813 was mapped to the region of amino acid residues 101–160 of E^rns where it was neither a neutralizing epitope nor essential to RNase activity. Furthermore, MAb CW813 was utilized as a capture antibody to develop a yE^rns-based indirect sandwich ELISA for detecting swine antibody to E^rns. The assay demonstrated a high sensitivity and specificity that may provide an alternative method for developing a diagnostic kit with easy manipulation and low cost.

Keywords: Classical swine fever virus; RNase activity; Monoclonal antibody; Sandwich ELISA

Optimized procedure to generate heavy isotope and selenomethionine-labeled proteins for structure determination using Escherichia coli-based expression systems by Zhaopeng Li; Manfred Nimtz; Ursula Rinas (pp. 823-833).

Generating sufficient quantities of labeled proteins represents a bottleneck in protein structure determination. A simple protocol for producing heavy isotope as well as selenomethionine (Se-Met)-labeled proteins was developed using T7-based Escherichia coli expression systems. The protocol is applicable for generation of single-, double-, and triple-labeled proteins (¹⁵N, ¹³C, and ²H) in shaker flask cultures. Label incorporation into the target protein reached 99% and 97% for ¹⁵N and ¹³C, respectively, and 75% of (non-exchangeable) hydrogen for ²H labeling. The expression yields and final cell densities (OD600 ∼16) were the same as for the production of non-labeled protein. This protocol is also applicable for Se-Met labeling, leading to Se-Met incorporation into the target protein of 70% or 90% using prototrophic or methionine auxotrophic E. coli strains, respectively.

Keywords: Escherichia coli ; Recombinant protein production; Stable heavy isotope labeling; Selenomethionine labeling; Autoinduction; Defined medium

Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments? by Sandrine Paisse; Robert Duran; Frédéric Coulon; Marisol Goñi-Urriza (pp. 835-844).

The diversity of alkB-related alkane hydroxylase sequences and the relationship between alkB gene expression and the hydrocarbon contamination level have been investigated in the chronically polluted Etang-de-Berre sediments. For this purpose, these sediments were maintained in microcosms and submitted to a controlled oil input miming an oil spill. New degenerated PCR primers targeting alkB-related alkane hydroxylase sequences were designed to explore the diversity and the expression of these genes using terminal restriction fragment length polymorphism fingerprinting and gene library analyses. Induction of alkB genes was detected immediately after oil addition and their expression detected only during 2 days, although the n-alkane degradation was observed throughout the 14 days of incubation. The alkB gene expression within triplicate microcosms was heterogeneous probably due to the low level of alkB transcripts. Moreover, the alkB gene expression of dominant OTUs has been observed in unoiled microcosms indicating that the expression of this gene cannot be directly related to the oil contamination. Although the dominant alkB genes and transcripts detected were closely related to the alkB of Marinobacter aquaeolei isolated from an oil-producing well, and to alkB genes related to the obligate alkanotroph Alcanivorax borkumensis, no clear relationship between the oil contamination and the expression of the alkB genes could be established. This finding suggests that in such coastal environments, alkB gene expression is not a function relevant enough to monitor bacterial response to oil contamination.

Keywords: Alkane hydroxylase; Gene expression; Oil contamination; T-RFLP; alkB diversity

Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge by Francisca A. Luesken; Theo A. van Alen; Erwin van der Biezen; Carla Frijters; Ger Toonen; Christel Kampman; Tim L. G. Hendrickx; Grietje Zeeman; Hardy Temmink; Marc Strous; Huub J. M. Op den Camp; Mike S. M. Jetten (pp. 845-854).

Recently discovered microorganisms affiliated to the bacterial phylum NC10, named “Candidatus Methylomirabilis oxyfera”, perform nitrite-dependent anaerobic methane oxidation. These microorganisms could be important players in a novel way of anaerobic wastewater treatment where ammonium and residual dissolved methane might be removed at the expense of nitrate or nitrite. To find suitable inocula for reactor startup, ten selected wastewater treatment plants (WWTPs) located in The Netherlands were screened for the endogenous presence of M. oxyfera using molecular diagnostic methods. We could identify NC10 bacteria with 98% similarity to M. oxyfera in nine out of ten WWTPs tested. Sludge from one selected WWTP was used to start a new enrichment culture of NC10 bacteria. This enrichment was monitored using specific pmoA primers and M. oxyfera cells were visualized with fluorescence oligonucleotide probes. After 112 days, the enrichment consumed up to 0.4 mM NO ₂ ⁻ per day. The results of this study show that appropriate sources of biomass, enrichment strategies, and diagnostic tools existed to start and monitor pilot scale tests for the implementation of nitrite-dependent methane oxidation in wastewater treatment at ambient temperature.

Keywords: Methylomirabilis oxyfera ; NC10 phylum; Methanotroph; Denitrification; Nitrogen removal; Anaerobic wastewater treatment; Anaerobic oxidation; pmoA primers

Anthrahydroquinone-2,6,-disulfonate (AH₂QDS) increases hydrogen molar yield and xylose utilization in growing cultures of Clostridium beijerinckii by Xiaofeng Ye; Eberhard Morgenroth; Xinyu Zhang; Kevin Thomas Finneran (pp. 855-864).

H₂ production and xylose utilization were investigated using the fermentative culture Clostridium beijerinckii NCIMB 8052. Adding anthrahydroquinone-2,6-disulfonate (AH₂QDS) increased the extent of xylose utilization by 56% and hydrogen molar yield by 24–37%. Enhanced hydrogen molar yield correlated with increased xylose utilization and increases in the acetate/butyrate product ratio. An electron balance indicated that AH₂QDS shifted the electrons from the butyric acid pathway (NADH-dependent pathway) to the acetic acid pathway (non-NADH-dependent pathway), putatively creating a surplus of reducing equivalents that were then available for hydrogen production. These data demonstrate that hydrogen yield and xylose utilization can be manipulated by amending redox active molecules into growing cultures. This will impact biohydrogen/biofuel production by allowing physiological manipulations of growing cells for increased (or decreased) output of selected metabolites using amendments that are not consumed during the reactions. Although the current yield increases are small, they suggest a target for cellular alterations. In addition, increased xylose utilization will be critical to the fermentation of pretreated lignocellulosic feedstocks, which may have higher xylose content.

Keywords: Hydrogen production; Hydrogen molar yield; Xylose utilization; Electron shuttling compounds

Comparison of separate hydrolysis and fermentation and simultaneous saccharification and fermentation processes for ethanol production from wheat straw by recombinant Escherichia coli strain FBR5 by Badal C. Saha; Nancy N. Nichols; Nasib Qureshi; Michael A. Cotta (pp. 865-874).

Ethanol production by recombinant Escherichia coli strain FBR5 from dilute acid pretreated wheat straw (WS) by separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) was studied. The yield of total sugars from dilute acid (0.5% H₂SO₄) pretreated (160 °C, 10 min) and enzymatically saccharified (pH 5.0, 45 °C, 72 h) WS (86 g/l) was 50.0 ± 1.4 g/l. The hydrolyzate contained 1,184 ± 19 mg furfural and 161 ± 1 mg hydroxymethyl furfural per liter. The recombinant E. coli FBR5 could not grow at all at pH controlled at 4.5 to 6.5 in the non-abated wheat straw hydrolyzate (WSH) at 35 °C. However, it produced 21.9 ± 0.3 g ethanol from non-abated WSH (total sugars, 44.1 ± 0.4 g/l) in 90 h including the lag time of 24 h at controlled pH 7.0 and 35 °C. The bioabatement of WS was performed by growing Coniochaeta ligniaria NRRL 30616 in the liquid portion of the pretreated WS aerobically at pH 6.5 and 30 °C for 15 h. The bacterium produced 21.6 ± 0.5 g ethanol per liter in 40 h from the bioabated enzymatically saccharified WSH (total sugars, 44.1 ± 0.4 g) at pH 6.0. It produced 24.9 ± 0.3 g ethanol in 96 h and 26.7 ± 0.0 g ethanol in 72 h per liter from bioabated WSH by batch SSF and fed-batch SSF, respectively. SSF offered a distinct advantage over SHF with respect to reducing total time required to produce ethanol from the bioabated WS. Also, fed-batch SSF performed better than the batch SSF with respect to shortening the time requirement and increase in ethanol yield.

Keywords: Ethanol; Recombinant ethanologenic Escherichia coli ; Wheat straw hydrolyzate; Separate hydrolysis and fermentation; Simultaneous saccharification and fermentation

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Applied Microbiology and Biotechnology (v.92, #4)

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Applied Microbiology and Biotechnology (v.92, #4)