Check out our New Publishers' Select for Free Articles

Applied Microbiology and Biotechnology (v.75, #1)

The potential of cloud point system as a novel two-phase partitioning system for biotransformation by Zhilong Wang (pp. 1-10).

Although the extractive biotransformation in two-phase partitioning systems have been studied extensively, such as the water–organic solvent two-phase system, the aqueous two-phase system, the reverse micelle system, and the room temperature ionic liquid, etc., this has not yet resulted in a widespread industrial application. Based on the discussion of the main obstacles, an exploitation of a cloud point system, which has already been applied in a separation field known as a cloud point extraction, as a novel two-phase partitioning system for biotransformation, is reviewed by analysis of some topical examples. At the end of the review, the process control and downstream processing in the application of the novel two-phase partitioning system for biotransformation are also briefly discussed.

Keywords: Nonionic surfactant; Cloud point system; Two-phase partitioning system; Biotransformation

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges by Jonathan Kennedy; Julian R. Marchesi; Alan D. W. Dobson (pp. 11-20).

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.

Keywords: Metagenomics; Marine sponges; Natural products

Extracellular enzymes and the pathogenesis of nematophagous fungi by Jinkui Yang; Baoyu Tian; Lianming Liang; Ke-Qin Zhang (pp. 21-31).

Nematophagous fungi are an important group of soil microorganisms that can suppress the populations of plant-parasitic nematodes. The pathogenic mechanisms of nematophagous fungi are diverse: They can be parasitical–mechanical through producing specialized capturing devices, or toxin-dependent. During infections, a variety of virulence factors may be involved against nematodes by nematophagous fungi. In this review, we present up-to-date information on the modes of infection by nematophagous fungi. The roles of extracellular hydrolytic enzymes and other virulence factors involved in infection against nematodes were summarized. The biochemical properties and peptide sequences of a special group of enzymes, the serine proteases, were compared, and their implications in infections were discussed. We also discussed the impact of emerging new techniques on our understanding of this unique group of fungi.

Chemical and enzymatic routes to dihydroxyacetone phosphate by Michael Schümperli; René Pellaux; Sven Panke (pp. 33-45).

Stereoselective carbon–carbon bond formation with aldolases has become an indispensable tool in preparative synthetic chemistry. In particular, the dihydroxyacetone phosphate (DHAP)-dependent aldolases are attractive because four different types are available that allow access to a complete set of diastereomers of vicinal diols from achiral aldehyde acceptors and the DHAP donor substrate. While the substrate specificity for the acceptor is rather relaxed, these enzymes show only very limited tolerance for substituting the donor. Therefore, access to DHAP is instrumental for the preparative exploitation of these enzymes, and several routes for its synthesis have become available. DHAP is unstable, so chemical synthetic routes have concentrated on producing a storable precursor that can easily be converted to DHAP immediately before its use. Enzymatic routes have concentrated on integrating the DHAP formation with upstream or downstream catalytic steps, leading to multi-enzyme arrangements with up to seven enzymes operating simultaneously. While the various chemical routes suffer from either low yields, complicated work-up, or toxic reagents or catalysts, the enzymatic routes suffer from complex product mixtures and the need to assemble multiple enzymes into one reaction scheme. Both types of routes will require further improvement to serve as a basis for a scalable route to DHAP.

Keywords: Dihyroxyacetone phosphate; Aldolases; Multi-step reactions

Expression of the Escherichia coli pntAB genes encoding a membrane-bound transhydrogenase in Corynebacterium glutamicum improves l-lysine formation by Armin Kabus; Tobias Georgi; Volker F. Wendisch; Michael Bott (pp. 47-53).

A critical factor in the biotechnological production of l-lysine with Corynebacterium glutamicum is the sufficient supply of NADPH. The membrane-integral nicotinamide nucleotide transhydrogenase PntAB of Escherichia coli can use the electrochemical proton gradient across the cytoplasmic membrane to drive the reduction of NADP⁺ via the oxidation of NADH. As C. glutamicum does not possess such an enzyme, we expressed the E. coli pntAB genes in the genetically defined C. glutamicum lysine-producing strain DM1730, resulting in membrane-associated transhydrogenase activity of 0.7 U/mg protein. When cultivated in minimal medium with 10% (w/v) carbon source, the presence of transhydrogenase slightly reduced glucose consumption, whereas the consumption of fructose, glucose plus fructose, and, in particular, sucrose was stimulated. Biomass was increased by pntAB expression between 10 and 30% on all carbon sources tested. Most importantly, the lysine concentration was increased in the presence of transhydrogenase by ∼10% on glucose, ∼70% on fructose, ∼50% on glucose plus fructose, and even by ∼300% on sucrose. Thus, the presence of a proton-coupled transhydrogenase was shown to be an efficient way to improve lysine production by C. glutamicum. In contrast, pntAB expression had a negative effect on growth and glutamate production of C. glutamicum wild type.

Keywords: Corynebacterium glutamicum ; Escherichia coli ; Lysine production; Glutamate production; Glucose; Fructose; Sucrose; Nicotinamide nucleotide transhydrogenase; pntAB

Ergosterol production from molasses by genetically modified Saccharomyces cerevisiae by Xiuping He; Xuena Guo; Nan Liu; Borun Zhang (pp. 55-60).

Ergosterol is an economically important metabolite produced by fungi. Recombinant Saccharomyces cerevisiae YEH56(pHXA42) with increased capacity of ergosterol formation was constructed by combined overexpression of sterol C-24(28) reductase and sterol acyltransferase in the yeast strain YEH56. The production of ergosterol by this recombinant strain using cane molasses (CM) as an inexpensive carbon source was investigated. An ergosterol content of 52.6 mg/g was obtained with 6.1 g/l of biomass from CM medium containing 60 g/l of total sugar in 30 h in shake flask. The ergosterol yield was enhanced through the increasing cell biomass by supplementation of urea to a concentration of 6 g/l in molasses medium. Fermentation was performed in 5-l bioreactor using the optimized molasses medium. In batch fermentation, the effect of agitation velocity on ergosterol production was examined. The highest ergosterol yield was obtained at 400 rpm that increased 60.4 mg/l in comparison with the shake flask culture. In fed-batch fermentation, yeast cells were cultivated, firstly, in the starting medium containing molasses with 20 g/l of total sugar, 1.68 g/l of phosphate acid, and 6 g/l of urea (pH 5.4) for 5 h, then molasses containing 350 g/l of total sugar was fed exponentially into the bioreactor to keep the ethanol level in the broth below 0.5%. After 40 h of cultivation, the ergosterol yield reached 1,707 mg/l, which was 3.1-fold of that in the batch fermentation.

Keywords: Ergosterol; Combined overexpression; Sterol C-24(28) reductase; Sterol acyltransferase; Molasses; Fed-batch fermentation

Impact of increasing NaCl concentrations on the performance and community composition of two anaerobic reactors by O. Lefebvre; S. Quentin; M. Torrijos; J. J. Godon; J. P. Delgenès; R. Moletta (pp. 61-69).

The anaerobic treatment of saline effluents using halophilic and halotolerant microbial consortia is of major interest. Inhibition of anaerobic digestion is known to occur at high salt content. However, it seems that the suitable adaptation of an anaerobic sludge makes possible the treatment of saline wastewater. In this study, a non-saline anaerobic sludge was inoculated in two anaerobic batch reactors operating with a different substrate (distillery vinasse and ethanol) and subjected to increasing NaCl concentrations. The performance of the digesters appeared to be highly dependent on the nature of the substrate, and a similar level of inhibition (i.e. around 90% of the specific loading rate and specific methanogenic activity) was stated at 10 g l⁻¹ of NaCl with distillery vinasse and 60 g l⁻¹ of NaCl with ethanol. The characterization of the microflora and its adaptation to increasing NaCl conditions were also investigated using molecular tools based on the analysis of genomic 16S rDNA. The microbial communities revealed a high diversity that could be maintained in both reactors despite the increase in NaCl concentrations.

Keywords: Anaerobic SBR; Halotolerance; Microbial community; 16S ribosomal RNA

Extremely high alkaline protease from a deep-subsurface bacterium, Alkaliphilus transvaalensis by Tohru Kobayashi; Jie Lu; Zhijun Li; Vo Si Hung; Atsushi Kurata; Yuji Hatada; Ken Takai; Susumu Ito; Koki Horikoshi (pp. 71-80).

A new high-alkaline protease (ALTP) was purified to homogeneity from a culture of the strictly anaerobic and extremely alkaliphilic Alkaliphilus transvaalensis. The molecular mass was 30 kDa on sodium dodecyl sulfate–polyacrylamide gel electrophoresis. The enzyme showed the maximal caseinolytic activity higher than pH 12.6 in KCl–NaOH buffer at 40°C. Hydrolysis of the oxidized insulin B-chain followed by mass spectrometric analysis of the cleaved products revealed that as many as 24 of the total 29 peptide bonds are hydrolyzed in a block-cutting manner, suggesting that ALTP has a widespread proteolytic functions. Calcium ion had no effect on the activity and stability of ALTP, unlike known subtilisins. The deduced amino acid sequence of the enzyme comprised 279 amino acids plus 97 prepropeptide amino acids. The amino acid sequence of mature ALTP was confirmed by capillary liquid chromatography coupled to tandem mass spectrometry, which was the 93% coverage of the deduced amino acid sequence. The mature enzyme showed moderate homology to subtilisin LD1 from the alkaliphilic Bacillus sp. strain KSM-LD1 with 64% identity, and both enzymes formed a new subcluster at an intermediate position among true subtilisins and high-alkaline proteases in a phylogenetic tree of subtilase family A. ALTP is the first high-alkaline protease reported from a strict anaerobe in this family.

Keywords: Serine protease; Subtilisin; Subtilase family A; Deep subsurface; Alkaliphilus transvaalensis

An alkaline protease from fresh fruiting bodies of the edible mushroom Pleurotus citrinopileatus by L. Cui; Q. H. Liu; H. X. Wang; T. B. Ng (pp. 81-85).

A protease was purified from fresh fruiting bodies of the edible mushroom Pleurotus citrinopileatus. The isolation procedure included ion exchange chromatography on DEAE-cellulose, CM-cellulose, and Q-Sepharose and fast protein liquid chromatography-gel filtration on Superdex 75. The protease was unadsorbed on DEAE-cellulose and Q-Sepharose, but adsorbed on CM-cellulose. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the protease demonstrated a single band with a molecular mass of 28 kDa. The protease showed an optimal pH at 10 and an optimal temperature at 50°C. The activity of the protease was not affected by EDTA, indicating that it is not a metalloprotease. The protease exhibited a higher activity in the presence of K⁺ and Li⁺, but its activity was potently inhibited by Al³⁺, Cu²⁺, and Hg²⁺ ions. It manifested a K _m of 3.44 mg/ml and a V _max of 0.139 mg ml⁻¹ min⁻¹. It was devoid of ribonuclease and antifungal activities.

Keywords: Mushroom; Protease; Fruiting bodies

Screening of β-fructofuranosidase-producing microorganisms and effect of pH and temperature on enzymatic rate by Rubén Cuervo Fernandez; Cristiane Angélica Ottoni; Elda Sabino da Silva; Rosa Mitiko Saito Matsubara; José Márcio Carter; Luis Roberto Magossi; Maria Alice Alves Wada; Maria Filomena de Andrade Rodrigues; Beatriz Guilarte Maresma; Alfredo Eduardo Maiorano (pp. 87-93).

Seventeen different strains of filamentous fungi were grown in batch cultures to compare their abilities for the production of β-fructofuranosidase. Three of them, Aspergillus oryzae IPT-301, Aspergillus niger ATCC 20611 and strain IPT-615, showed high production with total fructosyltransferase activity higher than 12,500 units l⁻¹. In addition, the β-fructofuranosidases of those strains have a high fructosyltransferase activity-to-hydrolytic activity ratio. The temperature and pH effects on the sucrose-β-fructofuranosidase reaction rate were studied using a 2² factorial experimental design. The comparative analysis of the tested variable coefficients shows that the variable pH contributes mostly to the changes in the fructosyltransferase and hydrolytic rates and in the V _t/V _h ratio. At 40 and 50°C, there were no significant differences between the fructosyltransferase and hydrolytic velocities of these enzymes.

Keywords: β-fructofuranosidase; Fructosyltransferase; Fructooligosaccharides; Aspergillus

Secretory expression of a heterologous nattokinase in Lactococcus lactis by Xiaobo Liang; Lixin Zhang; Jin Zhong; Liandong Huan (pp. 95-101).

Nattokinase has been reported as an oral health product for the prevention of atherosclerosis. We developed a novel strategy to express a nattokinase from Bacillus subtilis in a live delivery vehicle, Lactococcus lactis. Promoter P nis_Z and signal peptide SP_Usp were used for inducible and secretory expression of nattokinase in L. lactis. Western blotting analysis demonstrated that nattokinase was successfully expressed, and about 94% of the enzyme was secreted to the culture. The recombinant nattokinase showed potent fibrinolytic activity, equivalent to 41.7 urokinase units per milliliter culture. Expression and delivery of such a fibrinolytic enzyme in the food-grade vehicle L. lactis would facilitate the widespread application of nattokinase in the control and prevention of thrombosis diseases.

L-Tyrosine production by deregulated strains of Escherichia coli by Tina Lütke-Eversloh; Gregory Stephanopoulos (pp. 103-110).

The excretion of the aromatic amino acid l-tyrosine was achieved by manipulating three gene targets in the wild-type Escherichia coli K12: The feedback-inhibition-resistant (fbr) derivatives of aroG and tyrA were expressed on a low-copy-number vector, and the TyrR-mediated regulation of the aromatic amino acid biosynthesis was eliminated by deleting the tyrR gene. The generation of this l-tyrosine producer, strain T1, was based only on the deregulation of the aromatic amino acid biosynthesis pathway, but no structural genes in the genome were affected. A second tyrosine over-producing strain, E. coli T2, was generated considering the possible limitation of precursor substrates. To enhance the availability of the two precursor substrates phosphoenolpyruvate and erythrose-4-phosphate, the ppsA and the tktA genes were over-expressed in the strain T1 background, increasing l-tyrosine production by 80% in 50-ml batch cultures. Fed-batch fermentations revealed that l-tyrosine production was tightly correlated with cell growth, exhibiting the maximum productivity at the end of the exponential growth phase. The final l-tyrosine concentrations were 3.8 g/l for E. coli T1 and 9.7 g/l for E. coli T2 with a yield of l-tyrosine per glucose of 0.037 g/g (T1) and 0.102 g/g (T2), respectively.

Keywords: l-tyrosine; Aromatic amino acid; Escherichia coli ; Metabolic engineering

MPK1 gene is required for filamentous growth induced by isoamyl alcohol in Saccharomyces cerevisiae strains from the alcoholic fermentation by Guilherme Tadeu Vancetto; Sandra Regina Ceccato-Antonini (pp. 111-115).

The aim of this study was to evaluate the MPK1 (SLT2) gene deletion upon filamentous growth induced by isoamyl alcohol (IAA) in two haploid industrial strains of Saccharomyces cerevisiae using oligonucleotides especially designed for a laboratory S. cerevisiae strain. The gene deletion was performed by replacing part of the open reading frames from the target gene with the KanMX gene. The recombinant strains were selected by their resistance to G418, and after deletion confirmation by polymerase chain reaction, they were cultivated in a yeast extract peptone dextrose medium + 0.5% IAA to evaluate the filamentous growth in comparison to wild strains. Mpk1 derivatives were obtained for both industrial yeasts showing the feasibility of the oligonucleotides especially designed for a laboratory strain (Σ1278b) by Martinez-Anaya et al. (In yeast, the pseudohyphal phenotype induced by isoamyl alcohol results from the operation of the morphogenesis checkpoint. J Cell Sci 116:3423–3431, 2003). The filamentation rate in these derivatives was significantly lower for both strains, as induced by IAA. This drastic reduction in the filamentation ability in the deleted strains suggests that the gene MPK1 is required for IAA-induced filamentation response. The growth curves of wild and derivative strains did not differ substantially. It is not known yet whether the switch to filamentous growth affects the fermentative characteristics of the yeast or other physiological traits. A genetically modified strain for nonfilamentous growth would be useful for these studies, and the gene MPK1 could be a target gene. The feasibility of designed oligonucleotides for this deletion in industrial yeast strains is shown.

Keywords: Saccharomyces cerevisiae ; Filamentation; MPK1 ; Isoamyl alcohol

Multimerization and fusion expression of bovine lactoferricin derivative LfcinB15-W4,10 in Escherichia coli by Zi-gang Tian; Da Teng; Ya-lin Yang; Jin Luo; Xing-jun Feng; Ying Fan; Fan Zhang; Jian-hua Wang (pp. 117-124).

Antimicrobial peptides are promising candidates for therapeutic and industrial application owing to their broad spectrum. In this work, a cost-effective method for expression of a potent antimicrobial peptide, bovine lactoferricin derivative LfcinB15-W4,10, has been developed. The oligonucleotide encoding the peptide was linked to generate different oligomeric oligonucleotide segments containing from one to nine but eight tandem copies which was inserted individually to the E. coli expression vector pET32a. The thioredoxin fusion peptides were successfully expressed and detected with different molecular weight on SDS gel, respectively. Among the monomer and other multimeric peptides, the tetramer was expressed at the highest level. After purification, more than 10 mg of tetramer with 99% purity was obtained from 1 l culture and exhibited similar antimicrobial activity as synthetic LfcinB15-W4,10 monomer. The expression system in this study provides a potential production method for lactoferricin derivatives and other antimicrobial peptides in research and industrial applications.

Keywords: Antimicrobial peptides; Bovine lactoferricin; Multimerization; Fusion expression; Escherichia coli

Susceptibility of staphylococcal biofilms to enzymatic treatments depends on their chemical composition by P. Chaignon; I. Sadovskaya; Ch. Ragunah; N. Ramasubbu; J. B. Kaplan; S. Jabbouri (pp. 125-132).

Bacterial infections are serious complications after orthopaedic implant surgery. Staphylococci, with Staphylococcus epidermidis as a leading species, are the prevalent and most important species involved in orthopaedic implant-related infections. The biofilm mode of growth of these bacteria on an implant surface protects the organisms from the host’s immune system and from antibiotic therapy. Therapeutic agents that disintegrate the biofilm matrix would release planktonic cells into the environment and therefore allow antibiotics to eliminate the bacteria. An addition of a biofilm-degrading agent to a solution used for washing–draining procedures of infected orthopaedic implants would greatly improve the efficiency of the procedure and thus help to avoid the removal of the implant. We have previously shown that the extracellular staphylococcal matrix consists of a poly-N-acetylglucosamine (PNAG), extracellular teichoic acids (TAs) and protein components. In this study, we accessed the sensitivity of pre-formed biofilms of five clinical staphylococcal strains associated with orthopaedic prosthesis infections and with known compositions of the biofilm matrix to periodate, Pectinex Ultra SP, proteinase K, trypsin, pancreatin and dispersin B, an enzyme with a PNAG-hydrolysing activity. We also tested the effect of these agents on the purified carbohydrate components of staphylococcal biofilms, PNAG and TA. We found that the enzymatic detachment of staphylococcal biofilms depends on the nature of their constituents and varies between the clinical isolates. We suggest that a treatment with dispersin B followed by a protease (proteinase K or trypsin) could be capable to eradicate biofilms of a variety of staphylococcal strains on inert surfaces.

Keywords: Staphylococcus ; Biofilm detachment; Enzymatic treatment

Cellulose biosynthesis pathway is a potential target in the improved treatment of Acanthamoeba keratitis by Ricky Dudley; Selwa Alsam; Naveed Ahmed Khan (pp. 133-140).

Acanthamoeba is an opportunistic protozoan pathogen that can cause blinding keratitis as well as fatal granulomatous encephalitis. One of the distressing aspects in combating Acanthamoeba infections is the prolonged and problematic treatment. For example, current treatment against Acanthamoeba keratitis requires early diagnosis followed by hourly topical application of a mixture of drugs that can last up to a year. The aggressive and prolonged management is due to the ability of Acanthamoeba to rapidly adapt to harsh conditions and switch phenotypes into a resistant cyst form. One possibility of improving the treatment of Acanthamoeba infections is to inhibit the ability of these parasites to switch into the cyst form. The cyst wall is partially made of cellulose. Here, we tested whether a cellulose synthesis inhibitor, 2,6-dichlorobenzonitrile (DCB), can enhance the effects of the antiamoebic drug pentamidine isethionate (PMD). Our findings revealed that DCB can block Acanthamoeba encystment and may improve the antiamoebic effects of PMD. Using in vitro assays, the findings revealed that DCB enhanced the inhibitory effects of PMD on Acanthamoeba binding to and cytotoxicity of the host cells, suggesting the cellulose biosynthesis pathway as a novel target for the improved treatment of Acanthamoeba infections.

Keywords: Acanthamoeba ; Cysts; Therapy; Encystment; Pentamidine; 2,6-Dichlorobenzonitrile

Functional identification of the gene bace16 from nematophagous bacterium Bacillus nematocida by Qiuhong Niu; Xiaowei Huang; Lin Zhang; Lihui Lian; Yunxia Li; Juan Li; Jinkui Yang; Keqin Zhang (pp. 141-148).

Bacillus nematocida is a Gram-positive bacterium capable of killing nematodes. Our recent studies identified an extracellular serine protease Bace16 in B. nematocida as a candidate of pathogenic factor in the infection against nematodes, which displayed a high similarity with the serine protease family subtilisin BPN’, and the MEROPS ID is S08.034. To further confirm the roles that bace16 played in the mechanism of nematocidal pathogenesis, recombinant mature Bace16 (rm-Bace16) was expressed in Escherichia coli strain BL21 using pET-30 vector system. Bioassay experiments demonstrated that the purified recombinant protease had the ability to degrade nematode cuticles and kill nematodes. In addition, a bace16 knockout mutant of B. nematocida constructed by homologous recombination showed considerably lower proteolytic activity and less than 50% nematocidal activity than the wild-type strain. These results confirmed that Bace16 could serve as an important virulence factor during the infectious process.

Inventory and monitoring of wine microbial consortia by Vincent Renouf; Olivier Claisse; Aline Lonvaud-Funel (pp. 149-164).

The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation, respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity. PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production. Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries, in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified. The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated from very old vintages. B. bruxellensis and O. oeni were the most frequent.

Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR by David M. Stevenson; Paul J. Weimer (pp. 165-174).

Relative quantification real-time PCR was used to quantify several bacterial species in ruminal samples from two lactating cows, each sampled 3 h after feeding on two successive days. Abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and eubacterial domain-level primers. Bacterial populations showed a clear predominance of members of the genus Prevotella, which comprised 42% to 60% of the bacterial rRNA gene copies in the samples. However, only 2% to 4% of the bacterial rRNA gene copies were represented by the classical ruminal Prevotella species Prevotella bryantii, Prevotella ruminicola and Prevotella brevis. The proportion of rRNA gene copies attributable to Fibrobacter succinogenes, Ruminococcus flavefaciens, Selenomonas ruminantium and Succinivibrio dextrinosolvens were each generally in the 0.5% to 1% range. Proportions for Ruminobacter amylophilus and Eubacterium ruminantium were lower (0.1% to 0.2%), while Butyrivibrio fibrisolvens, Streptococcus bovis, Ruminococcus albus and Megasphaera elsdenii were even less abundant, each comprising <0.03% of the bacterial rRNA gene copies. The data suggest that the aggregate abundance of the most intensively studied ruminal bacterial species is relatively low and that a large fraction of the uncultured population represents a single bacterial genus.

Keywords: Bovine; PCR; Prevotella ; Primers; Real-time PCR; Rumen

Influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by Sphingomonas sp. strain PheB4 by Yin Zhong; Tiangang Luan; Xiaowei Wang; Chongyu Lan; Nora F. Y. Tam (pp. 175-186).

The influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated when Sphingomonas sp. strain PheB4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (PMSM) or nutrient broth (NB). The NB-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate PAHs compared to the PMSM-grown culture. The concentrations of PAH metabolites were also lower in NB-grown culture than in PMSM-grown culture, suggesting that NB-grown culture removed metabolites at a faster rate, particularly, for metabolites produced from cometabolic degradation of a binary mixture of PAHs. Cometabolic pathways of single PAH (anthracene, fluorene, or fluoranthene) in NB-grown culture showed similarity to that in PMSM-grown culture. However, cometabolic pathways of mixed PAHs were more diverse in NB-grown culture than that in PMSM-grown culture. These results indicated that nutrient rich medium was effective in enhancing cometabolic degradation of mixed PAHs concomitant with a rapid removal of metabolites, which could be useful for the bioremediation of mixed PAHs contaminated sites using Sphingomonas sp. strain PheB4.

Keywords: Biodegradation; Cometabolism; Solid phase microextraction; Mangrove ecosystems

Control of struvite precipitation by selective removal of $${ ext{NH}}^{{ ext{ + }}}_{{ ext{4}}} $$ with dialyzer/zeolite in an anaerobic membrane bioreactor by Junhong Kim; Chung-Hak Lee; Kwang-Ho Choo (pp. 187-193).

This study focused on the mitigation of membrane fouling caused by struvite precipitation using a dialyzer/zeolite (D/Z) unit in an anaerobic membrane bioreactor. The D/Z unit was designed to selectively remove $${ ext{NH}}^{{ ext{ + }}}_{{ ext{4}}} $$ ions, one of the main components of the inorganic foulant, struvite. The maximum mass transfer coefficient for $${ ext{NH}}^{{ ext{ + }}}_{{ ext{4}}} $$ through the dialyzer was estimated to be 0.92 l m⁻²h⁻¹, whereas the Na-substituted zeolite had the highest ion exchange capacity with respect to ammonium among intact or differently pretreated zeolites. During a single passage of dialysate through the zeolite column, substantial $${ ext{NH}}^{{ ext{ + }}}_{{ ext{4}}} $$ removal (in excess of 90%) was achieved, leading to the reduction in struvite precipitation in the digester. The D/Z unit played a significant role in controlling struvite precipitation, thereby enhancing permeate flux for the case of the ceramic membrane, in which struvite fouling would be more pronounced compared to the polymeric membrane. For the polymeric membrane, however, no significant improvement in flux was observed even with the D/Z unit because the fouling of the polymeric membrane was mainly due to the deposition of biomass rather than the struvite precipitation.

Keywords: Dialysis; Anaerobic digestion; Membrane bioreactor; Struvite; Zeolite

Effect of nitrate and nitrite on sulfide production by two thermophilic, sulfate-reducing enrichments from an oil field in the North Sea by Krista M. Kaster; Alexander Grigoriyan; Gary Jennneman; Gerrit Voordouw (pp. 195-203).

Thermophilic sulfate-reducing bacteria (tSRB) can be major contributors to the production of H₂S (souring) in oil reservoirs. Two tSRB enrichments from a North Sea oil field, NS-tSRB1 and NS-tSRB2, were obtained at 58°C with acetate-propionate-butyrate and with lactate as the electron donor, respectively. Analysis by rDNA sequencing indicated the presence of Thermodesulforhabdus norvegicus in NS-tSRB1 and of Archaeoglobus fulgidus in NS-tSRB2. Nitrate (10 mM) had no effect on H₂S production by mid-log phase cultures of NS-tSRB1 and NS-tSRB2, whereas nitrite (0.25 mM or higher) inhibited sulfate reduction. NS-tSRB1 did not recover from inhibition, whereas sulfate reduction activity of NS-tSRB2 recovered after 500 h. Nitrite was also effective in souring inhibition and H₂S removal in upflow bioreactors, whereas nitrate was similarly ineffective. Hence, nitrite may be preferable for souring prevention in some high-temperature oil fields because it reacts directly with sulfide and provides long-lasting inhibition of sulfate reduction.

Keywords: Thermophilic; Sulfate-reducing bacteria; Hydrogen sulfide; Souring; Nitrate; Nitrite; Nitrate-reducing bacteria

Characteristics and stability of aerobic granules cultivated with different starvation time by Yong-Qiang Liu; Joo-Hwa Tay (pp. 205-210).

The characteristics of aerobic granules at steady state and the effects of starvation time on the stability of aerobic granules during the long-term operation were investigated in three sequencing batch reactors (SBRs R1–R3). The SBRs were operated with a cycle time of 1.5, 4.0, and 8.0 h, respectively, which resulted in a starvation time of 0.8, 3.3, and 7.3 h in three reactors, respectively. Results showed that aerobic granules were successfully cultivated in the three reactors, but the granules in R2 with a starvation time of 3.3 h showed the highest density and the best settleability at steady state. It is obvious that the starvation time has an optimum value in terms of settleability of granules. In addition, it was found that the coexistence of a minority of fluffy granules with smooth granules was the potential unstable factor in R1 with a starvation time of 0.8 h at the steady state. The sudden dominance of fluffy granules in R1 after the 160-day operation led to the operation failure of the reactor R1, whereas the granules in R2 with a starvation time of 3.3 h and R3 with a starvation time of 7.3 h showed good stability during the long-term operation. As short starvation time leads to the instability of granules, and long starvation time is not advisable for practical application due to low efficiency, starvation time should be controlled in a reasonable range.

Keywords: Aerobic granules; Starvation; Characteristics; Stability; SBR

Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge by Joke Geets; Michaël de Cooman; Lieven Wittebolle; Kim Heylen; Bram Vanparys; Paul De Vos; Willy Verstraete; Nico Boon (pp. 211-221).

In order to improve wastewater treatment processes, a need exists for tools that rapidly give detailed insight into the community structure of activated sludge, supplementary to chemical and physical data. In this study, the advantages of microarrays and quantitative polymerase chin reaction (PCR) methods were combined into a real-time PCR assay that allows the simultaneous quantification of phylogenetic and functional genes involved in nitrification and denitrification processes. Simultaneous quantification was possible along a 5-log dynamic range and with high linear correlation (R ² > 0.98). The specificity of the assay was confirmed by cloning and sequencing analyses of PCR amplicons obtained from activated sludge. The real-time assay was validated on mixed liquid samples of different treatment plants, which varied in nitrogen removal rate. The abundance of ammonia oxidizers was in the order of magnitude of 10⁶ down to 10⁴ ml⁻¹, whereas nitrite oxidizers were less abundant (10³–10¹ order of magnitude). The results were in correspondence with the nitrite oxidation rate in the sludge types. As for the nirS, nirK, and nosZ gene copy numbers, their abundance was generally in the order of magnitude of 10⁸–10⁵. When sludge samples were subjected to lab-scale perturbations, a decrease in nitrification rate was reflected within 18 h in the copy numbers of nitrifier genes (decrease with 1 to 5 log units), whereas denitrification genes remained rather unaffected. These results demonstrate that the method is a fast and accurate tool for the analysis of the (de)nitrifying community structure and size in both natural and engineered environmental samples.

Keywords: SYBR Green I real-time PCR; 16S rRNA gene; amoA ; Nitrite oxidoreductase; nosZ ; nirS ; nirK ; Activated sludge

Dose–response relationships and statistical performance of a battery of bacterial gene profiling assays by F. Dardenne; I. Nobels; W. De Coen; R. Blust (pp. 223-234).

Because of increasing awareness and legislative demands, there is a demand for the development and use of biological assays for the assessment of the toxicity of chemicals, environmental samples. Recently, a growing number of bacterial reporter assays have been developed and implemented. Nevertheless, little data is published on the performance of these assays in terms of analytical parameters. We present results on a battery of 14 transgenic Escherichia coli strains carrying different promoter::reporter fusions. Growth characteristics and basal expression levels were modeled and fitted, data show that growth curves should be taken into account during test development. Our study shows that the induction profiles reflect the mode of action, e.g., paraquat clearly induces the soxRS operon. The sensitivity of the assay compares well to that of whole organism tests, e.g., fish and Daphnia for polar organics. Metal toxicity is detected less efficiently, e.g., cadmium is detected near the LC50 of carp, considered a relatively insensitive species towards cadmium. The assay variability ranges from 10 to 40% depending on the strain, comparable to that of other bioassays. The variability was shown to be determined by the intrinsic traits of the promoter–strain combination, not by operating conditions.

Keywords: Gene profiling assay; Stress gene; Ecotoxicology; E. coli ; Assay performance

Sections

Personal tools

Applied Microbiology and Biotechnology (v.75, #1)

Sections

Personal tools

Local resources

Applied Microbiology and Biotechnology (v.75, #1)