Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment

The oxidation of ammonia plays a significant role in the transformation of fixed nitrogen in the global nitrogen cycle. Autotrophic ammonia oxidation is known in three groups of microorganisms. Aerobic ammonia-oxidizing bacteria and archaea convert ammonia into nitrite during nitrification. Anaerobic ammonia-oxidizing bacteria (anammox) oxidize ammonia using nitrite as electron acceptor and producing atmospheric dinitrogen. The isolation and cultivation of all three groups in the laboratory are quite problematic due to their slow growth rates, poor growth yields, unpredictable lag phases, and sensitivity to certain organic compounds. Culture-independent approaches have contributed importantly to our understanding of the diversity and distribution of these microorganisms in the environment. In this review, we present an overview of approaches that have been used for the molecular study of ammonia oxidizers and discuss their application in different environments

Activity and stability of immobilized penicillin amidase at low pH values

Penicillin amidase is being applied widely in the production of semi-synthetic beta-lactam antibiotics. Usually the processes are at pH 7-8, but for many new applications the range of pH 3-6 is of interest too. Therefore, we studied the activity of penicillin amidase at 25 degreesC in potassium phosphate buffer of pH 3.7-9, as well as its stability in potassium phosphate buffer of pH 3-6. At each pH, the enzyme was stable during at least 32 days. On the other hand, immobilized penicillin amidase incubated in butyl acetate lost its stability, showing after 32 days a decrease of 52% in relation to its initial enzymatic activity value. In phosphate buffer, the enzyme showed the highest activity at pH 8-9. A gradual decrease to about 20% of this activity occurred when the pH was decreased to 3.7. At even lower pH, the enzyme activity could not be determined with the assay that was used due to a very low stability of penicillin G (PenG). The course of penicillin G conversion and 6-aminopenicillanic acid (APA) production, during enzymatic hydrolysis at pH 4, could be quantitatively described by a simple model when the thermodynamic equilibrium of the hydrolysis was taken into account. (C) 2003 Elsevier B.V. All rights reserved.271293

Surfactant-aided size-exclusion chromatography for the purification of immunoglobulin G

In the production of monoclonal antibodies, separate chains of the antibody are often present in the product mixture as well as other contaminating proteins. These fragments should be removed from the whole antibodies. This paper shows the purification of monoclonal immunoglobulin G (IgG) from its heavy chain contaminant. The heavy chain fragment is simulated experimentally using bovine serum albumin (BSA), which has approximately the same molecular weight. The purification is performed using traditional size-exclusion chromatography (SEC) and using surfactant-aided SEC (SASEC), testing two different surfactants (C12E23 and Tween20) and two different gels (Sephacryl S200HR and Sephacryl S300 HR). Pulse experiments show that with SASEC both BSA and IgG are more distributed towards the solid phase than compared to using SEC. This effect is larger on IgG, the largest component than on BSA. As a consequence, azeotropes will be formed at a specific surfactant concentration. Above this concentration the selectivity is reversed and increased to values higher than obtained with conventional SEC. At 7.5% (w/w) of C12E23, BSA actually elutes before IgG. These experiments further show that when using SASEC larger productivity, higher yields and lower solvent consumption can be achieved without loss of purity of IgG when compared to conventional SEC. Mathematical simulation of the separation of BSA and IgG using simulated moving bed (SMB) chromatography indicates a large increase in productivity when applying a surfactant gradient in SASEC SMB compared to conventional isocratic SEC-SMB. Furthermore, solvent consumption reductions with a factor 15 prove possible as well as concentrating the IgG by a factor 2

Solution crystallization kinetics of 6-aminopenicillanic acid

Semisynthetic penicillins, derived from 6-aminopenicillanic acid (APA), constitute an important group of antibiotics. APA is produced by enzymatic hydrolysis of penicillin G (PenG). This study concerns the determination of the crystallization kinetics of APA in the presence of other components that may be present after the PenG hydrolysis, i.e., remaining PenG and the byproduct phenylacetic acid. This evaluation is based on the analyses of growth rate and crystal size distribution, at pH 4 and 5. The results show that the impurities have no significant influence on the APA crystallization, within the range of pH and impurity concentrations evaluated. A mathematical model, based on the population balance, gives a good prediction of the crystallization rate and crystal size distribution with a single set of parameters.45206740674

Liquid-Liquid Extraction of Fermentation Inhibiting Compounds in Lignocellulose Hydrolysate

Several compounds that are formed or released during hydrolysis of lignocellulosic biomass inhibit the fermentation of the hydrolysate. The use of a liquid extractive agent IS Suggested as a method for removal of these fermentation inhibitors. The method can be applied before or during the fermentation. For a series of alkanes and alcohols, partition coefficients were measured at low concentrations of the inhibiting compounds furfural, hydroxymethyl furfural, vanillin, syringaldehyde, coniferyl aldehyde, acetic acid, as well as for ethanol as the fermentation product. Carbon dioxide production was measured during fermentation in the presence of each organic solvent to indicate its biocompatibility. The feasibility of extractive fermentation of hydrolysate was investigated by ethanolic glucose fermentation in synthetic medium containing several concentrations of furfural and vanillin and in the presence of decanol, oleyl alcohol and oleic acid. Volumetric ethanol productivity with 6 g/L vanillin in the medium increased twofold with 30% volume oleyl alcohol. Decanol showed interesting extractive properties for most fermentation inhibiting compounds, but it is not Suitable for in situ application due to its poor biocompatibility.102513541360Netherlands Ministry of Economic AffairsB-Basic partner organization

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

12 páginas, 6 figuras, 1 tabla.Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter–spring (that is, the 0 oC slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer—autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC−1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC−1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC−1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments.This research was supported by grants CRENYC CGL2006-12058 and PIRENA CGL2009-13318 to EOC, and CONSOLIDER grant GRACCIE CSD2007-00067 from the Spanish Office of Science and Innovation (MICINN). JCA benefits from a Juan de la Cierva postdoctoral fellow (MICINN).Peer reviewe