Investigation of volatile metabolites during growth of Escherichia coli and Pseudomonas aeruginosa by needle trap-GC-MS.

A new method for the growth-dependent headspace analysis of bacterial cultures by needle trap (NT)-gas chromatography-mass spectrometry (GC-MS) was established. NTs were used for the first time as enrichment technique for volatile organic compounds (VOCs) in the headspace of laboratory cultures. Reference strains of Escherichia coli and Pseudomonas aeruginosa were grown in different liquid culture media for 48 h at 36 °C. In the course of growth, bacterial culture headspace was analysed by NT-GC-MS. In parallel, the abiotic release of volatile organic compounds (VOC) from nutrient media was investigated by the same method. By examination of microbial headspace samples in comparison with those of uninoculated media, it could be clearly differentiated between products and compounds which serve as substrates. Specific microbial metabolites were detected and quantified during the stationary growth phase. P. aeruginosa produced dimethyl sulfide (max. 125 µg L(-1) < limits of quantification (LOQ)), 1-undecene (max. 164 µg L(-1)) and 2-nonanone (max. 200 µg L(-1)), whereas E. coli produced carbon disulfide, butanal and indole (max. 149 mg L(-1)). Both organisms produced isoprene.

Efficient computation of interacting model systems.

Physiological processes in the human body can be predicted by mathematical models. Medical Decision Support Systems (MDSS) might exploit these predictions when optimizing therapy settings. In critically ill patients depending on mechanical ventilation, these predictions should also consider other organ systems of the human body. In a previously presented framework we combine elements of three model families: respiratory mechanics, cardiovascular dynamics and gas exchange. Computing combinations of moderately complex submodels showed to be computationally costly thus limiting the applicability of those model combinations in an MDSS. A decoupled computing approach was therefore developed, which enables individual evaluation of every submodel. Direct model interaction is not possible in separate calculations. Therefore, interface signals need to be substituted by estimates. These estimates are iteratively improved by increasing model detail in every iteration exploiting the hierarchical structure of the implemented model families. Simulation error converged to a minimum after three iterations. Maximum simulation error showed to be 1.44% compared to the original common coupled computing approach. Simulation error was found to be below measurement noise generally found in clinical data. Simulation time was reduced by factor 34 using one iteration and factor 13 using three iterations. Following the proposed calculation scheme moderately complex model combinations seem to be applicable for model based decision support.

Complementation of Sulfolobus solfataricus PBL2025 with an α-mannosidase: effects on surface attachment and biofilm formation.

Compared to Sulfolobus solfataricus P2, the S. solfataricus mutant PBL2025 misses 50 genes (SSO3004-3050), including genes coding for a multitude of enzymes possibly involved in sugar degradation or metabolism. We complemented PBL2025 with two of the missing proteins, the α-mannosidase (SSO3006, Ssα-man) and the ß-galactosidase LacS (SSO3019), and performed comparative fluorescence microscopy and confocal laser scanning microscopy to analyze the recombinant strains. We demonstrated that the Ssα-man complemented strain resembled the S. solfataricus P2 behavior with respect to attachment of cells to glass and growth of cells in static biofilms. During expression of the Ssα-man, but not LacS, glucose and mannose-containing extracellular polymeric substance (EPS) levels changed in the recombinant strain during surface attachment and biofilm formation. These results suggest that the Ssα-man might be involved in the modulation of the EPS composition and/or in the de-mannosylation of the glycan tree, which is attached to extracellular glycosylated proteins in S. solfataricus. On the other hand, LacS expression in PBL2025 reduced the carbohydrate content of the isolated total EPS implying a role in the modulation of the produced EPS during static biofilm formation. These are the first enzymes identified as playing a role in archaeal EPS formation.

Faecal indicator bacteria in river biofilms.

Biofilms in surface waters primarily consist of allochthonous microorganisms. Under conditions of pollution faecally derived bacteria may interact with these biofilms. Total coliform bacteria, Escherichia coli and intestinal enterococci are used to monitor source water quality, indicating faecal pollution and the possible presence of enteric pathogens. In the present study the occurrence of faecal indicators was investigated in biofilms (epilithic biofilms, sediments) of German rivers. All of the biofilms contained significant concentrations of these bacteria, which were several orders of magnitude lower compared with the total cell number and the number of culturable heterotrophic plate count bacteria indicating that faecal indicator bacteria represented a minor fraction of the whole biofilm communities. The biofilms displayed approximately two orders of magnitude higher concentrations of total coliforms, E. coli and enterococci compared with the overlying water. Identification of coliform and enterococcal isolates from the biofilms revealed the presence of species which are known to be opportunistic pathogens. Overall, the results of the present study show that faecal indicator bacteria can survive in the presence of high cell densities of the authochthonous microflora in epilithic biofilms and sediments, suggesting that these biofilms may act as a reservoir for bacterial pathogens in polluted rivers.

Simultaneous visualisation of biofouling, organic and inorganic particle fouling on separation membranes.

Fouling is a major problem in membrane processes of water treatment. It can be caused by the deposition of inorganic and organic particulate material, and of microbial cells which may subsequently form biofilms. In practice, usually more than one foulant participates in the formation of membrane deposits. Knowledge of the composition of fouling layers is important for the development of appropriate countermeasures. For this purpose, an experimental system was established for the generation and microscopic visualisation of mixed deposits, using fluorescently labelled model foulants: (i) drinking-water bacteria stained with nucleic acid-specific dyes (biofouling), (ii) synthetic clay mineral laponite stained with rhodamine 6G (inorganic particle fouling), and (iii) fluorescently labelled polystyrene microspheres (organic particle fouling). Polycarbonate and polyethersulfone membranes were challenged with these foulants by dead-end filtration. On the basis of different fluorescent labels, the single foulants in these mixed deposits could be visualised separately by confocal laser scanning microscopy which, in combination with image analysis, allowed the generation of three-dimensional views of the complete deposits. This method offers the possibility for the estimation of quantitative surface coverage by foulants and for the determination of the efficacy of cleaning measures with respect to the removal of different foulants.

Contamination potential of drinking water distribution network biofilms.

Drinking water distribution system biofilms were investigated for the presence of hygienically relevant microorganisms. Early biofilm formation was evaluated in biofilm reactors on stainless steel, copper, polyvinyl chloride (PVC) and polyethylene coupons exposed to unchlorinated drinking water. After 12 to 18 months, a plateau phase of biofilm development was reached. Surface colonization on the materials ranged between 4 x 10(6) and 3 x 10(7) cells/cm2, with heterotrophic plate count (HPC) bacteria between 9 x 10(3) and 7 x 10(5) colony-forming units (cfu)/cm2. Established biofilms were investigated in 18 pipe sections (2 to 99 years old) cut out from distribution pipelines. Materials included cast iron, galvanized steel, cement and PVC. Colonization ranged from 4 x 10(5) to 2 x 10(8) cells/cm2, HPC levels varied between 1 and 2 x 10(5) cfu/cm2. No correlation was found between extent of colonization and age of the pipes. Using cultural detection methods, coliform bacteria were rarely found, while Escherichia coli, Pseudomonas aeruginosa and Legionella spp. were not detected in the biofilms. In regular operation, distribution system biofilms do not seem to be common habitats for pathogens. However, nutrient-leaching materials like rubber-coated valves were observed with massive biofilms which harboured coliform bacteria contaminating drinking water.

Interaction between alginates and manganese cations: identification of preferred cation binding sites.

Algal and bacterial alginates have been studied by means of 13C NMR spectroscopy in presence of paramagnetic manganese ions in order to reveal the nature of their interaction with bivalent cations. It is found that the mannuronate blocks bind manganese cations externally near their carboxylate groups, while guluronate blocks show the capability to integrate Mn2+ into pocket-like structures formed by adjacent guluronate residues. In alternating mannuronate-guluronate blocks, manganese ions preferentially locate in a concave structure formed by guluronate-mannuronate pairs. Partial acetylation of the alginate generally reduces its capability to interact with bivalent cations, however, the selectivity of the binding geometry is conserved. The results may serve as a hint for the better understanding of the alginate gelation in presence of calcium ions.

Metagenome survey of biofilms in drinking-water networks.

Most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. Therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. First, a sequence analysis of 650 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to the Proteobacteria: Only a small fraction of the 16S rRNA sequences were highly similar to rRNA sequences from Actinobacteria, low-G+C gram-positives and the Cytophaga-Flavobacterium-Bacteroides group. Our second strategy included a snapshot genome sequencing approach. Homology searches in public databases with 5,000 random sequence clones from a small insert library resulted in the identification of 2,200 putative protein-coding sequences, of which 1,026 could be classified into functional groups. Similarity analyses indicated that significant fractions of the genes and proteins identified were highly similar to known proteins observed in the genera Rhizobium, Pseudomonas, and Escherichia: Finally, we report 144 kb of DNA sequence information from four selected cosmid clones, of which two formed a 75-kb overlapping contig. The majority of the proteins identified by whole-cosmid sequencing probably originated from microbes closely related to the alpha-, beta-, and gamma-Proteobacteria: The sequence information was used to set up a database containing the phylogenetic and genomic information on this model microbial community. Concerning the potential health risk of the microbial community studied, no DNA or protein sequences directly linked to pathogenic traits were identified.

Monomer composition and sequence of alginates from Pseudomonas aeruginosa.

Alginates from four strains of Pseudomonas aeruginosa, one mucoid strain isolated from a technical water system, one strain isolated from a patient with cystic fibrosis and two mutants of this strain with a defect which affects the O-acetylation of the extracellular alginate, have been isolated and analysed for monomer composition and sequence by 13C-nuclear magnetic resonance (NMR) spectroscopy. The detected contributions of different monomer triplets (triads) were compared with values expected from a statistical chain constitution based on the given monomer ratio. While a typical algal alginate presents a nearly statistical distribution of uronic acids in the polymer chain, a strong deviation from the statistical arrangement of mannuronate (M) and guluronate (G) was found in the alginate of the mucoid strains of P. aeruginosa, being most expressed for the triad MMM. This feature is partially lost in the alginate from the mutant strains, indicating that the O-acetylation is linked to a mechanism which takes influence on the chain sequence. The strong preference for MG-pairs in the parent strain of P. aeruginosa may be connected to a stronger binding of cations in the MG-vicinity.

Uniaxial compression measurement device for investigation of the mechanical stability of biofilms.

The mechanical stability of biofilms is important for biotechnology, as sloughing of the biomass due to mechanical failure of the biofilm matrix can lead to severe interferences with biofilm processes. In cases of biofouling, biofilms have to be removed, in which case their mechanical stability must be overcome. The apparent modulus of elasticity and the yield strength as obtained from uniaxial compression experiments can be taken as parameters indicative for the mechanical stability of a biofilm. A film rheometer is presented which allows for the determination of these quantities, using model biofilms of Pseudomonas aeruginosa grown on membrane filters. The compressive stress-strain behaviour up to the point of failure is recorded at a compression speed of 1 microm s(-1). In accordance with the stress-strain curve, the investigated biofilm can be described as viscoelastic material, which demonstrates plastic flow properties. The extracellular polymeric substances (EPS), which keep biofilms together, form a temporary network of fluctuating junction points. Above the yield point, the gel structure fails and the system behaves as a highly viscous fluid. The apparent modulus of elasticity and the yield point are considered to be useful parameters for characterizing the mechanical properties of biofilms.

Relevance of microbial extracellular polymeric substances (EPSs)--Part I: Structural and ecological aspects.

Extracellular polymeric substances are the construction materials for microbial aggregates such as biofilms, flocs ("planktonic biofilms") and sludge. Their major components are not only polysaccharides but also proteins and in some cases lipids, with minor contents of nucleic acids and other biopolymers. In the EPS, biofilm organisms can establish stable arrangements and function multicellularly as synergistic microconsortia. The matrix facilitates the retention of exoenzymes, cellular debris and genetic material; it can be considered as a microbial recycling yard. Gradients can develop due to the physiological activity and the fact that diffusive mass transport prevails over convective transport in the matrix. Biofilm cells tolerate higher concentrations of many biocides. The EPS matrix sequesters nutrients from the water phase. In photosynthetic communities, EPS molecules can function as light transmitters and provide photons to organisms located deeper in a microbial mat. The EPS matrix is a dynamic system, constructed by the organisms and responding to environmental changes. It enables the cells to function in a manner similar to multicellular organisms.

Influence of calcium ions on the mechanical properties of a model biofilm of mucoid Pseudomonas aeruginosa.

The mechanical properties of biofilms and in particular their mechanical strength is of great importance for both biofilm reactors and for the removal of undesired biofilms as in cases of biofouling and biocorrosion. By uniaxial compression measurements, it is possible to determine the apparent elastic or Young's modulus and the yield stress as parameters for mechanical stability. This was performed with a recently developed device, using model biofilms of mucoid strain Pseudomonas aeruginosa SG81. The biofilms were grown on membrane filters placed on nutrient agar medium with different concentrations of calcium ions. The compressive stress-strain behaviour up to failure was recorded at a compression speed of 1 micron s-1. The apparent Young's modulus, representing the stiffness of the biofilm, and the yield stress obtained from the stress--strain diagram were used for the description of mechanical properties of biofilms. A certain critical concentration of calcium ions was found where the Young's modulus of the P. aeruginosa biofilms increases strongly and subsequently remains constant for higher calcium concentrations. This behaviour is explained by the presence of calcium ions crosslinking alginate, which is the major component of the extracellular polymeric substances produced by the mucoid P. aeruginosa strain used in this investigation.

Relevance of microbial extracellular polymeric substances (EPSs)--Part II: Technical aspects.

Extracellular polymeric substances (EPSs) are involved in both detrimental and beneficial consequences of microbial aggregates such as biofilms, flocs and biological sludges. In biofouling, they are responsible for the increase of friction resistance, change of surface properties such as hydrophobicity, roughness, colour, etc. In biocorrosion of metals they are involved by their ability to bind metal ions. In bioweathering, they contribute by their complexing properties to the dissolution of minerals. The EPSs represent a sorption site for pollutants such as heavy metal ions and organic molecules. This can lead to a burden in wastewater sludge; on the other hand, the sorption properties can be used for water purification. Other biotechnological uses of EPS exploit their contribution to viscosity, e.g., in food, paints and oil-drilling 'muds'; their hydrating properties are also used in cosmetics and pharmaceuticals. Furthermore, EPSs may have potential uses as biosurfactants, e.g., in tertiary oil production, and as biological glue. EPSs are an interesting component of all biofilm systems and still hold a large biotechnological potential.

Capability of mucoid Pseudomonas aeruginosa to survive in chlorinated water.

Mucoid strains of Pseudomonas aeruginosa are characterized by an overproduction of the extracellular polysaccharide alginate. When suspended into chlorinated swimming-pool water or drinking water samples, mucoid bacteria revealed enhanced survival compared with isogenic nonmucoid cells. Removal of slime from mucoid bacteria abolished chlorine resistance, addition of purified alginate to washed bacteria again enhanced survival. Thus, alginate-containing slime confers protection on P. aeruginosa against chlorine and may contribute to survival of these bacteria in chlorinated water systems.

The role of intermolecular interactions: studies on model systems for bacterial biofilms.

The mechanical stability of biofilms and other microbial aggregates is of great importance for both the maintenance of biofilm processes and the removal of undesired biofilms. The binding forces are weak interactions such as London dispersion forces, electrostatic interactions and hydrogen bonds. In a first attempt to rank their contribution, the viscosity of solutions of extracellular polymeric substances (EPS) from a mucoid strain of Pseudomonas aeruginosa is measured. In order to distinguish the binding forces, substances are chosen which individually address the different types of bonds. Polyacrylic acid is identified as a suitable model system for EPS when molecular interactions are studied. Electrostatic interactions and hydrogen bonds are found to be the dominating forces among macromolecules within the biofilm.

Characterization of mucoid Pseudomonas aeruginosa strains isolated from technical water systems.

The occurrence of mucoid Pseudomonas aeruginosa strains was investigated in water samples and surface material from non-clinical aquatic environments. Ten of 81 environmental isolates displayed a mucoid colony type after incubation at 36 degrees C for 24 h on Pseudomonas Isolation Agar. The mucoid strains obtained exclusively from surfaces of technical water systems were characterized in terms of medium-dependent expression of mucoid colonial phenotype, exoenzyme profile, pigment production and O-antigen type. The mucoid strains secreted substantially higher quantities of carbohydrate and uronic acid-containing material compared to non-mucoid environmental isolates. Major slime components of the mucoid strains were identified as O-acetylated alginates that contained higher proportions of mannuronate than guluronate monomer residues and were composed of blocks of poly-mannuronate and poly-mannuronate/guluronate, whereas blocks of poly-guluronate were absent. The results suggest that surfaces in aquatic environments may represent a natural habitat for mucoid (i.e. alginate-overproducing) strains of Ps. aeruginosa with properties similar to clinical mucoid strains.

A major Pseudomonas aeruginosa clone common to patients and aquatic habitats.

The genomic relatedness of 573 Pseudomonas aeruginosa strains from environmental and clinical habitats was examined by digesting the genome with the rare-cutting enzyme SpeI. Thirty-nine strains were collected from environmental habitats mainly of aquatic origin, like rivers, lakes, or sanitary facilities. Four hundred fifty strains were collected from 76 patients with cystic fibrosis (CF) treated at four different centers, and 25 additional clinical isolates were collected from patients suffering from other diseases. Twenty-nine P. aeruginosa isolates were collected from the environment of one CF clinic. Thirty strains from culture collections were of environmental and clinic origin. A common macrorestriction fingerprint pattern was found in 13 of 46 CF patients, 5 of 29 environmental isolates from the same hospital, in a single ear infection isolate from another hospital, and 8 of 38 isolates from aquatic habitats about 300 km away from the CF clinic. The data indicate that closely related variants of one major clone (called clone C) persisted in various spatially and temporally separated habitats. Southern analysis of the clonal variants with six gene probes and two probes for genes coding for rRNA revealed almost the same hybridization patterns. With the exception of the phenotypically rapidly evolving CF isolates, the close relatedness of the strains of the clone was also shown by their identical responses in pyocin typing, phage typing, and serotyping. Besides clone C, three other P. aeruginosa clones were isolated from more than one clinical or environmental source.

An outer membrane protein characteristic of mucoid strains of Pseudomonas aeruginosa.

SDS-polyacrylamide gel electrophoresis of outer membrane (OM) proteins of different mucoid strains of P. aeruginosa revealed a protein of about 54 kDa that was absent in nonmucoid strains. This 54 kDa protein was expressed under iron-restricted and iron sufficient growth conditions. Electrophoretic mobility of the 54 kDa protein was modified by the solubilization temperature as well as by the addition of lipopolysaccharide and alginate prior to electrophoresis. Treatment of OMs with octylglucoside/KCl or SDS completely extracted the 54 kDa protein at low temperatures. The possible role of this protein in biosynthesis and/or excretion of bacterial alginate is discussed.

Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extraintestinal Escherichia coli isolates.

Fimbrial adhesins and hemolysins contribute to pathogenicity of extraintestinal Escherichia coli isolates causing urinary tract infections (UTI), sepsis and new born meningitis (NBM). Using gene cloning techniques and pulse field electrophoresis in combination with Southern hybridizations it was demonstrated that the genetic determinants coding for P and 'P-related' fimbrial adhesins and hemolysins are closely linked on the chromosomes of different pathogenic E. coli wild-type isolates. For two UTI strains, 536 (O6:K15) and J96 (O4:K6), a co-deletion of the linked gene clusters coding for hemolysin and fimbriae was observed. The deleted DNA regions which also comprise flanking DNA sequences were termed 'pathogenicity DNA islands'. Such 'pathogenicity DNA islands' were also detected in the genome of O18:K1 isolates of OMP type 6 but were absent on the chromosomes of O18:K1 strains of OMP type 9. A mutant strain, 536-22 was selected from rat kidneys after intraurethral infection of animals with the wild-type parental strain 536. This particular isolate also shows deletions of 'pathogenicity islands' leading to a non-pathogenic phenotype. It is therefore concluded that excisions of 'pathogenicity islands' from chromosomes of pathogenic E. coli strains are not restricted to the laboratory but also occur in vivo. The generation of deletions may represent a general mechanism of bacterial virulence modulation.