Effect of biostimulation and bioaugmentation on degradation of polyurethane buried in soil.

This work investigated biostimulation and bioaugmentation as strategies for removing polyurethane (PU) waste in soil. Soil microcosms were biostimulated with the PU dispersion agent "Impranil" and/or yeast extract or were bioaugmented with PU-degrading fungi, and the degradation of subsequently buried PU was determined. Fungal communities in the soil and colonizing buried PU were enumerated on solid media and were analyzed using denaturing gradient gel electrophoresis (DGGE). Biostimulation with yeast extract alone or in conjunction with Impranil increased PU degradation 62% compared to the degradation in untreated control soil and was associated with a 45% increase in putative PU degraders colonizing PU. Specific fungi were enriched in soil following biostimulation; however, few of these fungi colonized the surface of buried PU. Fungi used for soil bioaugmentation were cultivated on the surface of sterile wheat to form a mycelium-rich inoculum. Wheat, when added alone to soil, increased PU degradation by 28%, suggesting that wheat biomass had a biostimulating effect. Addition of wheat colonized with Nectria haematococca, Penicillium viridicatum, Penicillium ochrochloron, or an unidentified Mucormycotina sp. increased PU degradation a further 30 to 70%, suggesting that biostimulation and bioaugmentation were operating in concert to enhance PU degradation. Interestingly, few of the inoculated fungi could be detected by DGGE in the soil or on the surface of the PU 4 weeks after inoculation. Bioaugmentation did, however, increase the numbers of indigenous PU-degrading fungi and caused an inoculum-dependent change in the composition of the native fungal populations, which may explain the increased degradation observed. These results demonstrate that both biostimulation and bioaugmentation may be viable tools for the remediation of environments contaminated with polyurethane waste.

Programmed cell death in the aspergilli and other filamentous fungi.

Programmed cell death (PCD), in which cells actively participate in their own death through the activation of defined pathways, has long been established as an important developmental pathway in metazoan systems but it is only recently that evidence for a primitive form of PCD in the fungi has come to light. While much of the evidence for this comes from studies in the yeast Saccharomyces cerevisiae, recent evidence strongly suggests the presence of a metacaspase (primitive orthologues of the mammalian caspases) independent and dependent pathways in the Aspergilli which can be activated by deleterious environmental stimuli such as starvation, oxidative stress and antifungal agents as well as developmentally during sporulation. Bioinformatic evidence for these pathways suggests that the PCD pathway(s) is more complex in the Aspergilli compared to yeasts.

CADRE: the Central Aspergillus Data REpository.

CADRE is a public resource for housing and analysing genomic data extracted from species of Aspergillus. It arose to enable maintenance of the complete annotated genomic sequence of Aspergillus fumigatus and to provide tools for searching, analysing and visualizing features of fungal genomes. By implementing CADRE using Ensembl, a framework is in place for storing and comparing several genomes: the resource will thus expand by including other Aspergillus genomes (such as Aspergillus nidulans) as they become available. CADRE is accessible at http://www.cadre. man.ac.uk.

Choline: its role in the growth of filamentous fungi and the regulation of mycelial morphology.

Choline is an essential metabolite for the growth of filamentous fungi. It occurs most notably as a component of the major membrane phospholipid, phosphatidyl choline (lecithin), and fulfills a major role in sulphate metabolism in the form of choline-o-sulphate in many species. Choline is usually synthesised endogenously, but exogenous choline can also be taken up, either to compensate for metabolic deficiencies in choline-requiring mutants such as those of Aspergillus nidulans and Neurospora crassa, or as a normal function by species such as Fusarium graminearum which do not require added choline for growth. F. graminearum has a highly specific constitutive uptake system for this purpose. Recent studies have begun to indicate that choline also plays an important role in hyphal and mycelial morphology. Over a wide range of concentrations, choline influences mycelial morphology, apparently by controlling branch initiation. At high concentrations of added choline, branching is inhibited but specific growth rate is unaffected, leading to the production of rapidly extending, sparsely branched mycelia. Reduction of choline concentration allows a progressive increase in branching. Additionally, in choline-requiring mutants which have a very reduced content of choline, multiple tip-formation and apical branching occurs. Just prior to cessation of growth in choline-starved cultures of A. nidulans choline-requiring mutants, hyphal morphology changes due to a brief phase of unpolarised growth to produce spherical swellings called balloons, at or near hyphal apices. The precise mechanism by which choline affects fungal morphology is not yet known, although in A. nidulans it appears to be at least partially due to the influence of membrane composition on the synthesis of the hyphal wall polymer chitin. Several hypotheses for the possible mode of action of choline in affecting fungal morphology are discussed here.

Choline transport in Fusarium graminearum A 3/5.

Fusarium graminearum A 3/5 possesses a high affinity system (Km = 32 +/- 8 microM; mean +/- SE) for uptake of choline, which was shown to be energy-dependent and constitutive. The maximum rate of choline uptake by this system was repressed by ammonia and glucose, showing a three-fold increase in maximum activity after nitrogen (2 h) or carbon (4 h) starvation. The system was highly specific for choline with only dimethylethanolamine (Ki = 198 +/- 29 microM), betaine aldehyde (Ki = 95 +/- 14 microM) and chlorocholine (Ki = 352 +/- 40 microM) acting as competitive inhibitors. Hemicholinium-3 acted as a mixed (non-competitive) inhibitor (KIES = 1.9 +/- 0.6 microM; KIE = 3.6 +/- 1.9 microM).

Relationships between phosphatidylcholine content, chitin synthesis, growth, and morphology of Aspergillus nidulans choC.

The phosphatidylcholine (PC) content of Aspergillus nidulans choC was varied by growing the auxotroph in medium containing various concentrations of choline chloride. Direct linear correlations were observed between PC content and in vivo chitin synthase activity, between in vivo chitin synthase activity and mean hyphal extension rate, and between mean hyphal extension rate and hyphal growth unit length; hyphal growth unit length is a measure of hyphal branching. Further, there was a correlation between PC content and colony radial growth rate. Thus, membrane composition is an important determinant of both hyphal (and colony) extension rate and mycelial morphology.

Combined use of growth rate correlated and growth rate independent promoters for recombinant glucoamylase production in Fusarium venenatum.

Fusarium venenatum JeRS 325, a strain which produces recombinant glucoamylase under control of a growth rate independent promoter was transformed with a plasmid carrying the Aspergillus niger glucoamylase gene under control of its own growth rate correlated promoter. Some disruption of the original recombinant genes occurred and at pH 5.8 the double transformant did not produce as much glucoamylase as JeRS 325 in batch culture. However, the double transformant still produced as much glucoamylase as JeRS 325 in fed-batch cultures, illustrating the potential for the combined use of growth rate independent and dependent promoters to improve production of recombinant proteins in fed-batch culture systems.

Multiple isomers of phosphatidyl inositol monophosphate and inositol bis- and trisphosphates from filamentous fungi.

The range of inositol phosphates and inositol phospholipids present in three filamentous fungi, Neurospora crassa, Fusarium graminearum and Phanerochaete chrysosporium has been investigated by HPLC analysis. The profiles obtained demonstrate that two isomers of phosphatidyl inositol monophosphate are present, and that an apparent complexity in the number of isomers of inositol bis- and trisphosphates is found in filamentous fungi that has not been observed in animal or plant cells.

Effect of pH on hen egg white lysozyme production and evolution of a recombinant strain of Aspergillus niger.

An Aspergillus niger strain (B1) transformed to produce mature hen egg white lysozyme (HEWL) from a glucoamylase fusion protein under control of the A. niger glucoamylase promoter was grown in glucose-limited chemostat culture at a dilution rate of 0.07 h-1 at various pH values. Maximum HEWL production (9.3 mg g-1; specific production rate = 0.65 mg g-1 per h) was obtained at pH 4.5. However, in chemostat culture, HEWL production was not stable at any pH tested. After 240 h in steady state, specific production decreased to only 0.03 +/- 0.01 and 0.24 +/- 0.02 mg g-1 per h at pH 6.5 and 4.5, respectively. Some isolates removed from the chemostat cultures had lost copies of the HEWL gene and when grown in shake flask cultures all of the isolates produced less HEWL than the parental strain. Morphological mutants with similar phenotypes were isolated at all pHs, but their rate of increase in the population was pH dependent, with cultures at low pH (< 4.5) being more morphologically stable than cultures at high (> 4.5) pH. The selective advantage of these mutants was also generally dependent on pH. Both yellow pigment producing mutants and brown sporulation mutants had higher selective advantages over the parental strain at high than at low pH, regardless of the pH at which they were isolated. However, the selective advantage of densely sporulating mutants was independent of pH.

A glucoamylase::GFP gene fusion to study protein secretion by individual hyphae of Aspergillus niger.

Although Aspergillus niger is used as a host for heterologous protein production, yields are generally lower than those obtained for homologous proteins. Mechanisms of protein secretion and the secretory pathway in filamentous fungi are poorly characterised, although there is evidence to suggest that secretion occurs by a mechanism similar to that in other eukaryotes, but with proteins destined for secretion being directed to the hyphal tip. We report on a method using a glucoamylase: GFP gene fusion which allows us for the first time to monitor, in vivo, protein secretion in A. niger at the single hyphal level. A synthetic green fluorescent protein (sGFP(S65T)) was fused to truncated A. niger glucoamylase (GLA:499). Southern blot analysis of transformants confirmed that the gene fusion had successfully integrated into the A. niger genome. Confocal and fluorescence microscopy revealed that the GLA::GFP fusion protein is fluorescent in A. niger and appears to be directed to the hyphal tip. In young mycelia, hyphal cell wall fluorescence is apparent and immunogold labelling of GFP confirmed that GFP was partially localised within the hyphal cell wall. Using Western blotting, extracellular GLA::GFP was detected only in culture filtrates of young mycelia grown in a soya milk medium. The actin inhibitor latrunculin B was used to disrupt the secretion process, and its effects on the distribution of GLA::GFP were monitored.

The relationship between pipe material and biofilm formation in a laboratory model system.

The aim of this study was to compare biofilm accumulation and heterotrophic bacterial diversity on three pipe materials-cast iron, medium density polyethylene (MDPE), and unplasticised polyvinyl chloride (uPVC) - using a laboratory model system run over a short period (21 d) and a longer period (7 months). Newly Modified Robbins Devices (nMRD) were run in parallel, each containing 25 discs of one material with cold tap water flowing through the devices at 3 ml min(-1) (Reynolds Number 9.05) for 21 d. The numbers of bacteria on each material increased exponentially between 0 and 11 d when the biofilm viable count remained constant. The mean doubling times of the heterotrophic population on the materials during the exponential phase was 13.2 h for cast iron and 15.6 h for MDPE and uPVC. The same experiment was repeated under different environmental conditions with a lower temperature, higher free chlorine and lower number of organisms ml(-1) of incoming water. The exponential phase lengthened to 16 d but the steady state count remained the same. The mean viable count after 21 d and after 7 months was on average 97% higher on cast iron than on the other materials. Very few different colony types were isolated from each material with the largest number (nine) recovered from cast iron. The numbers of planktonic bacteria in the effluent water leaving each of the nMRDs directly correlated with the numbers in the biofilm phase on each of the materials. In addition the distribution and thickness of the biofilms on the MDPE and uPVC were observed using confocal scanning laser microscopy. In conclusion, MDPE and uPVC support the lowest numbers of bacteria in a steady state biofilm in the short term (21 d) and over a longer term (7 months). The diversity of heterotrophic bacteria was greatest on cast iron.

Influence of starvation, surface attachment and biofilm growth on the biocide susceptibility of the biodeteriogenic yeast Aureobasidium pullulans.

AIM: To investigate the effect of starvation, surface attachment and growth in a biofilm on the susceptibility of Aureobasidium pullulans to the biocides 2-n-octyl-4-isothiazolin-3-one (OIT) and sodium hypochlorite (NaOCl). METHODS AND RESULTS: Fluorescence loss from a green fluorescent protein (GFP)-transformed strain was used to monitor real-time loss in viability as previously described in situ in 96-well plates. Exponential phase, yeast-like (YL) cells were settled in the bottom of the wells as a low-density monolayer (LDM) and were susceptible to all biocide concentrations (25-100 mug ml(-1)). The exponential phase YL cells were either starved for 48 h in suspension or starved for 48 h as LDMs in the wells. Starvation in both cases led to a small reduction in susceptibility to the biocides. In contrast, 48-h biofilms grown in malt extract broth showed an apparent lack of susceptibility to 25 and 50 mug ml(-1) OIT and to 25-100 mug ml(-1) NaOCl. However, when the OIT concentration was increased to compensate for the higher cell density in the biofilm, the biofilms were found to be equally susceptible to the LDM. CONCLUSIONS: Starvation of A. pullulans YL cells either in suspension or as attached LDM resulted in a decrease in susceptibility to low concentrations of both OIT and NaOCl while the apparent reduced susceptibility of mature biofilms was due to the increase in biofilm cell density rather than true biofilm resistance per se. SIGNIFICANCE AND IMPACT OF THE STUDY: Monitoring fluorescence loss from the GFP-transformed strain of A. pullulans can be used as a fast and reliable method for monitoring cell death in real time as a response to biocide and antimicrobial challenge.

Fungal colonization of soil-buried plasticized polyvinyl chloride (pPVC) and the impact of incorporated biocides.

Plasticized polyvinyl chloride (pPVC) with or without incorporated biocides was buried in grassland and forest soil for up to 10 months. The change with time in viable counts of fungi on the plastic surface was followed, together with the percentage capable of clearing the two plasticizers dioctyl adipate (DOA) and dioctyl phthalate (DOP). With time fungal total viable counts (TVC) on control pPVC increased and the fraction able to clear DOA was considerably higher than the average estimated in both soil types. A total of 92 fungal morphotypes were isolated from grassland soil and 42 from forest soil with the greatest variety of fungal isolates observed on control pPVC. The incorporation of biocides into pPVC affected both fungal TVC and the richness of species isolated. The biocides NCMP [n-(trichloromethylthio)phthalimide], OBPA (10,10'-oxybisphenoxarsine) and OIT (2-n-octyl-4-isothiazolin-3-one) were the most effective in grassland soil, and TCMP [2,3,5,6-tetrachloro-4-(methylsulphonyl)pyridine] and NCMP the most effective in forest soil. In grassland soil, Penicillium janthinellum established as a principal colonizer and was recovered from all pPVC types. DOP clearers were found at much lower levels than DOA clearers, with Doratomyces spp. being the most efficient. At the end of 10 months the physical properties of the pPVC were altered; changes in stiffness were the most significant for heavily colonized grassland-buried pPVC samples, whereas in forest soil, the extensibility of the pPVC was affected more than the stiffness. These results suggest that fungi are important colonizers of pPVC buried in soil and that enrichment of soil fungi capable of clearing DOA occurs during colonization of the plastic surface. The results also demonstrate that incorporated biocides have a marked impact on the richness of species colonizing the pPVC surface.

Molecular species of phosphatidylethanolamine from continuous cultures of Saccharomyces pastorianus syn. carlsbergensis strains.

Saccharomyces pastorianus syn. carlsbergensis strain 34/70 is well known to be the most used strain for lager beer production. The difference between this strain and very closely related strain 34/78 is the latter's greater flocculating character. This single physiological trait can cause technical difficulties in beer production. The aim of this study was to determine whether lipid analysis by a combination of thin layer chromatography (TLC) with electrospray ionization mass spectrometry (ESI-MS) could be used as a strain-typing technique in order to distinguish S. pastorianus syn. carlsbergensis strain 34/70 from strain 34/78. Both strains (34/70 and 34/78) were harvested after continuous culture under standard conditions. Polar lipids were then extracted from lyophilized cultures and analysed by TLC in order to separate phospholipid families. Phosphatidylethanolamine (PE) was extracted and investigated using ESI-MS, to gain further information on individual molecular species. Using TLC analysis, lipids were separated corresponding to standards for PE, phosphatidylcholine (PC), phosphatidylglycerol (PG), cardiolipin (CL), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA) and sphingomyelin (SM). ESI-MS of the PE band, separated by TLC, showed that electrospray mass spectra were highly reproducible for repeat cultures. Novel findings were that both brewing strains displayed major phospholipid peaks with m/z 714, PE (34 : 2) m/z 742, PE (36 : 2) and m/z 758, PE (37 : 1). However, strain 34/78 had additional peaks of m/z 700, PE (33 : 2) and m/z 728, PE (35 : 2). Strain 34/70 had an extra peak with m/z 686 PE (32 : 2). We conclude that combined TLC/ESI-MS can distinguish between S. pastorianus syn. carlsbergensis 34/70 and 34/78 and may be a useful typing technique for differentiation of closely related yeast strains. This novel approach may aid quality assurance and could be suitable for yeast collections and larger industrial companies.

A preliminary analysis of the process of protein secretion and the diversity of putative secreted hydrolases encoded in Aspergillus fumigatus: insights from the genome.

The genome sequence of Aspergillus fumigatus has enabled the annotation of genes likely to encode secreted enzymes that may be important in underpinning the natural lifestyle of the fungus and its pathogenicity. We summarize the data from the genome sequence relevant to both the process of protein secretion and the predicted hydrolase enzymes secreted by A. fumigatus.

Effects of validamycin A on the morphology, growth and sporulation of Rhizoctonia cerealis, Fusarium culmorum and other fungi.

All Basidiomycotina screened were sensitive to validamycin A, whereas most Ascomycotina and all Mucorales and Oomycetes were insensitive. Studies with Rhizoctonia cerealis and Fusarium culmorum showed that, in semi-solid culture, the antibiotic caused a decrease in colony radial growth rate and that this was associated with a decrease in mean hyphal extension rate and an increase in hyphal branching. However, the antibiotic did not alter the morphology of R. cerealis grown in liquid culture (shaken or stationary). Validamycin A caused a reduction in the number and viability of conidia produced by F. culmorum.

In situ quantification of biocide efficacy using GFP transformed Aureobasidium pullulans.

AIMS: To develop a real-time in situ method to quantify loss of viability of Aureobasidium pullulans PRAFS8 cells attached to plasticized polyvinyl chloride (pPVC) with incorporated biocides, and to use the method to compare biocide efficacy in situ. METHODS AND RESULTS: A. pullulans PRAFS8, transformed with green fluorescent protein (GFP), was used to quantify the efficacy of a range of biocides incorporated into pPVC. Experimentally, it was found that a density of 1.53 x 10(6) yeast cells per cm(2) of pPVC was optimal as increasing the density of the yeast cells to 6.12 x 10(6) cm(-2) attached to pPVC containing the biocide 2-n-octyl-4-isothiazolin-3-one (OIT) decreased the rate of fluorescence loss. A strong positive correlation between fluorescence and viable yeast cell number was observed and fluorescence was used as a direct indicator of cell viability. The effectiveness of five commercial biocides, commonly incorporated into pPVC at their in-use concentrations, was tested against yeast cells attached to the pPVC surface. The loss of fluorescence and hence viability in situ was quantified using image analysis. The biocides N-(trichloromethylthio) phthalimide (NCMP), 10,10'-oxybisphenoxarsine (OBPA), OIT and 2,3,5,6-tetrachloro-4-(methylsulphonyl) pyridine (TCMP) caused complete loss of fluorescence within 30-50 h. In contrast the biocide dichloro-octyl-isothiazoline caused only 55 +/- 15% fluorescence loss after 50 h. Starvation of the yeast cells in suspension for 24 h prior to attachment reduced their initial sensitivity to OBPA, NCMP, OIT and TCMP by 15-20%, but eventually the fluorescence was also completely lost. CONCLUSIONS: The use of A. pullulans expressing cytosolic GFP enables the in situ quantification of loss of viability when cells are attached to pPVC with incorporated biocides. SIGNIFICANCE AND IMPACT OF THE STUDY: GFP fluorescence was used as a real-time indicator of cell viability and thus can be applied for direct quantification of the effectiveness of a broad range of biocides, incorporated into the polymer mass and used to protect a variety of plastics or other materials from microbial growth.

Exogenous cAMP and cGMP modulate branching in fusarium graminearum.

A study was made of the effects of adenosine 3',5'-cyclic monophosphate (cAMP), guanosine 3',5'-cyclic monophosphate (cGMP) and choline on the morphology and growth of a wild-type strain (A 3/5) and a highly branched, 'colonial' mutant strain (C106) of Fusarium graminearum. Addition of up to 50 mM-cAMP or cGMP to the medium had no effect on the specific growth rate of strain A 3/5. For strain A 3/5, but not for strain C106, exogenous cAMP caused significant decreases in both mean hyphal extension rate (E) and hyphal growth unit length (G), i.e. cAMP caused mycelia of strain A 3/5 to branch profusely. By contrast, for both strains, cGMP caused significant increases in both E and G, i.e. exogenous cGMP caused mycelia to branch more sparsely. The effects of exogenous cGMP and choline in increasing E and G were synergistic, but the effects of cGMP and choline counteracted the effect of cAMP. The mutant phenotype of strain C106 was not correlated with altered levels of endogenous cAMP or cGMP.

Effect of choline on the morphology, growth and phospholipid composition of Fusarium graminearum.

Studies were made of the growth kinetics, morphology and phospholipid composition of two strains of Fusarium graminearum, a wild-type strain (A3/5) and a highly branched variant (C106) which arose spontaneously during cultivation of A3/5. No significant difference was observed between the hyphal diameters of the two strains and therefore increased branching of C106 could not be explained in the terms of an increase in hyphal radius in the absence of a change in hyphal growth unit volume. The two strains had the same specific growth rate in batch culture and this was not affected by the addition of up to 1.5 mM-choline to the medium. However, choline increased the mean hyphal extension rate and colony radial growth rate of both strains and this response was correlated with the formation of mycelia which were more sparsely branched than mycelia grown on medium lacking choline. Addition of betaine, choline, ethanolamine, monomethylethanolamine or dimethylethanolamine (but not serine, glycine, dimethylglycine, methylamine, hydroxylamine or beta-hydroxyethylhydrazine) to the medium also resulted in appreciable increases in the colony radial growth rates of A3/5 (increased by about 130% for choline) and C106 (increased by about 25% for choline). No significant difference was observed between the phospholipid compositions of the two strains, and the addition of 100 microM-choline to the medium had no significant effect on the phospholipid composition of either strain.

A study of the protein secretory pathway of Aspergillus niger using a glucoamylase-GFP fusion protein.

The effect of various treatments that block protein secretion was visualized in Aspergillus niger using a strain expressing a glucoamylase-GFP fusion protein. Cold shock caused the retention of the fusion protein in a reticulate network (ER) with brighter nodes that may represent Golgi bodies. Treatment of germlings with brefeldin A (BFA) also initially caused accumulation within the ER but prolonged exposure led to the formation and targeting of the fusion protein to vacuoles from the ER. Disruption of actin with cytochalasin A initially led to a faint diffuse accumulation and ultimately to the formation of aggregated bodies which were not vacuoles, suggesting that the actin cytoskeleton is important in secretory vesicle transport. Disruption of microtubules with nocodazole led to hyperbranching but did not cause intracellular accumulation, suggesting that microtubules play a role in directing vesicle transport rather than vesicle movement per se. Treatment of regenerating protoplasts confirmed that BFA and cytochalasin but not nocodazole inhibited protein secretion. When germlings were subjected to carbon starvation, vacuolation was rapidly initiated throughout the hyphae and GFP fluorescence was visible in some of the vacuoles, indicating retargeting of the fusion protein from the secretory pathway to the vacuoles.