Fungal Communities Associated with Degradation of Polyester Polyurethane in Soil

Soil fungal communities involved in the biodegradation of polyester polyurethane (PU) were investigated. PU coupons were buried in two sandy loam soils with different levels of organic carbon: one was acidic (pH 5.5), and the other was more neutral (pH 6.7). After 5 months of burial, the fungal communities on the surface of the PU were compared with the native soil communities using culture-based and molecular techniques. Putative PU-degrading fungi were common in both soils, as <45% of the fungal colonies cleared the colloidal PU dispersion Impranil on solid medium. Denaturing gradient gel electrophoresis showed that fungal communities on the PU were less diverse than in the soil, and only a few species in the PU communities were detectable in the soil, indicating that only a small subset of the soil fungal communities colonized the PU. Soil type influenced the composition of the PU fungal communities. Geomyces pannorum and a Phoma sp. were the dominant species recovered by culturing from the PU buried in the acidic and neutral soils, respectively. Both fungi degraded Impranil and represented >80% of cultivable colonies from each plastic. However, PU was highly susceptible to degradation in both soils, losing up to 95% of its tensile strength. Therefore, different fungi are associated with PU degradation in different soils but the physical process is independent of soil type.     

Fungal communities associated with degradation of polyester polyurethane in soil

Soil fungal communities involved in the biodegradation of polyester polyurethane (PU) were investigated. PU coupons were buried in two sandy loam soils with different levels of organic carbon: one was acidic (pH 5.5), and the other was more neutral (pH 6.7). After 5 months of burial, the fungal communities on the surface of the PU were compared with the native soil communities using culture-based and molecular techniques. Putative PU-degrading fungi were common in both soils, as <45% of the fungal colonies cleared the colloidal PU dispersion Impranil on solid medium. Denaturing gradient gel electrophoresis showed that fungal communities on the PU were less diverse than in the soil, and only a few species in the PU communities were detectable in the soil, indicating that only a small subset of the soil fungal communities colonized the PU. Soil type influenced the composition of the PU fungal communities. Geomyces pannorum and a Phoma sp. were the dominant species recovered by culturing from the PU buried in the acidic and neutral soils, respectively. Both fungi degraded Impranil and represented >80% of cultivable colonies from each plastic. However, PU was highly susceptible to degradation in both soils, losing up to 95% of its tensile strength. Therefore, different fungi are associated with PU degradation in different soils but the physical process is independent of soil type.     

Cloning and expression in Escherichia coli of apolyurethane-degrading enzyme from Pseudomonasfluorescens

A polyester polyurethane (PU)-degrading enzyme, PU esterase, derived from Pseudomonas fluorescens, a bacterium that utilizes polyester PU as the sole carbon source,was purified to homogeneity as indicated by sodium dodecyl sulfate-polyacrylamide gelelectrophoresis. This enzyme was a soluble, extracellular protein with a molecular mass of 48 kDa and was inhibited by phenylmethylsulfonylfluoride (PMSF). A genomic library of Ps.fluorescens was constructed using the Escherichia coli bacteriophage l vector lZAPII. A recombinant phage exhibiting activity against Impranil DLN was isolated. The geneencoding the polyurethanase (PUase) protein was subcloned into a plasmid expression vectorpT7-6 and expressed in E. coli. Upon expression, the PUase was secreted by the host,displayed esterase activity which was inhibited by PMSF, and in vivo ³⁵S-methionine labeling of the gene product encoded by the open reading frame of the clone insertrevealed a single polypeptide with a molecular mass of 48 kDa.     

Isolation and characterization of different promising fungi for biological waste management of polyurethanes

As a highly resistant polymer family, polyurethanes (PU) are responsible for increasing environmental issues. Then, PU biodegradation is a challenging way to develop sustainable waste management processes based on biological recycling. Since the metabolic diversity of fungi is a major asset for polymer degradation, nearly thirty strains were isolated from sampling on six different PU wastes-containing environments. A screening of the fungi on four thermoplastic PU (TPU) with different macromolecular architectures led to the selection of three strains able to use two polyester PU as sole carbon source: Alternaria sp., Penicillium section Lanata-Divaricata and Aspergillus section flavi. Weight loss, FT-IR, Scanning Electron Microscopy and Size Exclusion Chromatography analyses revealed that these three fungi degrade slightly and similarly a fatty acid dimer-based TPU while variability of degradation was noticed on a polycaprolactone-based TPU. On this last TPU, robust analysis of the degraded polymers showed that the Penicillium strain was the best degrading microorganism. Membrane enzymes seemed to be involved in this degradation. It is the first time that a strain of Penicillium of the section Lanata-Divaricata displaying PU biodegradation ability is isolated. These newly discovered fungi are promising for the development of polyester PU waste management process.     

Characterization of the Polyurethanolytic Activity of Two Alicycliphilus sp. Strains Able To Degrade Polyurethane and N-Methylpyrrolidone

Two bacterial strains (BQ1 and BQ8) were isolated from decomposed soft foam. These were selected for their capacity to grow in a minimal medium (MM) supplemented with a commercial surface-coating polyurethane (PU) (Hydroform) as the carbon source (MM-PUh). Both bacterial strains were identified as Alicycliphilus sp. by comparative 16S rRNA gene sequence analysis. Growth in MM-PUh showed hyperbolic behavior, with BQ1 producing higher maximum growth (17.8 ± 0.6 mg·ml⁻¹) than BQ8 (14.0 ± 0.6 mg·ml⁻¹) after 100 h of culture. Nuclear magnetic resonance, Fourier transform infrared (IR) spectroscopy, and gas chromatography-mass spectrometry analyses of Hydroform showed that it was a polyester PU type which also contained N-methylpyrrolidone (NMP) as an additive. Alicycliphilus sp. utilizes NMP during the first stage of growth and was able to use it as the sole carbon and nitrogen source, with calculated K_s values of about 8 mg·ml⁻¹. Enzymatic activities related to PU degradation (esterase, protease, and urease activities) were tested by using differential media and activity assays in cell-free supernatants of bacterial cultures in MM-PUh. Induction of esterase activity in inoculated MM-PUh, but not that of protease or urease activities, was observed at 12 h of culture. Esterase activity reached its maximum at 18 h and was maintained at 50% of its maximal activity until the end of the analysis (120 h). The capacity of Alicycliphilus sp. to degrade PU was demonstrated by changes in the PU IR spectrum and by the numerous holes produced in solid PU observed by scanning electron microscopy after bacterial culture. Changes in the PU IR spectra indicate that an esterase activity is involved in PU degradation.     

Isolation of a <Emphasis Type="Italic">Pseudomonas</Emphasis><Emphasis Type="Italic">aeruginosa</Emphasis> strain from soil that can degrade polyurethane diol

Polyurethane diol (PUR-diol), a synthetic polymer, is widely used as a modifier for water-soluble resins and emulsions in wood appliances and auto coatings. Non-biodegradability of polyurethanes (PUR) and PUR-based materials poses a threat to environment that has led scientists to isolate microbes capable of degrading PUR. However, the bio-degradation of PUR-diol has not yet been reported. In this study, we report isolation of a soil bacterium that can survive using PUR-diol as sole carbon source. PUR-diol degradation by the organism was confirmed by thin layer chromatographic analysis of the conditioned medium obtained after the growth wherein a significant reduction of PUR-diol was observed compared to non-inoculated medium. To quantify the PUR-diol degradation, a sensitive assay based on High Performance Thin Layer Chromatography has been developed that showed 32% degradation of PUR-diol by the organism in 10 days. Degradation kinetics showed the maximal depletion of PUR-diol during logarithmic growth of the organism indicating a direct relation between the growth and PUR-diol degradation. Mutagenic study and GC-MS analysis revealed that esterase activity is involved in this degradation event. The ribotyping and metabolic fingerprinting analysis showed that this organism is a strain of Pseudomonous aeruginosa (P. aeruginosa). It has also been observed that this strain is able to degrade Impranil DLN™, a variety of commercially available PUR. Therefore this study identifies a new bacterium from soil that has the potential to reduce PUR-related waste burden and adds a new facet to diverse functional activities of P. aeruginosa.     

Degradation of polyester polyurethane by newly isolated Pseudomonas aeruginosa strain MZA-85 and analysis of degradation products by GC–MS

In this report, a polyester polyurethane (PU) degrading bacterium, designated as strain MZA-85, was isolated from soil through enrichment. The bacterium was identified through 16S rRNA gene sequencing; it was completely matched with Pseudomonas aeruginosa type strain. The degradation of PU film pieces by P. aeruginosa strain MZA-85 was investigated by scanning electron microscopy (SEM), Fourier transformed infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM micrographs of PU film pieces, treated with strain MZA-85, revealed changes in the surface morphology. FTIR spectrum showed increase in organic acid functionality and corresponding decrease in ester functional group. GPC results revealed increase in polydispersity, which shows that long chains of polyurethane polymer are cleaved into shorter chains by microbial action. The bacterium was found to produce cell associated esterases based on p-Nitrophenyl acetate (pNPA) hydrolysis assay. 1,4-Butanediol and adipic acid monomers were detected by gas chromatography–mass spectrometry (GC–MS), which were produced as a result of hydrolysis of ester linkages in PU by cell bound esterases. Strain MZA-85 not only depolymerized PU but also mineralized it into CO₂ and H₂O, as indicated by increase in cells growth in the presence of degradation products as well as detection of CO₂ evolution through Sturm test. From the results presented above, it is finally concluded that P. aeruginosa strain MZA-85, as well as its enzymes, can be applied in the process of biochemical monomerization for the pure monomers recycling.     

Lon Protease Influences Antibiotic Production and UV Tolerance of Pseudomonas fluorescens Pf-5

Pseudomonas fluorescens Pf-5 is a soil bacterium that suppresses plant pathogens due in part to its production of the antibiotic pyoluteorin. Previous characterization of Pf-5 revealed three global regulators, including the stationary-phase sigma factor ς^S and the two-component regulators GacA and GacS, that influence both antibiotic production and stress response. In this report, we describe the serine protease Lon as a fourth global regulator influencing these phenotypes in Pf-5. lon mutants overproduced pyoluteorin, transcribed pyoluteorin biosynthesis genes at enhanced levels, and were more sensitive to UV exposure than Pf-5. The lon gene was preceded by sequences that resembled promoters recognized by the heat shock sigma factor ς³² (ς^H) of Escherichia coli, and Lon accumulation by Pf-5 increased after heat shock. Therefore, ς^H represents the third sigma factor (with ς^S and ς⁷⁰) implicated in the regulation of antibiotic production by P. fluorescens. Lon protein levels were similar in stationary-phase and exponentially growing cultures of Pf-5 and were not positively affected by the global regulator ς^S or GacS. The association of antibiotic production and stress response has practical implications for the success of disease suppression in the soil environment, where biological control organisms such as Pf-5 are likely to encounter environmental stresses.     

Novel Lectin-Like Bacteriocins of Biocontrol Strain Pseudomonas fluorescens Pf-5

Bacteriocin LlpA, produced by Pseudomonas sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol. 185:897-908, 2003). Biocontrol strain Pseudomonas fluorescens Pf-5 contains two llpA-like genes, named llpA1_Pf-5 and llpA2_Pf-5. Recombinant Escherichia coli cells expressing llpA1_Pf-5 or llpA2_Pf-5 acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA_BW11M1 antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1_Pf-5 and LlpA2_Pf-5 are able to inhibit P. fluorescens strains, as well as the related mushroom pathogen Pseudomonas tolaasii. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.     

Chemical intervention in bacterial lignin degradation pathways: Development of selective inhibitors for intradiol and extradiol catechol dioxygenases

Bacterial lignin degradation could be used to generate aromatic chemicals from the renewable resource lignin, provided that the breakdown pathways can be manipulated. In this study, selective inhibitors of enzymatic steps in bacterial degradation pathways were developed and tested for their effects upon lignin degradation. Screening of a collection of hydroxamic acid metallo-oxygenase inhibitors against two catechol dioxygenase enzymes, protocatechuate 3,4-dioxygenase (3,4-PCD) and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), resulted in the identification of selective inhibitors D13 for 3,4-PCD (IC₅₀ 15 μM) and D3 for MhpB (IC₅₀ 110 μM). Application of D13 to Rhodococcus jostii RHA1 in minimal media containing ferulic acid led to the appearance of metabolic precursor protocatechuic acid at low concentration. Application of 1 mM disulfiram, an inhibitor of mammalian aldehyde dehydrogenase, to R. jostii RHA1, gave rise to 4-carboxymuconolactone on the β-ketoadipate pathway, whereas in Pseudomonas fluorescens Pf-5 disulfiram treatment gave rise to a metabolite found to be glycine betaine aldehyde.     

Fungi are the predominant micro-organisms responsible for degradation of soil-buried polyester polyurethane over a range of soil water holding capacities

AIMS: To investigate the relationship between soil water holding capacity (WHC) and biodegradation of polyester polyurethane (PU) and to quantify and identify the predominant degrading micro-organisms in the biofilms on plastic buried in soil. METHODS AND RESULTS: High numbers of both fungi and bacteria were recovered from biofilms on soil-buried dumb-bell-shaped pieces of polyester PU after 44 days at 15-100% WHC. The tensile strength of the polyester PU was reduced by up to 60% over 20-80% soil WHC, but no reduction occurred at 15, 90 or 100% soil WHC. A PU agar clearance assay indicated that fungi, but not bacteria were, the major degrading organisms in the biofilms on polyester PU and 10-30% of all the isolated fungi were able to degrade polyester PU in this assay. A 5.8S rDNA sequencing identified 13 strains of fungi representing the three major colony morphology types responsible for PU degradation. Sequence homology matches identified these strains as Nectria gliocladioides (five strains), Penicillium ochrochloron (one strain) and Geomyces pannorum (seven strains). Geomyces pannorum was the predominant organism in the biofilms comprising 22-100% of the viable polyester PU degrading fungi. CONCLUSIONS: Polyester PU degradation was optimum under a wide range of soil WHC and the predominant degrading organisms were fungi. SIGNIFICANCE AND IMPACT OF THE STUDY: By identifying the predominant degrading fungi in soil and studying the optimum WHC conditions for degradation of PU it allows us to better understand how plastics are broken down in the environment such as in landfill sites.     

Comparative study on the influence of fluoride on lipid peroxidation and antioxidants levels in the different brain regions of well-fed and protein undernourished rats

Effects of fluoride on the levels of Lipid peroxidation (LP) and antioxidant enzymes in the brain regions of protein undernourished (PU) and well-fed rats (WF) rats exposed to 100 ppm fluoride in drinking water were investigated. The results indicate that the mean body weights and the total brain weights of PU rats as well as those given fluoride (both WF and PU) were significantly (P < 0.05) lower than their respective controls. The weights of different brain regions were also significantly reduced (P < 0.05) in PU rats compared to WF rats except in the brain stem. Fluoride ingestion diminished the weights of WF and PU rats affecting the cerebrum only (in the case of PU rats) and the cerebellum of both WF and PU rats without an effect on the brain stem of both WF and PU. Additionally, increased LP was observed in the cerebrum and cerebellum of PU rats but after fluoride ingestion, 30% increase in LP was observed only in the cerebrum. In the brain stem however, protein undernutrition was accompanied with a significant reduction in LP but the region seems insensitive to fluoride. There were significant reductions (P < 0.05) in CAT, SOD and GSH in all the brain regions (except the GSH level in the brain stem only) of PU rats. Fluoride induced reduction in the activity of CAT in the three brain regions and on SOD activity in cerebrum only for WF rats but no effect of fluoride on all the antioxidants studied in the three brain regions for PU rats. It is concluded that WF and PU rats responded differently to fluoride toxicity. However, it seems that at the dosage used, fluoride toxicity may be a direct effect on the antioxidant enzymes.     

Pivotal role of O-antigenic polysaccharide display in the sensitivity against phage tail-like particles in environmental Pseudomonas kin competition

Environmental pseudomonads colonize various niches including insect and plant environments. When invading these environments, bacteria are confronted with the resident microbiota. To oppose with closely related strains, they rely on narrow-spectrum weaponry such as tailocins, i.e., phage tail-like particles. Little is known about the receptors for these tailocins especially among phylogenetically closely related species. Here, we studied the interaction between an R-tailocin from Pseudomonas protegens CHA0 and a targeted kin, Pseudomonas protegens Pf-5. Using genome-wide transposon insertion sequencing, we identified that lipopolysaccharides are involved in the sensitivity of Pf-5 towards the tailocin of CHA0. By generating Pf-5 lipopolysaccharide mutants and exposing them to extracted tailocin, we specified the two O-antigenic polysaccharides (O-PS) targeted by the tailocin. We affirmed the role of these O-PS through competition assays in vitro as well as in insects. Further, we demonstrate that O-PS are double-edge swords that are responsible for the sensitivity of P. protegens towards tailocins and phages produced by their kin, but shield bacteria from the immune system of the insect. Our results shed light on the trade-off that bacteria are confronted with, where specific O-PS decorations can both be of benefit or disadvantage depending on the host environment and its bacterial inhabitants.Subject terms: Bacteriophages, Environmental microbiology     

The clonogenic potential of hematopoietic stem cells and mesenchymal stromal cells in various hematologic diseases: a pilot study

Background aimsMesenchymal stromal cells (MSC) are the most popular cells used in regenerative medicine and biotechnology. The clonogenic potential of these cells is defined by colony-forming unit-fibroblasts (CFU-F). It is well known that there is an interaction between hematopoietic cells and stromal cells in disease formation pathogenesis. Therefore we hypothesized that there should be a quantitative and qualitative relationship between MSC colonies (CFU-F) and hematopoietic stem cell colonies (colony-forming unit-granulocyte-macrophages; CFU-GM) among patients with and without hematologic diseases.MethodsForty-two patients were included in this study. Patients were divided into three groups: group A, patients with hematologic malignancies (n = 20); group B, patients with bone marrow (BM) failure (n = 11); group C, patients without hematologic diseases (n = 11). BM aspirates were plated in different densities for CFU-F culture. The plating density was the same for CFU-GM culture.ResultsCFU-GM colonies grew in 90% of group A cells and all of group B and C cells (P = 0.0001). CFU-F colonies became visible on the ninth day of plating in group A and on the eight day in groups B and C. There was no statistically significant difference between the groups for the duration of CFU-F colony formation (P = 0.12). There were differences in the morphology of the colonies among the groups.ConclusionsThis is the first study that has compared the clonogenic potential of stromal cells and hematopoietic stem cells in the same subjects with and without hematologic diseases. No correlation was shown between the clonogenic potential of stromal cells and hematopoietic cells.     

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.The polyester polyurethanes (PU) are a diverse group of synthetic polymers with many industrial and commercial applications, including insulating and packaging foams, fibers, fabrics, and synthetic leather goods (20). These polymers contain intramolecular bonds analogous to those found in biological macromolecules (such as ester and urethane linkages), making them susceptible to enzymatic degradation and assimilation by environmental microbial communities (17, 42). The susceptibility of plastics to biodegradation is of increasing importance as the generation of plastic waste material continues to increase and plastics now comprise more than 30% of household waste in the United States (32). By exploiting the biodegradability of plastics such as PU, bioremediation by microorganisms in the environment shows great potential for reducing the burden of plastic waste.Although the diversity of natural microbial populations often means that the potential for waste remediation exists at polluted sites, factors such as absence of electron acceptors or donors, low nitrogen or phosphorus availability, or a lack of induction of the metabolic pathways responsible for degradation can inhibit waste remediation. In these cases, addition of exogenous nutrients can enhance the degradation of waste, a process known as biostimulation. Biostimulation of in situ microbial communities has been used to enhance the degradation of crude oil (22, 29), tetrachloroethene (19), diesel fuel (24, 28), and polyaromatic hydrocarbons (41).If communities native to polluted sites lack significant populations of waste degraders, microbes with the desired phenotypes can be added exogenously in a process known as bioaugmentation. This approach has been successfully used to remediate a wide range of waste products, from hydrocarbons (8, 34) to heavy metals (15, 16). Numerous PU-degrading organisms have been isolated from a range of environments (6, 9, 26, 30), and this has provided a large reservoir of organisms for potential bioaugmentation of PU waste.This study was the first study to assess the potential of biostimulation and bioaugmentation as methods for accelerating the degradation of PU waste in the environment. The response of fungal communities in soil microcosms to (i) addition of nutrients or (ii) a large influx of PU-degrading fungi was investigated using culture-based and molecular techniques, and the effect of these treatments on the degradation of PU coupons buried in these microcosms was determined.     

Biodegradation of malathion by <Emphasis Type="Italic">Brevibacillus</Emphasis> sp. strain KB2 and <Emphasis Type="Italic">Bacillus cereus</Emphasis> strain PU

We report here the degradation of a pesticide, malathion, by Brevibacillus sp. strain KB2 and Bacillus cereus strain PU, isolated from soil samples collected from malathion contaminated field and an army firing range respectively. Both the strains were cultured in the presence of malathion under aerobic and energy-limiting conditions. Both strains grew well in the medium having malathion concentration up to 0.15%. Reverse phase HPLC–UV analysis indicated that Strain KB2 was able to degrade 72.20% of malaoxon (an analogue of malathion) and 36.22% of malathion, while strain PU degraded 87.40% of malaoxon and 49.31% of malathion, after 7 days of incubation. The metabolites mal-monocarboxylic acid and mal-dicarboxylic acid were identified by Gas chromatography/mass spectrometry. The factors affecting biodegradation efficiency were investigated and effect of malathion concentration on degradation rate was also determined. The strain was analyzed for carboxylesterase activity and maximum activity 210 ± 2.5 U ml⁻¹ and 270 U ± 2.7 ml⁻¹ was observed for strains KB2 and PU, respectively. Cloning and sequencing of putative malathion degrading carboxylesterase gene was done using primers based PCR approach.     

Soil and vegetation recovery following alien tree clearing in the Eastern Cape Province of South Africa

The impact of alien tree clearing on soil and vegetation recovery remains largely understudied. This study focused on changes in soil and vegetation properties following Acacia removal. The aim was to quantify the long‐term consequences of alien clearing. Paired cleared (old – 15 years; medium – 11 years; recent – 6 years) and uncleared sites were selected along the Palmiet catchment in Eastern Cape Province, South Africa. Various soil physico‐chemical properties (soil moisture, pH, P, N, C, K, Na, Ca, Mg and soil repellency) and vegetation diversity measures were studied on 10 m × 10 m plots. Results indicate that measured soil nutrients are significantly (P < 0.05) lower in cleared than in uncleared sites. However, comparisons among cleared sites alone indicate that soil properties are recovering with older cleared sites having higher (P < 0.05) nutrients than recent cleared sites. Soils in uncleared sites are more repellent than soil in cleared sites. Vegetation recovery in cleared sites was taking place with older cleared sites having higher native species diversity than recently cleared site. We conclude that the removal of alien plants could have caused a reduction in soil nutrients. However, as native vegetation recovers on cleared sites, soil nutrients are gradually improving.     

Identification and characterization of a novel nitrilase from <Emphasis Type="Italic">Pseudomonas fluorescens</Emphasis> Pf-5

Nitrile groups are catabolized to the corresponding acid and ammonia through one-step reaction involving a nitrilase. Here, we report the use of bioinformatic and biochemical tools to identify and characterize the nitrilase (NitPf5) from Pseudomonas fluorescens Pf-5. The nitPf5 gene was identified via sequence analysis of the whole genome of P. fluorescens Pf-5 and subsequently cloned and overexpressed in Escherichia coli. DNA sequence analysis revealed an open-reading frame of 921 bp, capable of encoding a polypeptide of 307 amino acids residues with a calculated isoelectric point of pH 5.4. The enzyme had an optimal pH and temperature of 7.0°C and 45°C, respectively, with a specific activity of 1.7 and 1.9 μmol min⁻¹ mg protein⁻¹ for succinonitrile and fumaronitrile, respectively. The molecular weight of the nitrilase as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration chromatography was 33,000 and 138,000 Da, respectively, suggesting that the enzyme is homotetrameric. Among various nitriles, dinitriles were the preferred substrate of NitPf5 with a K _m = 17.9 mM and k _cat/K _m = 0.5 mM⁻¹ s⁻¹ for succinonitrile. Homology modeling and docking studies of dinitrile and mononitrile substrate into the active site of NitPf5 shed light on the substrate specificity of NitPf5. Although nitrilases have been characterized from several other sources, P. fluorescens Pf-5 nitrilase NitPf5 is distinguished from other nitrilases by its high specific activity toward dinitriles, which make P. fluorescens NitPf5 useful for industrial applications, including enzymatic synthesis of various cyanocarboxylic acids.     

Comparative study on the dynamics and performances of Apis mellifera jemenitica and imported hybrid honeybee colonies in southwestern Saudi Arabia

The aims of this study were to assess the seasonal population dynamics and evaluate the performance of Apis mellifera jemenitica (local bee) and introduced hybrid honeybee colonies in the lowlands and highlands of southwestern Saudi Arabia. Data regarding the performance and population dynamics parameters such as brood and adult bee population, amounts of stored pollen and nectar were gathered from the two races (25 colonies of each) for one year (April 2013 through March 2014), and statistically tested. The results indicated that at low lands, local bee colonies maintained relatively high brood and adult bee populations (P < 0.05) than introduced honeybee colonies and produced more (P < 0.05) honey. The local bee colonies were able to hoard three times more (P < 0.05) pollen and built more (P < 0.05) queen cells than introduced bees in both the low and highland areas. The annual survival rate of local bee colonies was almost double (P < 0.05) than that of introduced honeybee colonies. Moreover, local bees had greater (P < 0.05) adult bee and brood populations than imported, throughout the year. The relatively good performance of local colonies could be due to their long year’s adaptation to cope with resource scarcity and unpredictable environmental conditions of the regions. The possible reasons for the dwindling of the imported hybrid colonies could be due to continuing to exhibit adaptive characteristics of their original that might not fit well with the new environment.     

Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids

Lignins are complex natural polymers resulting from oxidative coupling of, primarily, 4-hydroxyphenylpropanoids. An understanding of their nature is evolving as a result of detailed structural studies, recently aided by the availability of lignin-biosynthetic-pathway mutants and transgenics. The currently accepted theory is that the lignin polymer is formed by combinatorial-like phenolic coupling reactions, via radicals generated by peroxidase-H₂O₂, under simple chemical control where monolignols react endwise with the growing polymer. As a result, the actual structure of the lignin macromolecule is not absolutely defined or determined. The ``randomness'' of linkage generation (which is not truly statistically random but governed, as is any chemical reaction, by the supply of reactants, the matrix, etc.) and the astronomical number of possible isomers of even a simple polymer structure, suggest a low probability of two lignin macromolecules being identical. A recent challenge to the currently accepted theory of chemically controlled lignification, attempting to bring lignin into line with more organized biopolymers such as proteins, is logically inconsistent with the most basic details of lignin structure. Lignins may derive in part from monomers and conjugates other than the three primary monolignols (p-coumaryl, coniferyl, and sinapyl alcohols). The plasticity of the combinatorial polymerization reactions allows monomer substitution and significant variations in final structure which, in many cases, the plant appears to tolerate. As such, lignification is seen as a marvelously evolved process allowing plants considerable flexibility in dealing with various environmental stresses, and conferring on them a striking ability to remain viable even when humans or nature alter ``required'' lignin-biosynthetic-pathway genes/enzymes. The malleability offers significant opportunities to engineer the structures of lignins beyond the limits explored to date. Abbreviations: 4CL – 4-coumarate:CoA ligase; C3H –p-coumarate 3-hydroxylase; HCT –p-hydroxycinnamoyl-CoA: quinate shikimate p-hydroxycinnamoyltransferase; CCoAOMT – caffeoyl-CoA O-methyltransferase; CCR – cinnamoyl-CoA reductase; F5H – ferulate 5-hydroxylase; CAld5H – coniferaldehyde 5-hydroxylase; COMT – caffeic acid O-methyltransferase; AldOMT – (5-hydroxyconifer)aldehyde O-methyltransferase; CAD – cinnamyl alcohol dehydrogenase; NMR – nuclear magnetic resonance (spectroscopy); DFRC – derivatization followed by reductive cleavage; TIZ – tosylation, iodination, zinc (a DFRC method); DHP – dehydrogenation polymer.