Primary biodegradation of amine oxide and quaternary ammonium amphiphiles

Biodegradation of two amphiphilic “soft” antimicrobially active derivatives of lauric (dodecanoic) acid, a quaternary ammonium salt and an amine oxide bearing an amide or ester group, was followed using microorganisms from activated sludge. Primary biodegradation was determined by ion-selective electrodes, total biodegradation as the chemical oxygen demand. Though organic ammonium salts quickly undergo primary biodegradation, the rest of the molecule is difficult to destroy. In contrast, amine oxides are easily biodegradable.     

Development of a treatment solution for reductive dechlorination of hexachloro-1,3-butadiene in vadose zone soil

The biodegradation of chlorinated organics in vadose zone soils is challenging owing to the presence of oxygen, which inhibits reductive dehalogenation reactions and consequently the growth of dehalorespiring microbes. In addition, the hydraulic conductivity of vadose zone soils is typically high, hence attempts to remediate such zones with biostimulation solutions are often unsuccessful due to the short residence times for these solutions to act upon the native bacterial community. In this study we have identified sodium alginate as a hydrogel polymer that can be used to increase the residence time of a nutrient solution in an unsaturated sandy soil. Additionally we have identified neutral red as a redox active compound that can catalyse the reductive dechlorination of the chlorinated organic hexachloro-1,3-butadiene by activated sludge fed with lactate and acetate. Finally we have shown that a nutrient solution amended with neutral red and sodium alginate can lower the redox potential and reduce hexachloro-1,3-butadiene concentrations in a contaminated vadose zone soil.     

Biodegradation of high explosive production effluent containing RDX and HMX by denitrifying bacteria

The biodegradation of high explosive production effluent containing RDX (royal demolition explosive) and HMX (high melting-point explosive) in the presence of denitrifying bacterial isolates was investigated. The effluent collected from HMX production plant containing acetic acid, ammonium nitrate and explosive residue with water and other organic nitro bodies was used. The diluted and neutralized effluent was subjected to biodegradation using Pseudomonas (HPB1) and two Bacillus (HPB2, HPB3) denitrifying bacterial isolates. Samples were analysed by HPLC for qualitative and quantitative analysis of remaining RDX and HMX. The results indicate that the HMX and RDX was biodegraded under denitrifying conditions. The isolate Pseudomonas (HPB1) was found to be an efficient biodegrading strain for HMX. However, the isolate Pseudomonas (HPB1) was found to have lower biodegradation activity for RDX as compared to the denitrifying strain Bacillus (HPB2). Denitrifying bacteria Bacillus (HPB2) was found to be the most efficient strain for the biodegradation of RDX and HMX containing effluent neutralized with sodium bicarbonate. The biotransformation activity for HMX and RDX was lower for the isolate Bacillus (HPB2) in the effluent neutralized with ammonia. Removal of nitrate from the effluent containing HMX and RDX by the three denitrifying bacteria was also studied. Denitrifying bacteria Pseudomonas (HPB1) showed the maximum nitrate reduction in the presence of both the neutralizing agents- sodium bicarbonate and ammonia.     

Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation

Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics-contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.     

The Effects of Cyanobacterial Exudates on Bacterial Growth and Biodegradation of Organic Contaminants

The pulp and paper industry largely depends on the biodegradation activities of heterotrophic bacteria to remove organic contaminants in wastewater prior to discharge. Our recent discovery of extensive cyanobacterial communities in pulp and paper waste treatment systems led us to investigate the potential impacts of cyanobacterial exudates on growth and biodegradation efficiency of three bacterial heterotrophs. Each of the three assessed bacteria represented different taxa commonly found in pulp and paper waste treatment systems: a fluorescent Pseudomonad, an Ancylobacter aquaticus strain, and a Ralstonia eutropha strain. They were capable of utilizing phenol, dichloroacetate (DCA), or 2,4-dichlorophenoxyacetic acid (2,4-D), respectively. Exudates from all 12 cyanobacterial strains studied supported the growth of each bacterial strain to varying degrees. Maximum biomass of two bacterial strains positively correlated with the total organic carbon content of exudate treatments. The combined availability of exudate and a known growth substrate (i.e., phenol, DCA, or 2,4-D) generally had a synergistic affect on the growth of the Ancylobacter strain, whereas mixed effects were seen on the other two strains. Exudates from four representative cyanobacterial strains were assessed for their impacts on phenol and DCA biodegradation by the Pseudomonas and Ancylobacter strains, respectively. Exudates from three of the four cyanobacterial taxa repressed phenol biodegradation, but enhanced DCA biodegradation. These dissimilar impacts of cyanobacterial exudates on bacterial degradation of contaminants suggest a species-specific association, as well as a significant role for cyanobacteria during the biological treatment of wastewaters.     

Estimation of Biodegradation Potential of Xenobiotic Organic Chemicals

A method is described to estimate the biodegradation potential of soluble, insoluble, and unknown organic chemicals. The method consists of two stages: (i) generation of a microbial inoculum in a bench scale semicontinuous activated sludge system during which microorganisms are acclimated to test material and the removal of dissolved organic carbon is monitored and (ii) biodegradability testing (CO₂ evolution) in a defined minimal medium containing the test material as the sole carbon and energy source and a dilute bacterial inoculum obtained from the supernatant of homogenized activated sludge generated in the semicontinuous activated sludge system. Removal and biodegradation are measured using nonspecific methods, at initial concentrations of 5 to 10 mg of dissolved organic carbon per liter. Biodegradability data are accurately described by a nonlinear computer model which allows the rate and extent of biodegradation for different compounds to be compared and statistically examined. The evaluation of data generated in the combined removability-biodegradability system allows the biodegradation potential of a variety of xenobiotic organic chemicals to be estimated.     

A proteomics strategy for the analysis of bacterial biodegradation pathways

Bacterial biodegradation (bioremediation) is the use of microorganisms to break down organic materials into simpler compounds; it plays a pivotal role in the clean-up of hazardous wastes in the environment. Following the completion of genome sequencing in bacteria capable of biodegradation, functional genomic studies have played a major role in obtaining information on bacterial biodegradation pathways. Novel proteomics technologies have recently been developed to make it possible to analyze global protein expression. Proteomics can also provide important information on the life cycle, regulation, and post-translational modification of proteins induced under specific conditions. Proteomics technologies have been applied to the comprehensive study of bacterial biodegradation. In this paper, we introduce the proteomics technologies applicable to bacterial biodegradation studies, review the results of the proteomics analysis of representative biodegrading bacteria, and discuss the potential use of proteomics technologies in future biodegradation studies.     

Microbial community changes during organic solid waste treatment analyzed by double gradient-denaturing gradient gel electrophoresis and fluorescence in situ hybridization

The bacterial community present during semicontinuous treatment of organic solid waste under alkaline and high-temperature conditions was studied. PCR-amplified 16S rDNA fragments were analyzed by double gradient-denaturing gradient gel electrophoresis (DGGE). The band pattern was stable during the steady state of the treatment phase, and the major bands resulting from individual treatments had the same DNA sequence with good reproducibility. No sequence in the DNA database of isolated bacteria showed close similarity to this sequence, the closest relative being Bacillus licheniformis with less than 97% similarity. The conditions for fluorescence in situ hybridization (FISH) were determined without the need to obtain extracts of the bacterial cells. An oligonucleotide probe was designed to detect the microorganisms found in the DGGE analysis. FISH analysis showed that the bacterium corresponding to the major bands accounted for 30% of the total eubacterial cell count at the steady state. These results indicate that this bacterium is a key microorganism in the biodegradation process.     

The role of indoleacetaldehyde in IAA production from tryptophan by plants and by their epiphytic bacteria

Tryptophan, tryptamine, or indolepyruvic acid were applied to 2 systems: a bacterial (pea stem sections containing the epiphytic bacteria) and a plant system (pea stem sections under sterile conditions). In the plant system, the production of indoleacetic acid and indoleethanol (tryptophol) from each applied indole derivative is clearly reduced by the aldehyde reagents bisulfite and dimedon, respectively. Indoleacetaldehyde is chromatographically detected after alkaline liberation from its bisulfite addition product. In the bacterial system, the production of indoleacetic acid and indoleethanol is likewise reduced by bisulfite and dimedon. However, after tryptophan or tryptamine application, we could not detect indoleacetaldehyde in the described way. In one case only, namely tryptamine application to the bacterial system, indoleethanol production (contrary to indoleacetic acid production) is scarcely reduced by the aldehyde reagents. This indicates a bacterial pathway tryptamine → indoleethanol which bypasses indoleacetaldehyde.     

Comparison of anaerobic and aerobic biodegradation of mineralized skeletal structures in marine and estuarine conditions

The knowledge of the biodegradation rates is essential to studies of the biogeochemistry and ecology of aquatic systems. It helps us to quantify the production and uptake rates of chemical components and their recycling, and to understand the mechanisms and rates of organic matter accumulation in sediments. Experimental studies of biodegradation processes in six types of mineralized skeletons were performed in shallow-marine waters of Calvi Bay, Corsica and in estuarine waters of Roscoff, Brittany. Three types of mollusk shells, sea urchin skeletal plates, crab cuticle and fish vertebrae were exposed to oxic and anoxic conditions over periods of 15 days to 30 months. After recovery of the substrates, protein assays, bacterial counts and organic carbon analyses were performed.Quantitative protein assays and bacterial counts indicate that biodegradation of mineralized skeletal structures occurs at a slower rate in anoxic conditions than in oxic conditions. Bacterial analysis showed that in anoxic environment, less than 0.5% of the consumed organic matter is converted into bacterial biomass. The aerobic biodegradation rate was positively correlated with the organic content of the skeletons.Anoxic biodegradation of skeletons occurred at much slower rates in estuarine sediments than in shallow marine sediments. Preservation of skeletal structures in estuarine conditions appears to be correlated with the abundance of dissolved organic matter rather than with high sedimentation rates.     

6种土壤微生物提取剂的比较

比较了6种土壤微生物提取剂（6-偏磷酸钠溶液、焦磷酸钠溶液、磷酸盐缓;中液、林格溶液、NaCl溶液和水）对土壤细菌、真菌和放线菌数量的影响。结果表明：0．1％的6-偏磷酸钠（HMP）和焦磷酸钠（PYS）溶液（w／v）提取的细菌、真菌、放线菌数量最多,磷酸缓冲液（pH值7．2）对土壤真菌提取效率与焦磷酸钠和6-偏磷酸钠溶液相似,而对细菌和放线菌的提取效率则低于焦磷酸钠和6-偏磷酸钠溶液,其余3种提取剂的提取效率相对较低。     

Modeling of crude oil biodegradation using two phase partitioning bioreactor

In this work, crude oil biodegradation has been optimized in a solid‐liquid two phase partitioning bioreactor (TPPB) by applying a response surface methodology based d ‐optimal design. Three key factors including phase ratio, substrate concentration in solid organic phase, and sodium chloride concentration in aqueous phase were taken as independent variables, while the efficiency of the biodegradation of absorbed crude oil on polymer beads was considered to be the dependent variable. Commercial thermoplastic polyurethane (Desmopan®) was used as the solid phase in the TPPB. The designed experiments were carried out batch wise using a mixed acclimatized bacterial consortium. Optimum combinations of key factors with a statistically significant cubic model were used to maximize biodegradation in the TPPB. The validity of the model was successfully verified by the good agreement between the model‐predicted and experimental results. When applying the optimum parameters, gas chromatography‐mass spectrometry showed a significant reduction in n‐alkanes and low molecular weight polycyclic aromatic hydrocarbons. This consequently highlights the practical applicability of TPPB in crude oil biodegradation. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:797–805, 2014     

Automated fluorometric amino acid analysis: the determination of proline and hydroxyproline.

A fluorometric method for the automated determination of the imino acids proline and hydroxyproline has been developed. The assay is based on the postcolumn reaction of the imino acids with alkaline sodium hypochlorite, which yields oxidation products amenable to detection with fluorogenic amine reagents. The method is simple and can be adapted readily to high-sensitivity amino acid analyzers which use o-phthalaldehyde for detection. As little as 10 pmol proline and 20 pmol hydroxyproline can be determined accurately. Thus the full array of natural imino and amino acids can now be determined on a high-sensitivity amino acid analyzer using o-phthalaldehyde.     

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.     

Spatial Distribution of Bacterial Communities and Phenanthrene Degradation in the Rhizosphere of Lolium perenne L.

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.     

Removal of Nonvolatile Hydrophobic Compounds from Artificially and Naturally Contaminated Soils by Column Flotation

Removal of a nonvolatile paraffin oil from spiked soils using column flotation with countercurrent bubbles was explored at both ambient and elevated temperatures. Up to 80% of the contaminant was separated from the coarse fraction (250 to 800?µm) by flotation at 45°C using aqueous solutions of anionic and nonionic surfactants or alkali salt as collectors. With the 75 to 800?µm fraction, removal efficiencies of up to 65% was achieved. Sodium dodecyl-sulfate and Triton 100X at 50?ppm concentrations as well as sodium carbonate at pH 10 were found to yield similar removal efficiencies. Same surfactants were tested in soil washing experiments at similar and higher dosages. Removal efficiency by flotation was higher than those obtained by soil washing in all cases. In addition, as high surfactant dosage are not used in flotation, unlike in the case of soil washing, the problem of formation of stable emulsions was absent. Experiments with soil polluted by hydrocarbons from a contaminated site demonstrated the feasibility of the flotation process for decontamination of coarse (250 to 830?µm) fractions. A 70% reduction of petroleum hydrocarbon in soil was achieved as a result of flotation at 45°C using the above surfactants.     

Intensification of phenol biodegradation by humic substances

Phenol biodegradation was carried out in a batch system by the bacterial strain Cupriavidus metallidurans in the presence of potassium humate that was prepared by alkaline extraction from oxyhumolite. The experiments were focused on the assessment of the humate effect on biodegradation activity of the tested bacterial strain. The achieved results demonstrated that the humate has a positive influence on the biodegradation of phenol and reduces the incubation time necessary for phenol removal. Higher biodegradation rate and more intensive growth were observed during the cultivation in presence of humate in comparison to the cultivation without its addition. Adsorption of the humate on bacterial biomass was observed as well. Subsequently, a phenol biodegradation testing in a continuous-flow system using a biofilm reactor was also carried out. Although the reactor was inoculated by C. metallidurans only, the microbial composition under an aerobic non-aseptic condition during this long-term cultivation changed. The phenol removal efficiency obtained in the biofilm reactor was higher than 92% when phenol concentration in a treated medium was 1200 mg l⁻¹.     

Characterization of organic matter from animal manures after digestion by earthworms

The humification index (HI) values of three different manures and earthworm casts were calculated for three different extractant solutions (0.5M sodium hydroxide, 0.1M sodium pyrophosphate pH 7 and 0.1M sodium pyrophosphate plus 0.1M NaOH). The alkaline sodium pyrophosphate solution was found to be the most suitable because of both its extraction efficiency and the quality of the organic matter extracted which allows a good characterization of the stabilization degree attained by composting. Neutral sodium pyrophosphate extracts also show characteristic HI values for different samples but lower extraction efficiencies. The HI values for sodium hydroxide extracts show only little differences between manures and composts. The good correspondence found between HI data and isoelectric focusing (IEF) patterns confirmed on one side that humification indexes give a quantitative measure of the humification degree, on the other side that IEF is a suitable technique in order to obtain qualitative informations on organic matter stabilization in earthworm casts.     

N-(o-carboxybenzyl) chitosans: Novel chelating polyampholytes

The imine formed by chitosan with phthalaldehydic acid was reduced with sodium cyanoborohydride and the resulting N-(o-carboxybenzyl) chitosan (NCBC) was insolubilised with ethanol and acetone and obtained as a white, free-flowing powder, soluble in both acidic and alkaline solutions. A sample of NCBC with the following degrees of substitution: acetamido 42%±4%, N-(o-carboxybenzyl) amine 43%±3%, free amine 15%±1% and containing 16%±1% moisture, was characterised by IR and UV-Vis. spectrometry, titration and viscometry. The isoelectric point was 6·8; the pK_a values were 5·7 and 8·0. NCBC could be determined by UV-Vis. spectrophotometry in aqueous solutions at 274 nm; maximum viscosity of the solutions was observed at pH 4. Upon addition of NCBC to transition metal ion solutions (0·1–0·5 mm) chelation and insolubilisation took place immediately. The dependence of the collection percentage on pH, NCBC and metal ion concentrations was studied for nine metal ions.     

Degradation of sodium polyglyoxylate,a non-persistent metal sequestrant,in laboratory ecosystems

Summary Detergent builders such as zeolites, silicates and most organic polymers present concerns to some because of their environmental persistence. Sodium polyglyoxylate (SPG), on the other hand, is classified as readily biodegradable in a variety of aerobic and anaerobic biodegradation screening tests because it is extensively mineralized. Its persistence, however, is dependent on its rate of chemical hydrolysis to sodium glyoxylate, which is in turn controlled by parameters such as pH, temperature, metal ions and end capping group. The time for SPG's degradation ranges from a few hours at pH 5 to a few weeks at pH 9. Even though SPG is more persistent at alkaline pH values, it is rendered less bioavailable via precipitation/adsorption mechanisms. SPG's removal from and degradation in practically all ecosystems indicates that it will not have a significant impact on the environment with widespread use.