Rhizodegradation of PAHs differentially altered by C3 and C4 plants.

Pyrosequencing of 16S ribosomal RNA (rRNA) was employed to characterize bacterial communities colonizing the rhizosphere of plants with C3 and C4 photosynthetic pathways grown in soil contaminated with polycyclic aromatic hydrocarbons (PAHs) after 60 and 120 days. The results of this study exhibited a clear difference in bacterial diversity between the rhizosphere and non-rhizosphere samples and between the rhizospheres of the C3 and C4 plants after 120 days. In both C3 and C4 rhizospheres, an incremental change in PAHs degrading bacterial genera was observed in the 120th day samples compared to the 60th day ones.

Phytoremediation efficacy assessment of polycyclic aromatic hydrocarbons contaminated soils using garden pea (Pisum sativum) and earthworms (Eisenia fetida).

Endpoint assessment using biological systems in combination with the chemical analysis is important for evaluating the residual effect of contaminants following remediation. In this study, the level of residual toxicity of polycyclic aromatic hydrocarbons (PAHs) after 120 days of phytoremediation with five different plant species:- maize (Zea mays), Sudan grass (Sorghum sudanense), vetiver (Vetiveria zizanioides), sunflower (Helianthus annuus) and wallaby grass (Austrodanthonia sp.) has been evaluated by ecotoxicological tests such as root nodulation and leghaemoglobin assay using garden pea (Pisum sativum) and acute, chronic and genotoxicity assays using earthworm (Eisenia fetida).

Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria.

The biodegradation potential of three bacterial cultures isolated from the rhizosphere of maize (Zea mays) and Sudan grass (Sorghum sudanense) grown in PAHs contaminated soils to degrade benzo[a]pyrene (BaP) and pyrene (PYR) was assessed. Of the three bacterial cultures isolated, two belonged to Gram-positive bacteria of phylum Actinobacteria namely Arthrobacter sp. MAL3 and Microbacterium sp.

Metabolomics reveals defensive mechanisms adapted by maize on exposure to high molecular weight polycyclic aromatic hydrocarbons.

Polycyclic aromatic hydrocarbons are an important group of persistent organic pollutants. Using plants to remediate PAHs has been recognized as a cost-effective and environmentally friendly technique. However, the overall impact of PAHs on the regulation of plant metabolism has not yet been explored.

Comparison of plants with C3 and C4 carbon fixation pathways for remediation of polycyclic aromatic hydrocarbon contaminated soils.

The phytoremediation technique has been demonstrated to be a viable option for the remediation of polycyclic aromatic hydrocarbons (PAHs) contaminated sites. This study evaluated the potential applicability of plants with C3 and C4 carbon fixation pathways for the phytoremediation of recalcitrant high molecular weight (HMW) PAHs contaminated soil. A 60 and 120-day greenhouse study was conducted which showed higher degradation of HMW PAHs in soil grown with C4 plants when compared to C3 plants.

Rhodococcus wratislaviensis strain 9: An efficient p-nitrophenol degrader with a great potential for bioremediation.

A Gram-positive bacterium, Rhodococcus wratislaviensis strain 9, was isolated from groundwater contaminated with nitrophenolics and trichloroethene following enrichment culture technique. The cells of strain 9 grown on LB broth (uninduced) degraded 720 μM p-nitrophenol (PNP) within 12 h, and utilized as a source of carbon and energy. Orthogonal experimental design analysis to determine optimal conditions for biodegradation of PNP showed that pH had a significant positive effect (P ≤ .

Impact of plant photosystems in the remediation of benzo[a]pyrene and pyrene spiked soils.

The phytoremediation potential of 14 different plant species belonging to C3 and C4 carbon fixation pathway for soils spiked with polycyclic aromatic hydrocarbons (PAHs) such as benzo[a]pyrene (B[a]P) and pyrene (PYR) was investigated. A glasshouse experiment was conducted to measure the changes in morphological, physiological, biochemical parameters and the bioaccumulation and biodegradation ability of the plants in soils spiked with 48 and 194 mg kg of B[a]P and PYR, respectively. The per cent removal efficacy of B[a]P and PYR by the tested plant species over a period of 50 days was from 6 to 26% and 14 to 40% respectively.

Identification of a new operon involved in desulfurization of dibenzothiophenes using a metagenomic study and cloning and functional analysis of the genes.

The presence of sulphur-substituted hydrocarbons in fossil fuels are one of main reasons for the release of sulfur oxides into the environment. Dibenzothiophenes (DBT) are organic sulfur-containing molecules in crude oil, which have the potential for biological oxidation, with the sulphur being removed through an enzymatic cleavage of the CS bonds. Therefore, finding new strains that can desulfurize this compound has recently become a point of interest.

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis.

Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG-RAST, Actinomycetales (9.

The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil.

Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria).

A Review on the Genetics of Aliphatic and Aromatic Hydrocarbon Degradation.

Because of the high diversity of hydrocarbons, degradation of each class of these compounds is activated by a specific enzyme. However, most of other downstream enzymes necessary for complete degradation of hydrocarbons maybe common between different hydrocarbons. The genes encoding proteins for degradation of hydrocarbons, including the proteins required for the uptake of these molecules, the specific enzyme used for the initial activation of the molecules and other necessary degrading enzymes are usually arranged as an operon.

Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments.

Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate.

Enhanced removal of petroleum hydrocarbons using a bioelectrochemical remediation system with pre-cultured anodes.

Bioelectrochemical remediation (BER) systems such as microbial fuel cells (MFCs) have recently emerged as a green technology for the effective remediation of petroleum hydrocarbon contaminants (PH) coupled with simultaneous energy recovery. Recent research has shown that biofilms previously enriched for substrate degrading bacteria resulted in excellent performance in terms of substrate removal and electricity generation but the effects on hydrocarbon contaminant degradation were not examined. Here we investigate the differences between enriched biofilm anodes and freshly inoculated new anodes in diesel fed single chamber mediatorless microbial fuel cells (DMFC) using various techniques for the enhancement of PH contaminant remediation with concomitant electricity generation.

A second component of the SltA-dependent cation tolerance pathway in Aspergillus nidulans.

The transcriptional response to alkali metal cation stress is mediated by the zinc finger transcription factor SltA in Aspergillus nidulans and probably in other fungi of the pezizomycotina subphylum. A second component of this pathway has been identified and characterized. SltB is a 1272 amino acid protein with at least two putative functional domains, a pseudo-kinase and a serine-endoprotease, involved in signaling to the transcription factor SltA.

A pyrosequencing-based analysis of microbial diversity governed by ecological conditions in the Winogradsky column.

The Winogradsky column is used as a microcosm to mimic both the microbial diversity and the ecological relationships between the organisms in lake sediments. In this study, a pyrosequencing approach was used to obtain a more complete list of the microbial organisms present in such columns and their ratios in different layers of this microcosm. Overall, 27 different phyla in these columns were detected in these columns, most (20 phyla) belonged to bacteria.

A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria.

Hydrocarbons are relatively recalcitrant compounds and are classified as high-priority pollutants. However, these compounds are slowly degraded by a large variety of microorganisms. Bacteria are able to degrade aliphatic saturated and unsaturated hydrocarbons via both aerobic and anaerobic pathways.

The Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex in Aspergillus nidulans.

A mutation screen in Aspergillus nidulans uncovered mutations in the acdX gene that led to altered repression by acetate, but not by glucose. AcdX of A. nidulans is highly conserved with Spt8p of Saccharomyces cerevisiae, and since Spt8p is a component of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, the SAGA complex may have a role in acetate repression in A.

SAGA complex components and acetate repression in Aspergillus nidulans.

Alongside the well-established carbon catabolite repression by glucose and other sugars, acetate causes repression in Aspergillus nidulans. Mutations in creA, encoding the transcriptional repressor involved in glucose repression, also affect acetate repression, but mutations in creB or creC, encoding components of a deubiquitination system, do not. To understand the effects of acetate, we used a mutational screen that was similar to screens that uncovered mutations in creA, creB, and creC, except that glucose was replaced by acetate to identify mutations that were affected for repression by acetate but not by glucose.

Influence of nutrient mixtures on p-nitrophenol degradation by Stenotrophomonas sp. isolated from groundwater.

We isolated strain CERAR5, a Stenotrophomonas sp., from an aquifer contaminated with chlorinated hydrocarbons that utilizes up to 1.0 mM PNP within 62 h in M9 medium as a source of carbon and nitrogen.

CreA-mediated repression in Aspergillus nidulans does not require transcriptional auto-regulation, regulated intracellular localisation or degradation of CreA.

The major regulatory protein in carbon repression in Aspergillus nidulans is CreA. Strains constitutively over-expressing creA show normal responses to carbon repression, indicating that auto-regulation of creA is not essential for CreA-mediated regulation. In these strains, high levels of CreA are present whether cells are grown in repressing or derepressing conditions, indicating large-scale degradation of CreA does not play a key role.

Molecular characterization and analysis of the acrB gene of Aspergillus nidulans: a gene identified by genetic interaction as a component of the regulatory network that includes the CreB deubiquitination enzyme.

Mutations in the acrB gene, which were originally selected through their resistance to acriflavine, also result in reduced growth on a range of sole carbon sources, including fructose, cellobiose, raffinose, and starch, and reduced utilization of omega-amino acids, including GABA and beta-alanine, as sole carbon and nitrogen sources. The acrB2 mutation suppresses the phenotypic effects of mutations in the creB gene that encodes a regulatory deubiquitinating enzyme, and in the creC gene that encodes a WD40-repeat-containing protein. Thus AcrB interacts with a regulatory network controlling carbon source utilization that involves ubiquitination and deubiquitination.

Regulation by carbon and nitrogen sources of a family of cellulases in Aspergillus nidulans.

The total amount of Aspergillus nidulans secreted cellulases is affected by both the carbon and nitrogen source present in the medium, and is regulated directly and/or indirectly by the carbon metabolism regulators, CreA, CreB, and CreC, and the global nitrogen metabolism regulator, AreA. We have characterized two A. nidulans genes that encode exo-cellulases, and one gene that encodes an endo-cellulase which is additional to the previously described endo-cellulase encoding gene, eglA.

The WD40-repeat protein CreC interacts with and stabilizes the deubiquitinating enzyme CreB in vivo in Aspergillus nidulans.

Genetic dissection of carbon catabolite repression in Aspergillus nidulans has identified two genes, creB and creC, which, when mutated, affect expression of many genes in both carbon catabolite repressing and derepressing conditions. The creB gene encodes a functional deubiquitinating enzyme and the creC gene encodes a protein that contains five WD40 repeat motifs, and a proline-rich region. These findings have allowed the in vivo molecular analysis of a cellular switch involving deubiquitination.

Carbon catabolite repression in Aspergillus nidulans involves deubiquitination.

The best studied role of ubiquitination is to mark proteins for destruction by the proteasome but, in addition, it has recently been shown to promote macromolecular assembly and function, and alter protein function, thus playing a regulatory role distinct from protein degradation. Deubiquinating enzymes, the ubiquitin-processing proteases (ubps) and the ubiquitin carboxy-terminal hydrolases (uchs), remove ubiquitin from ubiquitinated substrates. We show here that the creB gene involved in carbon catabolite repression in Aspergillus nidulans encodes a functional member of the novel subfamily of the ubp family defined by the human homologue UBH1, thus implicating ubiquitination in the process of carbon catabolite repression.