Biodegradation of phosphonomycin by Rhizobium huakuii PMY1

The biodegradation by Rhizobium huakuii PMY1 of up to 10 mM phasphonomycin as a carbon, energy, and phosphorus source with accompanying P-1 release is described. This biodegradation represents a further mechanism of resistance to this antibiotic and a novel, phosphate-deregulated route for organophosphonate metabolism by Rhizobium spp.

Production of a broad specificity antibody for the development and validation of an optical SPR screening method for free and intracellular microcystins and nodularin in cyanobacteria cultures

A highly sensitive broad specificity monoclonal antibody was produced and characterised for microcystin detection through the development of a rapid surface plasmon resonance (SPR) optical biosensor based immunoassay. The antibody displayed the following cross-reactivity: MC-LR 100%; MC-RR 108%; MC-YR 68%; MC-LA 69%; MC-LW 71%; MC-LF 68%; and Nodularin 94%. Microcystin-LR was covalently attached to a CM5 chip and with the monoclonal antibody was employed in a competitive 4min injection assay to detect total microcystins in water samples below the WHO recommended limit (1µg/L). A 'total microcystin' level was determined by measuring free and intracellular concentrations in cyanobacterial culture samples as this toxin is an endotoxin. Glass bead beating was used to lyse the cells as a rapid extraction procedure. This method was validated according to European Commission Decision 96/23/EC criteria. The method was proven to measure intracellular microcystin levels, the main source of the toxin, which often goes undetected by other analytical procedures and is advantageous in that it can be used for the monitoring of blooms to provide an early warning of toxicity. It was shown to be repeatable and reproducible, with recoveries from spiked samples ranging from 74 to 123%, and had % CVs below 10% for intra-assay analysis and 15% for inter-assay analysis. The detection capability of the assay was calculated as 0.5ng/mL for extracellular toxins and 0.05ng/mL for intracellular microcystins. A comparison of the SPR method with LC-MS/MS was achieved by testing six Microcystis aeruginosa cultures and this study yielded a correlation R(2) value of 0.9989.

Re-inoculation of autoclaved soil as a non-sterile treatment for xenobiotic sorption and biodegradation studies

Autoclaved soil is commonly used for the study of xenobiotic sorption and as an abiotic control in biodegradation experiments. Autoclaving has been reported to alter soil physico-chemical and xenobiotic sorption characteristics such that comparison of autoclaved with non-autoclaved treatments in soil aging and bioavailability studies may yield misleading results. Experiments could be improved by using autoclaved soil re-inoculated with indigenous microorganisms as an additional or alternative non-sterile treatment for comparison with the sterile, autoclaved control. We examined the effect of autoclaving (3 x 1 h, 121°C, 103.5 KPa) on the physico-chemical properties of a silt loam soil (pH 7.2, 2.3% organic carbon) and the establishment of indigenous microorganisms reintroduced after autoclaving. Sterilisation by autoclaving significantly (p ≤ 0.05) decreased pH (0.6 of a unit) and increased concentrations of water-soluble organic carbon (WSOC; nontreated = 75 mg kg^-1; autoclaved = 1526 mg kg^-1). The initial first-order rate of ¹⁴C-2,4-dichloro-UL-phenol (2,4-DCP) adsorption to non-treated, autoclaved and re-inoculated soil was rapid (K₁ = 16.8-24.4 h^-1) followed by a slower linear phase (K₂). In comparison with autoclaved soil (0.038% day^-1), K₂ values were higher for re-inoculated (0.095% day^-1) and nontreated (0.181% day^-1) soil. This was attributed to a biological process. The Freundlich adsorption coefficient (K(f)) for autoclaved soil was significantly (p ≤ 0.05) higher than for re-inoculated or non-treated soil. Increased adsorption was attributed to autoclaving-induced changes to soil pH and solution composition. Glucose-induced respiration of autoclaved soil after re-inoculation was initially twice that in the non-treated control, but it decreased to control levels by day 4. This reduction corresponded to a depletion of WSOC. 2,4-DCP mineralisation experiments revealed that the inoculum of nonsterile soil (0.5 g) contained 2,4-DCP-degrading microorganisms capable of survival in autoclaved soil. The lag phase before detection of significant 2,4-DCP mineralisation was reduced (from 7 days to ≤3 days) by pre-incubation of re-inoculated soils for 7 and 14 days before 2,4-DCP addition. This was attributed to the preferential utilisation of WSOC prior to the onset of 2,4-DCP mineralisation. Cumulative ¹⁴CO₂ evolved after 21 days was significantly lower (p ≤ 0.05) from non-treated soil (25.3%) than re-inoculated soils (ca 45%). Experiments investigating sorption-biodegradation interactions of xenobiotics in soil require the physico-chemical properties of sterile and non-sterile treatments to be as comparable as possible. For fundamental studies, we suggest using re-inoculated autoclaved soil as an additional or alternative non-sterile treatment.

Biosensing 2,4-dichlorophenol toxicity during biodegradation by Burkholderia sp. RASC c2 in soil

Biodegradation of the model pollutant, 2,4-dichlorophenol (2,4-DCP) by Burkholderia sp. RASC c2, in contaminated soil was assessed by combining chemical analysis with a toxicity test using Escherichia coli HB101 pUCD607. E. coli HB101 pUCD607 was previously marked with luxCDABE genes, encoding bacterial bioluminescence and was used as an alternative to Microtox. Mineralization of ¹⁴C-2,4-DCP (196.2 μg g^-1 dry wt) in soil occurred rapidly after a 24 h lag. Correspondingly, 2,4-DCP concentrations in soil and soil water extracts decreased with time and concentrations in the latter were at background levels (<0.12 μg mL^-1) after day 2. Toxicity of soil water extracts to the lux-based biosensor also decreased with time. Mean light output of E. coli was stimulated by ~1.5 X control values in soil water extracts when concentrations of 2,4-DCP were approaching the limit of detection by HPLC but returned to values equivalent to those of controls when soil water 2,4-DCP concentrations were below the detection limit. No mineralization or microbial growth was detected in noninoculated microcosms. 2,4-DCP concentration in sterile controls decreased significantly with time as did toxicity to E. coli Lux-based E. coli was a sensitive biosensor of 2,4-DCP toxicity during biodegradation and results complemented chemical analysis.

Assessment of Anaerobic Biodegradation of Aromatic Hydrocarbons: The Impact of Molecular Biology Approaches

One of the most cost effective methods of pollution remediation is through natural attenuation where the resident microorganisms are responsible for the breakdown of pollutants (Dou et al. 2008). Other forms of bioremediation - such as analogue enrichment, composting and bio-venting - also use the microbes already present in a contaminated site to enhance the remediation process. In order for these approaches to be successful, in an industrial setting, some form of monitoring needs to take place enabling conclusions to be drawn about the degradation processes occurring. In this review we look at some key molecular biology techniques that have the potential to act as a monitoring tool for industries dealing with contaminated land. 

Engineering passive bioreactive barriers: risk-managing the legacy of industrial soil and groundwater pollution

Permeable reactive barriers are a technology that is one decade old, with most full-scale applications based on abiotic mechanisms. Though there is extensive literature on engineered bioreactors, natural biodegradation potential, and in situ remediation, it is only recently that engineered passive bioreactive barrier technology is being considered at the commercial scale to manage contaminated soil and groundwater risks. Recent full-scale studies are providing the scientific confidence in our understanding of coupled microbial (and genetic), hydrogeologic, and geochemical processes in this approach and have highlighted the need to further integrate engineering and science tools.

A Holocene record of human induced and natural environmental change from Lake Forsyth (Te Wairewa), New Zealand

A 1.2 m sediment core from Lake Forsyth, Canterbury, New Zealand, records the development of the catchment/lake system over the last 7000 years, and its response to anthropogenic disturbance following European settlement c. 1840 AD. Pollen was used to reconstruct catchment vegetation history, while foraminifera, chironomids, Trichoptera, and the abundance of Pediastrum simplex colonies were used to infer past environmental conditions within the lake. The basal 30 cm of core records the transition of the Lake Forsyth Basin from a tidal embayment to a brackish coastal lake. Timing of closure of the lake mouth could not be accurately determined, but it appears that Lake Forsyth had stabilised as a slightly brackish, oligo mesotrophic shallow lake by about 500 years BP. Major deforestation occurred on Banks Peninsula between 1860 AD and 1890 AD. This deforestation is marked by the rapid decline in the main canopy trees (Prumnopitys taxifolia (matai) and Podocarpus totara/hallii (totara/mountain totara), an increase in charcoal, and the appearance of grasses. At around 1895 AD, pine appears in the record while a willow (Salix spp.) appears somewhat later. Redundancy analysis (RDA) of the pollen and aquatic species data revealed a significant relationship between regional vegetation and the abundance of aquatic taxa, with the percentage if disturbance pollen explaining most (14.8%) of the constrained variation in the aquatic species data. Principle components analysis (PCA) of aquatic species data revealed that the most significant period of rapid biological change in the lakes history corresponded to the main period of human disturbance in the catchment. Deforestation led to increased sediment and nutrient input into the lake which was accompanied by a major reduction in salinity. These changes are inferred from the appearance and proliferation of freshwater algae (Pediastrum simplex), an increase in abundance and diversity of chironomids, and the abundance of cases and remains from the larvae of the caddisfly, Oecetis unicolor. Eutrophication accompanied by increasing salinity of the lake is inferred from a significant peak and then decline of P. simplex, and a reduction in the abundance and diversity of aquatic invertebrates. The artificial opening of the lake to the Pacific Ocean, which began in the late 1800s, is the likely cause of the recent increase in salinity. An increase in salinity may have also encouraged blooms of the halotolerant and hepatotoxic cyanobacteria Nodularia spumigena.