Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

A microbial fuel cell in contaminated ground delineated by electrical self-potential and normalized induced polarization data

There is a growing interest in the use of geophysical methods to aid investigation and monitoring of complex biogeochemical environments, for example delineation of contaminants and microbial activity related to land contamination. We combined geophysical monitoring with chemical and microbiological analysis to create a conceptual biogeochemical model of processes around a contaminant plume within a manufactured gas plant site. Self-potential, induced polarization and electrical resistivity techniques were used to monitor the plume. We propose that an exceptionally strong (>800 mV peak to peak) dipolar SP anomaly represents a microbial fuel cell operating in the subsurface. The electromagnetic and electrical geophysical data delineated a shallow aerobic perched water body containing conductive gasworks waste which acts as the abiotic cathode of microbial fuel cell. This is separated from the plume below by a thin clay layer across the site. Microbiological evidence suggests that degradation of organic contaminants in the plume is dominated by the presence of ammonium and its subsequent degradation. We propose that the degradation of contaminants by microbial communities at the edge of the plume provides a source of electrons and acts as the anode of the fuel cell. We hypothesize that ions and electrons are transferred through the clay layer that was punctured during the trial pitting phase of the investigation. This is inferred to act as an electronic conductor connecting the biologically mediated anode to the abiotic cathode. Integrated electrical geophysical techniques appear well suited to act as rapid, low cost sustainable tools to monitor biodegradation.

Biosensors for the analysis of microbiological and chemical contaminants in food

Increases in food production and the ever-present threat of food contamination from microbiological and chemical sources have led the food industry and regulators to pursue rapid, inexpensive methods of analysis to safeguard the health and safety of the consumer. Although sophisticated techniques such as chromatography and spectrometry provide more accurate and conclusive results, screening tests allow a much higher throughput of samples at a lower cost and with less operator training, so larger numbers of samples can be analysed. Biosensors combine a biological recognition element (enzyme, antibody, receptor) with a transducer to produce a measurable signal proportional to the extent of interaction between the recognition element and the analyte. The different uses of the biosensing instrumentation available today are extremely varied, with food analysis as an emerging and growing application. The advantages offered by biosensors over other screening methods such as radioimmunoassay, enzyme-linked immunosorbent assay, fluorescence immunoassay and luminescence immunoassay, with respect to food analysis, include automation, improved reproducibility, speed of analysis and real-time analysis. This article will provide a brief footing in history before reviewing the latest developments in biosensor applications for analysis of food contaminants (January 2007 to December 2010), focusing on the detection of pathogens, toxins, pesticides and veterinary drug residues by biosensors, with emphasis on articles showing data in food matrices. The main areas of development common to these groups of contaminants include multiplexing, the ability to simultaneously analyse a sample for more than one contaminant and portability. Biosensors currently have an important role in food safety; further advances in the technology, reagents and sample handling will surely reinforce this position.

Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495

Aminobacter lissarensis CC495 is an aerobic facultative methylotroph capable of growth on glucose, glycerol, pyruvate and methylamine as well as the methyl halides methyl chloride and methyl bromide. Previously, cells grown on methyl chloride have been shown to express two polypeptides with apparent molecular masses of 67 and 29 kDa. The 67 kDa protein was purified and identified as a halomethane:bisulfide/halide ion methyltransferase. This study describes a single gene cluster in A. lissarensis CC495 containing the methyl halide utilisation genes cmuB, cmuA, cmuC, orf 188, paaE and hutI The genes correspond to the same order and have a high similarity to a gene cluster found in Aminobacter ciceronei IMB-1 and Hyphomicrobium chloromethanicum strain CM2 indicating that genes encoding methyl halide degradation are highly conserved in these strains. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier, B.V. All rights reserved.

REMA: A computer-based mapping tool for analysis of restriction sites in multiple DNA sequences

REMA is an interactive web-based program which predicts endonuclease cut sites in DNA sequences. It analyses Multiple sequences simultaneously and predicts the number and size of fragments as well as provides restriction maps. The users can select single or paired combinations of all commercially available enzymes. Additionally, REMA permits prediction of multiple sequence terminal fragment sizes and suggests suitable restriction enzymes for maximally discriminatory results. REMA is an easy to use, web based program which will have a wide application in molecular biology research. Availability: REMA is written in Perl and is freely available for non-commercial use. Detailed information on installation can be obtained from Jan Szubert (jan.szubert@gmail.com) and the web based application is accessible on the internet at the URL http://www.macaulay.ac.uk/rema. Contact: b.singh@macaulay.ac.uk. (C) 2007 Elsevier B.V. All rights reserved.

Microbiological Profile of Aggressive Periodontitis in a Sudanese Population

Background: Several bacterial species have been identified as being associated with aggressive periodontitis (AgP) notably Aggregatibacter actinomycetemcomitans (Aa) and Porphyromonas gingivalis (Pg). There are limited data on bacterial associations with AgP in African populations. Objective: To investigate possible associations between specific bacteria and AgP in a Sudanese population. Methods: Subgingival plaque samples were collected from 93 (20 male, 73 female) Sudanese patients diagnosed with AgP and from 72 (23 male, 48 female) periodontally healthy Sudanese controls. Quantitative PCR was used to identify Aa, Pg, Treponema denticola (Td) and Fusobacterium nucleatum (Fn). The prevalence of these bacterial species was compared using Chi-square analysis. Odds ratios (OR) were calculated using standard methods. Results: The cases with AgP were well matched in age with the controls: 24.8 (SD 5.1) compared with 23.5 (SD 3.7) years, p=0.07. There was a significantly higher prevalence of Pg in AgP (73%) than in the controls (33%), p<0.0001. The OR for Pg to be associated with AgP was 5.44 (95% confidence intervals 2.78-10.64). In 26 (38%) of the AgP cases positive for Pg there were low levels of this bacterium (<100 copies). Both Td and Fn were identified in virtually all (>95%) the plaque samples studied from both AgP and controls. Aa was the least frequently identified species and was present in only 28% of AgP and 18% of controls, p=0.14. The OR for Aa to be associated with AgP was slightly increased at 1.76 (95% CI 0.83-3.74), however, this was not significant (p=0.14). Conclusion: In the Sudanese subjects studied Pg but not Aa was associated with AgP. There were very low levels of Pg in many of the plaque samples from AgP.

Biomarker responses to folic acid intervention in healthy adults: a meta-analysis of randomized controlled trials

BACKGROUND: The task of revising dietary folate recommendations for optimal health is complicated by a lack of data quantifying the biomarker response that reliably reflects a given folate intake.

OBJECTIVE: We conducted a dose-response meta-analysis in healthy adults to quantify the typical response of recognized folate biomarkers to a change in folic acid intake.

DESIGN: Electronic and bibliographic searches identified 19 randomized controlled trials that supplemented with folic acid and measured folate biomarkers before and after the intervention in apparently healthy adults aged ≥18 y. For each biomarker response, the regression coefficient (β) for individual studies and the overall pooled β were calculated by using random-effects meta-analysis.

RESULTS: Folate biomarkers (serum/plasma and red blood cell folate) increased in response to folic acid in a dose-response manner only up to an intake of 400 μg/d. Calculation of the overall pooled β for studies in the range of 50 to 400 μg/d indicated that a doubling of folic acid intake resulted in an increase in serum/plasma folate by 63% (71% for microbiological assay; 61% for nonmicrobiological assay) and red blood cell folate by 31% (irrespective of whether microbiological or other assay was used). Studies that used the microbiological assay indicated lower heterogeneity compared with studies using nonmicrobiological assays for determining serum/plasma (I(2) = 13.5% compared with I(2) = 77.2%) and red blood cell (I(2) = 45.9% compared with I(2) = 70.2%) folate.

CONCLUSIONS: Studies administering >400 μg folic acid/d show no dose-response relation and thus will not yield meaningful results for consideration when generating dietary folate recommendations. The calculated folate biomarker response to a given folic acid intake may be more robust with the use of a microbiological assay rather than alternative methods for blood folate measurement.

Quantitative analysis of methyl and propyl parabens in neonatal DBS using LC–MS/MS

Aim: Excipients are used to overcome the chemical, physical and microbiological challenges posed by developing formulated medicines. Both methyl and propyl paraben are commonly used in pediatric liquid formulations. There is no data on systemic exposure to parabens in neonates. The European Study of Neonatal Exposure to Excipients project has investigated this. Results & methodology: DBS sampling was used to collect opportunistic blood samples. Parabens were extracted from the DBS and analyzed using a validated LC-MS/MS assay.

Discussion & Conclusion: The above assay was applied to analyze neonatal DBS samples. The blood concentrations of parabens in neonates confirm systemic exposure to parabens following administration of routine medicines.