Effects of hydrocarbon contamination on soil microbial community and enzyme activity

Acknowledgment I would like to gratefully acknowledge the government of Saudi Arabia for the scholarship and financial support.Peer reviewedPublisher PD

Hazard and risk assessment of human exposure to toxic metals using in vitro digestion assay

Acknowledgements The authors, acknowledge with thanks DSR technical and financial support. Funding This project was funded by the Deanship of Scientific Research (DSR), King Abdulaziz University, Jeddah, under grant no. 1434-142-514. The authors, therefore, acknowledge with thanks DSR technical and financial support.Peer reviewedPublisher PD

Insights into the biodegradation of weathered hydrocarbons in contaminated soils by bioaugmentation and nutrient stimulation

Acknowledgements This work was supported by the LINK Bioremediation programme (BIOREM_35), the Environment Agency and the Biotechnology and Biological Sciences Research Council BBSRC (Grant BB/B512432/1). The authors also thank the UK Engineering and Physical Sciences Research Council (EPSRC) for financial support to carry out this work through a CASE award supported by the former FIRSTFARADAY (Environmental Sustainability KTN) partnership (Ref No. 5010978). The views expressed are authors’ alone and may not reflect the views or policies of their employing organisations.Peer reviewedPublisher PD

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation

Multimedia fate of petroleum hydrocarbons in the soil: Oil matrix of constructed biopiles

A dynamic multimedia fugacity model was used to evaluate the partitioning and fate of petroleum hydrocarbon fractions and aromatic indicator compounds within the soil: oil matrix of three biopiles. Each biopile was characterised by four compartments: air, water, soil solids and non-aqueous phase liquid (NAPL). Equilibrium partitioning in biopile A and B suggested that most fractions resided in the NAPL, with the exception of the aromatic fraction with an equivalent carbon number from 5 to 7 (EC5-7). In Biopile C, which had the highest soil organic carbon content (13%), the soil solids were the most important compartment for both light aliphatic fractions (EC5-6 and EC6-8) and aromatic fractions, excluding the EC16-21 and EC21-35. Our starting hypothesis was that hydrocarbons do not degrade within the NAPL. This was supported by the agreement between predicted and measured hydrocarbon concentrations in Biopile B when the degradation rate constant in NAPL was set to zero. In all scenarios, biodegradation in soil was predicted as the dominant removal process for all fractions, except for the aliphatic EC5-6 which was predominantly lost via volatilization. The absence of an explicit NAPL phase in the model yielded a similar prediction of total petroleum hydrocarbon (TPH) behaviour; however the predicted concentrations in the air and water phases were significantly increased with consequent changes in potential mobility. Further comparisons between predictions and measured data, particularly concentrations in the soil mobile phases, are required to ascertain the true value of including an explicit NAPL in models of this kind

Mineralisation of target hydrocarbons in three contaminated soils from former refinery facilities

This study investigated the microbial degradation of 14C-labelled hexadecane, octacosane, phenanthrene and pyrene and considered how degradation might be optimised in three genuinely hydrocarbon contaminated soils from former petroleum refinery sites. Hydrocarbon mineralisation by the indigenous microbial community was monitored over 23 d. Hydrocarbon mineralisation enhancement by nutrient amendment (biostimulation), hydrocarbon degrader addition (bioaugmentation) and combined nutrient and degrader amendment, was also explored. The ability of indigenous soil microflora to mineralise 14C-target hydrocarbons was appreciable; ≥ 16% mineralised in all soils. Generally, addition of nutrients or degraders increased the rates and extents of mineralisation of 14C-hydrocarbons. However, the addition of nutrients and degraders in combination had a negative effect upon 14C-octacosane mineralisation and resulted in lower extents of mineralisation in the three soils. In general, the rates and extents of mineralisation will be dependent upon treatment type, nature of the contamination and adaptation of the ingenious microbial communi

Optimising the biopiling of weathered hydrocarbons within a risk management framework.

Thirty years of research into petroleum microbiology and bioremediation have bypassed an important observation – that many hydrocarbon contaminated sites posing potential risks to human health harbour weathered, ‘mid-distillate’ or heavy oils rather than ‘fresh product’ (Pollard, 2003). Ex-situ biopiling is an important technology for treating soils contaminated with weathered hydrocarbons. However, its performance continues to be represented by reference to reductions in the hydrocarbon ‘load’ in the soils being treated, rather than reductions in the risks posed by the hydrocarbon contamination (Owens and Bourgouin, 2003; Tien et al., 1999). The absence of ‘risk’ from the vocabulary of many operators and remediation projects reduces stakeholder (regulatory, investor, landowner, and public) confidence in remediation technologies, and subsequently limits the market potential of these technologies. Stakeholder confidence in the biopiling of weathered hydrocarbons may be improved by demonstrating process optimisation within a validated risk ma