Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem

Challenges to evaluating complex interventions: a content analysis of published papers.

BACKGROUND: There is continuing interest among practitioners, policymakers and researchers in the evaluation of complex interventions stemming from the need to further develop the evidence base on the effectiveness of healthcare and public health interventions, and an awareness that evaluation becomes more challenging if interventions are complex.We undertook an analysis of published journal articles in order to identify aspects of complexity described by writers, the fields in which complex interventions are being evaluated and the challenges experienced in design, implementation and evaluation. This paper outlines the findings of this documentary analysis. METHODS: The PubMed electronic database was searched for the ten year period, January 2002 to December 2011, using the term "complex intervention*" in the title and/or abstract of a paper. We extracted text from papers to a table and carried out a thematic analysis to identify authors' descriptions of challenges faced in developing, implementing and evaluating complex interventions. RESULTS: The search resulted in a sample of 221 papers of which full text of 216 was obtained and 207 were included in the analysis. The 207 papers broadly cover clinical, public health and methodological topics. Challenges described included the content and standardisation of interventions, the impact of the people involved (staff and patients), the organisational context of implementation, the development of outcome measures, and evaluation. CONCLUSIONS: Our analysis of these papers suggests that more detailed reporting of information on outcomes, context and intervention is required for complex interventions. Future revisions to reporting guidelines for both primary and secondary research may need to take aspects of complexity into account to enhance their value to both researchers and users of research