RESUMEN
The sediment microbiome is a demographically diverse and functionally active biosphere. Ensuring that data acquired from sediment is truly representative of the microbiome is critical to achieving robust analyses. Sample storage and the processing and timing of nucleic acid purification after environmental sample extraction may fundamentally affect the detectable microbial community and thereby significantly alter resultant data. Direct sequencing of environmental samples is increasingly commonplace due to the advent of the portable Oxford Nanopore MinION sequencing device. Here we demonstrate that storing sediment subsamples at - 20 °C or storing the cores at 4 °C for 10 weeks prior to analysis, has a significant effect on the sediment microbiome analysed using sedimentary DNA (sedDNA), especially for Alpha-, Beta- and Deltaproteobacteria species. Furthermore, these significant differences are observed regardless of sediment type. We show that the taxa which are predominantly affected by storage are Proteobacteria, and therefore recommend on-site purifications are performed to ensure an accurate representation of these taxa are observed in the microbiome. Comparisons of sedimentary RNA (sedRNA) analyses, revealed substantial differences between samples purified and sequenced immediately on-site, samples that were frozen before transportation, and cores that were stored at 4 °C prior to analysis. Our data therefore suggest that a more accurate representation of the sediment microbiome demography and functionality may be achieved by environmental sequencing as rapidly as possible to minimise confounding effects of storage.
RESUMEN
Environmentally persistent aromatic hydrocarbons known as unresolved complex mixtures (UCMs) derived from crude oil can be accumulated by, and elicit toxicological responses in, marine organisms (e.g. mussels, Mytilus edulis). Comprehensive two-dimensional gas chromatography time-of-flight mass-spectrometry (GCxGC-ToF-MS) previously revealed that these UCMs included highly branched alkylated aromatic hydrocarbons. Here, the effects of biodegradation on the toxicity and chemical composition of an aromatic UCM hydrocarbon fraction isolated from Tia Juana Pesado (TJP) crude oil were examined. 48h exposure of mussels to the aromatic hydrocarbon fraction (F2) resulted in tissue concentrations of 900microgg(-1) (dry wt.) and approximately 45% decrease in clearance rate. Over 90% of the hydrocarbon burden corresponded to an UCM. Following a 5day recovery period, GCxGC-ToF-MS analysis of the tissues indicated depuration of most accumulated hydrocarbons and clearance rates returned to those observed in controls. To assess the potential of biodegradation to reduce UCM toxicity, TJP F2 was exposed to bacteria isolated from Whitley Bay, UK, for 46days. Mussels exposed to the undegraded TJP F2 from the abiotic control exhibited a reduction in clearance rate comparable with values for the pure crude oil TJP F2. Clearance rates of mussels exposed to biodegraded TJP F2 were statistically similar to seawater controls, suggesting biodegradation had reduced the TJP F2 toxicity. GCxGC-ToF-MS analysis revealed the same compound groups in the tissue of mussels exposed to pure TJP F2, undegraded TJP F2 and biodegraded TJP F2 samples; however >300 fewer compounds were observed in the biodegraded (954 compounds) compared to the undegraded TJP F2 (1261). The compound distributions were markedly different, possibly accounting for the decrease in toxicity. Extraction and analysis of pelleted bacterial cell material revealed that a significant proportion of the TJP F2 had adsorbed onto the cells. Thus extreme care must be taken in interpreting biodegradation data from recalcitrant UCM hydrocarbons.