Comparing DNA isolation and sequencing strategies for 16S rRNA gene amplicon analysis in biofilm containing environments.

Bacteria are primarily responsible for biological water treatment processes in constructed wetland systems. Gravel in constructed wetlands serves as an essential substrate onto which complex bacterial biofilms may successfully grow and evolve. To fully understand the bacterial community in these systems it is crucial to properly isolate biofilms and process DNA from such substrates. This study looked at how best to isolate bacterial biofilms from gravel substrates in terms of bacterial richness. It considered factors including the duration of agitation during extraction, extraction temperature, and enzyme usage. Further, the 16S taxonomy data subsequently produced from Illumina MiSeq reads (using the SILVA 132 ribosomal RNA (rRNA) database on the DADA2 pipeline) were compared with the 16S data produced from Oxford Nanopore Technologies (ONT) MinION reads (using the NCBI 16S database on the EPI2ME pipeline). Finally, performance was tested by comparing the taxonomy data generated from the Illumina MiSeq and ONT MinION reads using the same (SILVA 132) database. We found no significant differences in the effective number of species observed when using different bacterial biofilm detachment techniques. However, enzyme treatment enhanced the total concentration of DNA. In terms of wetland community profiles, relative abundance differences within each sample type were clearer at the genus level. For genus-level taxonomic classification, MinION sequencing with the EPI2ME pipeline (NCBI database) produced bacterial abundance information that was poorly correlated with that from the Illumina MiSeq and DADA2 pipelines (SILVA132 database). When using the same database for each sequencing technology (SILVA132), the correlation between relative abundances at genus-level improved from negligible to moderate. This study provides detailed information of value to researchers working on constructed wetlands regarding efficient biofilm detachment techniques for DNA isolation and 16 s metabarcoding platforms for sequencing and data analysis.

Recoverable resources from pot ale & spent wash from Scotch Whisky production.

Scotch Whisky is an important global commodity which generates extensive co-product known as pot ale or spent wash (> 10 L co-product per L whisky). Whilst this is often used as fertiliser or animal feed, a proportion requires disposal resulting in cost to the distillery along with the negative impact on the carbon footprint due to transportation. This study examined the composition of the soluble fraction of pot ale from twenty-two distilleries in Scotland in order to assess the potential for resource recovery and transition to a more circular economy. The results reinforced previous studies, demonstrating that pot ale is an excellent source of protein with a potential for recovery >150, 000 t per annum in Scotland based on Whisky production data. Lactic acid, an important industrial platform chemical, was the major organic acid produced with concentrations ranging from 0.3 to 6.6 g L -1, representing a potential opportunity for recovery for applications such as manufacture of biodegradable polylactic acid for plastics (> 15,000 t per annum based on mean values). Other important platform chemicals, succinic acid and lysine were also identified and considered in sufficient amounts for future use. Pot ale was also shown to contain significant amounts of critical raw materials, magnesium and phosphate, which could be reclaimed for use in fertiliser/feed supporting the development of a new circular economy whilst at the same time reducing the burden of mining and transportation on the environment. The data in this study demonstrated a potential 13.8 kt recoverable phosphate per annum representing more than half of the annual fertiliser consumption in Scotland. Whisky co-products can contribute to sustainable energy, food and platform chemicals with the added value that metal concentrations are not sufficiently high to prevent its utilisation.

Mobility of antimony, arsenic and lead at a former antimony mine, Glendinning, Scotland.

Elevated concentrations of antimony (Sb), arsenic (As) and lead (Pb) in upland organic-rich soils have resulted from past Sb mining activities at Glendinning, southern Scotland. Transfer of these elements into soil porewaters was linked to the production and leaching of dissolved organic matter and to leaching of spoil material. Sb was predominantly present in truly dissolved (<3 kDa) forms whilst As and Pb were more commonly associated with large Fe-rich/organic colloids. The distinctive porewater behaviour of Sb accounts for its loss from deeper sections of certain cores and its transport over greater distances down steeper sections of the catchment. Although Sb and As concentrations decreased with increasing distance down a steep gully from the main spoil heap, elevated concentrations (~6-8 and 13-20 µg L(-1), respectively) were detected in receiving streamwaters. Thus, only partial attenuation occurs in steeply sloping sections of mining-impacted upland organic-rich soils and so spoil-derived contamination of surface waters may continue over time periods of decades to centuries. CAPSULE ABSTRACT: Production and leaching of dissolved organic matter led to the concomitant transfer of truly dissolved Sb to soil porewaters. Leaching of spoil-derived Sb impacted on the quality of receiving stream waters.

Lipid increases in European eel (Anguilla anguilla) in Scotland 1986-2008: an assessment of physical parameters and the influence of organic pollutants.

Recruitment of the European eel (Anguilla anguilla) has fallen steadily in recent decades, with current levels understood to be at around 5% of those in the 1970s, and the species is now widely recognised as being endangered. Changes in ocean currents, climate shifts, habitat loss, overfishing, barriers to migration, increased predation, plastic litter and exposure to chemicals have all been postulated as potential causative factors. Several studies have shown a general decline in eel quality (lower lipid content and body condition) over time that may be linked to reduced reproductive success. In this study, data from an eel sampling campaign in 1987 are compared with recent data (2004-2008) for eels in Scotland to assess any temporal changes in eel quality indicators and also to assess any links between current levels of chemical exposure and eel quality. Mean lipid levels, as a percentage of wet muscle mass, were higher in 2004-2008 (37 ± 1.9% SE) than in 1986 (21 ± 0.9% SE). By contrast, mean body condition index (K) was slightly lower in the latter period. Considering the 2004-2008 samples, significant inter-site variation was observed for condition index K, while intra-site variation was observed for lipid content and physical parameters relative to age (i.e. mass/age, length/age and lipid/age ratios); however, the variations observed could not be linked to differences in chemical body burdens, indicating that no chemical impacts on the parameters assessed are discernible during the continental life stage of eels in Scotland.

Persistent organic pollutants (PCB, DDT, HCH, HCB & BDE) in eels (Anguilla anguilla) in Scotland: current levels and temporal trends.

Eels are an ideal biomonitor for persistent organic pollutants (POPs) because of their high lipid content, longevity and tendency to remain within a defined range during their freshwater life phase. This study investigated concentrations of POPs in eels (Anguilla anguilla) from 30 sites across Scotland, including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (BDEs), DDT (and metabolites), hexachlorocyclohexanes (alpha, beta, gamma-HCH), hexachlorobenzene (HCB), hexachlorobutadiene (HCBD) and pentachlorobenzene. Despite its EU-wide ban approximately 30 years ago, DDT and its derivatives were detected in almost all samples. PCB 153 and 138 were the most widely detected PCB congeners, while BDE 47 was the dominant BDE. Pentachlorobenzene was not detected, while HCBD was detected once only. alpha-HCH, beta-HCH and HCB concentrations were very low (generally <3 microg/kg or below detection). When compared with 1986 and 1995 data, the results revealed considerable decreases in p,p'-DDE concentrations. More drastic reductions were evident for gamma-HCH, reflecting the tightening restrictions on pesticide use imposed over the previous decades.