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The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

1The EU Animal By-Products Regulations generated the need for novel methods of 2 storage and disposal of dead livestock. Bioreduction prior to rendering or incineration has 3 been proposed as a practical and potentially cost-effective method; however, its 4 biosecurity characteristics need to be elucidated. To address this, Salmonella enterica 5 (serovars Senftenberg and Poona), Enterococcus faecalis, Campylobacter jejuni, 6Campylobacter coli and a lux-marked strain of Escherichia coli O157 were inoculated 7 into laboratory-scale bioreduction vessels containing sheep carcass constituents. Numbers 8 of all pathogens and the metabolic activity of E. coli O157 decreased significantly within 9 the liquor waste over time, and only E. faecalis remained detectable after three months. 10Only very low numbers of Salmonella spp. and E. faecalis were detected in bioaerosols, 11 and only at initial stages of the trial.

Endotoxin is a bioaerosol component that is known to cause respiratory effects in exposed populations. To date, most research focused on occupational exposure, whilst much less is known about the impact of emissions from industrial operations on downwind endotoxin concentrations. A review of the literature was undertaken, identifying studies that reported endotoxin concentrations in both ambient environments and around sources with high endotoxin emissions. Ambient endotoxin concentrations in both rural and urban areas are generally below 10 endotoxin units (EU) m−3; however, around significant sources such as compost facilities, farms, and wastewater treatment plants, endotoxin concentrations regularly exceeded 100 EU m−3. However, this is affected by a range of factors including sampling approach, equipment, and duration. Reported downwind measurements of endotoxin demonstrate that endotoxin concentrations can remain above upwind concentrations. The evaluation of reported data is complicated due to a wide range of different parameters including sampling approaches, temperature, and site activity, demonstrating the need for a standardised methodology and improved guidance. Thorough characterisation of ambient endotoxin levels and modelling of endotoxin from pollution sources is needed to help inform future policy and support a robust health-based risk assessment process.

Options for the storage and disposal of animal carcasses are extremely limited in the EU after the introduction of the EU Animal By-products Regulations (ABPR; EC/1774/2002), leading to animosity within the livestock sector and the call for alternative methods to be validated. Novel storage technologies such as bioreduction may be approved under the ABPR provided that they can be shown to prevent pathogen proliferation. We studied the survival of Enterococcus faecalis, Salmonella spp., E. coli O157 and porcine parvovirus in bioreduction vessels containing sheep carcasses for approximately 4 months. The vessels were operated under two different scenarios: (A) where the water within was aerated and heated to 40 °C, and (B) with no aeration or heating, to simulate vessel failure. Microbial analysis verified that pathogens were contained within the bioreduction vessel and indeed reduced in numbers with time under both scenarios. This study shows that bioreduction can provide an effective and safe on-farm storage system for livestock carcasses prior to ultimate disposal. The findings support a review of the current regulatory framework so that bioreduction is considered for approval for industry use within the EU.