Aim: To assess Pediococcus acidilactici as a dietary supplement for on‐growing red tilapia (Oreochromis niloticus). Methods and Results: Tilapia were fed either a control diet or control diet supplemented with Ped. acidilactici at 10⁷ CFU g⁻¹ for 32 days. Ped. acidilactici colonized the intestinal tract and significantly affected the intestinal microbial communities. PCR‐DGGE revealed direct antagonism of gastric Ped. acidilactici with an endogenous uncultured bacterium during a period of reverting to nonsupplemented feeding. Light microscopy revealed that gut integrity and leucocyte levels were unaffected by Ped. acidilactici; however, blood leucocyte levels and serum lysozyme activity were elevated after 14‐days' feeding. No significant improvements in growth performance were observed at the end of the trial (day 32), but survival was significantly higher in the probiotic group. Conclusions: The study demonstrates that oral supplementation of Ped. acidilactici modulates intestinal bacterial communities in on‐growing red tilapia and also stimulates some aspects of the nonspecific immune response. Significance and Impact of the study: To our knowledge this is the first study assessing the effects of probiotics on the gut microbiota of tilapia using culture‐independent methods. Such methods are crucial to understand the mechanisms which underpin and mediate host benefits.

This study investigated the effect of changes in organic loading rate (OLR) and feedstock on the volatile fatty acids (VFAs) production and their potential use as a bioengineering management tool to improve stability of anaerobic digesters. Digesters were exposed to one or two changes in OLR using the same or different co-substrates (Fat Oil and Grease waste (FOG) and/or glycerol). Although all the OLR fluctuations produced a decrease in biogas and methane production, the digesters exposed twice to glycerol showed faster recovery towards stable conditions after the second OLR change. This was correlated with the composition of the VFAs produced and their mode of production, from parallel to sequential, resulting in a more efficient recovery from inhibition of methanogenesis. The change in acids processing after the first OLR increase induced a shift in the microbial community responsible of the process optimisation when the digesters were exposed to a subsequent OLR increase with the same feedstock. When the digesters were exposed to an OLR change with a different feedstock (FOG), the recovery took 7d longer than with the same one (glycerol). However, the microbial community showed functional resilience and was able to perform similarly to pre-exposure conditions. Thus, changes in operational conditions can be used to influence microbial community structure for anaerobic digestion (AD) optimisation. Finally, shorter recovery times and increased resilience of digesters were linked to higher numbers of Clostridia incertae sedis XV, suggesting that this group may be a good candidate for AD bioaugmentation to speed up recovery after process instability or OLR increase.

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine ‐scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram‐positive bacteria, we found that the matrix for impingement should be phosphate‐buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in‐field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high ‐throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.

Particle size is a significant factor in determining the dispersal and inhalation risk from bioaerosols. Green-waste composting is a significant source of bioaerosols (including pathogens), but little is known about the distribution of specific taxa across size fractions. To characterise size fractionated bioaerosol emissions from a compost facility, we used a Spectral Intensity Bioaerosol Sensor (SIBS) to quantify total bioaerosols and qPCR and metabarcoding to quantify microbial bioaerosols. Overall, sub-micron bioaerosols predominated, but molecular analysis showed that most (>75%) of the airborne microorganisms were associated with the larger size fractions (>3.3 µm da). The microbial taxa varied significantly by size, with Bacilli dominating the larger, and Actinobacteria the smaller, size fractions. The human pathogen Aspergillus fumigatus dominated the intermediate size fractions (>50% da 1.1-4.7 µm), indicating that it has the potential to disperse widely and once inhaled may penetrate deep into the respiratory system. The abundance of Actinobacteria (>60% at da < 2.1 µm) and other sub-micron bioaerosols suggest that the main health effects from composting bioaerosols may come from allergenic respiratory sensitisation rather than directly via infection. These results emphasise the need to better understand the size distributions of bioaerosols across all taxa in order to model their dispersal and to inform risk assessments of human health related to composting facilities.

To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800mgkg-1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p=0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity.

454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.