Stochastic modelling of pesticide transport to drinking water sources via runoff and resulting human health risk assessment

A modelling framework was developed to facilitate a probabilistic assessment of health risks posed by pesticide exposure via drinking water due to runoff, with the inclusion of influential site conditions and in-stream processes. A Monte-Carlo based approach was utilised to account for the inherent variability in pesticide and population properties, as well as site and climatic conditions. The framework presented in this study was developed with an ability to integrate different data sources and adapt the model for various scenarios and locations to meet the users' needs. The results from this model can be used by farm advisors and catchment managers to identify lower risk pesticides for use for given soil and site conditions and implement risk mitigation measures to protect water resources. Pesticide concentrations in surface water, and their risk of regulatory threshold exceedances, were simulated for fifteen pesticides in an Irish case study. The predicted concentrations in surface water were then used to quantify the level of health risk posed to Irish adults and children. The analysis indicated that herbicides triclopyr and MCPA occur in the greatest concentrations in surface water, while mecoprop was associated with the highest potential for health risks. The study found that the modelled pesticides posed little risk to human health under current application patterns and climatic conditions in Ireland using international acceptable intake values. A sensitivity study conducted examined the impact seasonal conditions, timing of application, and instream processes, have on the transport of pesticides to drinking water.

Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health

Over the past two decades, whole food supplementation strategies have been leveraged to target mental health. In addition, there has been increasing attention on the ability of gut microbes, so called psychobiotics, to positively impact behaviour though the microbiota-gut-brain axis. Fermented foods offer themselves as a combined whole food microbiota modulating intervention. Indeed, they contain potentially beneficial microbes, microbial metabolites and other bioactives, which are being harnessed to target the microbiota-gut-brain axis for positive benefits. This review highlights the diverse nature of fermented foods in terms of the raw materials used and type of fermentation employed, and summarises their potential to shape composition of the gut microbiota, the gut to brain communication pathways including the immune system and, ultimately, modulate the microbiota-gut-brain axis. Throughout, we identify knowledge gaps and challenges faced in designing human studies for investigating the mental health-promoting potential of individual fermented foods or components thereof. Importantly, we also suggest solutions that can advance understanding of the therapeutic merit of fermented foods to modulate the microbiota-gut-brain axis.

Pesticide exposure and the microbiota-gut-brain axis

The gut microbiota exist within a dynamic ecosystem shaped by various factors that includes exposure to xenobiotics such as pesticides. It is widely regarded that the gut microbiota plays an essential role in maintaining host health, including a major influence on the brain and behaviour. Given the widespread use of pesticides in modern agriculture practices, it is important to assess the long-term collateral effects these xenobiotic exposures have on gut microbiota composition and function. Indeed, exposure studies using animal models have shown that pesticides can induce negative impacts on the host gut microbiota, physiology and health. In tandem, there is a growing body of literature showing that the effects of pesticide exposure can be extended to the manifestation of behavioural impairments in the host. With the increasing appreciation of the microbiota-gut-brain axis, in this review we assess whether pesticide-induced changes in gut microbiota composition profiles and functions could be driving these behavioural alterations. Currently, the diversity of pesticide type, exposure dose and variation in experimental designs hinders direct comparisons of studies presented. Although many insights presented, the mechanistic connection between the gut microbiota and behavioural changes remains insufficiently explored. Future experiments should therefore focus on causal mechanisms to examine the gut microbiota as the mediator of the behavioural impairments observed in the host following pesticide exposure.

Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner

Exposure to repeated social stress may cause maladaptive emotional reactions that can be reduced by healthy nutritional supplementation. Histaminergic neurotransmission has a central role in orchestrating specific behavioural responses depending on the homeostatic state of a subject, but it remains to be established if it participates in the protective effects against the insults of chronic stress afforded by a healthy diet. By using C57BL/6J male mice that do not synthesize histamine (Hdc-/-) and their wild type (Hdc+/+) congeners we evaluated if the histaminergic system participates in the protective action of a diet enriched with polyunsaturated fatty acids and vitamin A on the deleterious effect of chronic stress. Behavioural tests across domains relevant to cognition and anxiety were performed. Hippocampal synaptic plasticity, cytokine expression, hippocampal fatty acids, oxylipins and microbiota composition were also assessed. Chronic stress induced social avoidance, poor recognition memory, affected hippocampal long-term potentiation, changed the microbiota profile, brain cytokines, fatty acid and oxylipins composition of both Hdc-/- and Hdc+/+ mice. Dietary enrichment counteracted stress-induced deficits only in Hdc+/+ mice as histamine deficiency prevented almost all the diet-related beneficial effects. Interpretation: Our results reveal a previously unexplored and novel role for brain histamine as a mediator of many favorable effects of the enriched diet. These data present long-reaching perspectives in the field of nutritional neuropsychopharmacology.

Microbially-derived short-chain fatty acids impact astrocyte gene expression in a sex-specific manner

Recent investigations in neuroscience implicate the role of microbial-derived metabolites, such as short-chain fatty acids (SCFAs) in brain health and disease. The SCFAs acetate, propionate and butyrate have pleiotropic effects within the nervous system. They are crucial for the maturation of the brain's innate immune cells, the microglia, and modulate other glial cells through the aryl-hydrocarbon receptor. Investigations in preclinical and clinical models find that SCFAs exert neuroprotective and antidepressant affects, while also modulating the stress response and satiety. However, many investigations thus far have not assessed the impact of sex on SCFA activity. Our novel investigation tested the impact of physiologically relevant doses of SCFAs on male and female primary cortical astrocytes. We find that butyrate (0–25 ​μM) correlates with increased Bdnf and Pgc1-α expression, implicating histone-deacetylase inhibitor pathways. Intriguingly, this effect is only seen in females. We also find that acetate (0–1500 ​μM) correlates with increased Ahr and Gfap expression in males only, suggesting immune modulatory pathways. In males, propionate (0–35 ​μM) correlates with increased Il-22 expression, further suggesting immunomodulatory actions. These findings show a novel sex-dependent impact of acetate and butyrate, but not propionate on astrocyte gene expression.

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters

The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R ² = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R ² ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH₄ influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.

Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion

Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD.

Low-temperature anaerobic digestion is associated with differential methanogenic protein expression

Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes.

Draft genomic DNA sequence of the multi-resistant Sphingomonas sp. strain AntH11 isolated from an Antarctic hypolith

Hypoliths are microbial communities that live underneath translucent rocks in desert ecosystems and represent a key refuge niche in the Antarctic Dry Valleys. These cryptic microbial assemblages are crucial as they mediate numerous ecosystem processes. Here, we present the first draft genome of a hypolith isolate belonging to the α-proteobacterial class and the genus Sphingomonas. The draft genome of Sphingomonas sp. strain AntH11 shows the capacity of this organism to adapt to the extreme cold and arid conditions encountered in Antarctic desert soils. Our result also suggests that its metabolic versatility and multidrug resistance constitutes an opportunistic advantage in competition with other hypolith-colonizing microorganisms.

A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches

A co-extraction protocol that sequentially isolates core biopolymer fractions (DNA, RNA, protein) from edaphic microbial communities is presented. In order to confirm compatibility with downstream analyses, bacterial T-RFLP profiles were generated from the DNA- and RNA-derived fractions of an arid-based soil, with metaproteomics undertaken on the corresponding protein fraction.

Exploring mixed microbial community functioning: recent advances in metaproteomics

System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.