Monitoring bioaerosol and odour emissions from composting facilities - WR1121

Government policy requires that valuable resources should be recovered and recycled from biodegradable waste. A successful and growing organics recycling industry delivers this policy with composting being one of the principal technologies deployed to process suitable feedstock such as garden and food waste. Composting inevitably generates bioaerosols – particulate matter comprising cells or cellular components that are released into the air as a result of disturbance of composting feedstock or the processing of final product. Exposure to bioaerosols has the potential to be harmful to human and animal health. The Environment Agency adopts a precautionary and risk-based approach to the regulation of composting facilities which was developed on the basis of research by Wheeler et al. (2001) and which has been updated as new evidence has become available. The Environment Agency also requires site operators to monitor bioaerosols around their facilities using methods specified in a standard protocol which relies upon classical microbiology methods which are tried and tested but which are labour-intensive, slow and offer only a snapshot view of a highly dynamic system. A recent IOM review commissioned by Defra (Searl, 2009) on exposure-response relationships for bioaerosol emissions from waste treatment processes identified significant gaps in knowledge of exposure to bioaerosols and recommended that more research was needed into alternatives to viable microbial monitoring such as priority biomarkers (notably endotoxin) and potential surrogates such as particulate matter. The IOM review also concluded that there is a lack of information to support the development of appropriate stand-off distances. The overall aim of this project was to provide evidence on bioaerosol production, dispersion and potential exposures from composting facilities in support of future developments in policy and regulation of biowaste facilities. The objectives were: (i) to undertake a comprehensive set of standard and novel bioaerosol measurements at representative composting sites to assess comparability between different methods and also to measure spatial and temporal variations; and (ii) to determine the odour emissions and then compare these with bioaerosol emissions to see if odour is a marker of significant bioaerosol exposure. Standard (AfOR, 2009) and novel (CEN filter method, endotoxin, glucan, qPCR, real-time particulates) bioaerosols measurements were taken on a minimum of three to a maximum of six occasions over a twelve month period at four different composting facilities in England. The composting facilities were selected to represent sites of varying sizes (tonnages) and to allow a comparison of bioaerosol concentrations at standard open windrow sites versus a fully-contained site. Additional supporting information was collected including meteorological data at the time of sampling, observation of site operations and measurements of odour at one of the sites. Supporting bioaerosol and odour dispersion modelling was conducted at the site where the odour measurements were made. The spatial trend of bioaerosol concentrations described by Wheeler et al., (1991) and upon which EA regulatory policy is based was broadly corroborated by this dataset. Excursions above the EA acceptable levels at or beyond 250m from source were rare. Bioaerosol concentrations at the enclosed site were generally lower than at the open windrow sites. There was no evidence of a seasonal pattern in bioaerosol concentrations at any of the sites whereas between-sampling day variations were apparent. The cause(s) of these variations were not identified. No consistent relationship was observed between the concentration of bioaerosols measured by the two AfOR standard methods. The two methods displayed certain strengths and weakness in different situations. The IOM sampling device proved to be better suited to situations where high bioaerosol concentrations were encountered (close to source); the Andersen proving to be more effective in the lower concentration range typically found upwind of a site or at distance downwind from source. The higher volume filtration device tested in this project (referred to as the CEN method) produced data that did not consistently match either of the AfOR standard methods. This device demonstrated greater sensitivity than the IOM filter method but suffered drawbacks associated with its weight and a lack of ease of use in the field. Endotoxin concentrations were normally below the level recommended by the Dutch Expert Committee on Occupational Safety but occasional exceedances of this standard were detected at the larger open windrow sites. The majority of glucan measurements were below a widely referred to 10ng/m3 threshold. Significantly elevated concentrations were detected at one of the larger open windrow sites. The dynamic range of the qPCR method is wider (4-5-log) than either of the AfOR and the CEN methods. It is also quicker to carry out and has the potential for automation. The results from the qPCR method are mainly higher than standard AfOR methods, as the method does not distinguish viable and non-viable spores. The spatial distribution of Aspergillus fumigatus spores (by qPCR) along sampling transects, gives similar results compared to AfOR (and CEN) methods. Real time particle detection showed that both TSP and PM10 are correlated to Aspergillus fumigatus spore concentration. No consistent relationship was observed between odour and bioaerosol concentrations (although this was a limited dataset). The envelope of modelled (back-extrapolated) bioaerosol emission rates straddles several orders of magnitude. Distinguishing the influences of meteorological conditions on this variability was not possible. It was not possible to predict bioaerosol or odour emission rates with confidence. This continues to hamper confidence in modelling of odours and bioaerosols from open windrow facilities. The findings of this research have implications for the current standard monitoring protocol which should be reviewed accordingly. The findings of this multi-site survey accord with existing regulatory policy and are supportive of the general trend towards enclosed facilities. Notwithstanding this, continuing research is needed to enhance the database on emission from bioaerosol and odour abatement technologies (e.g. biofilters); to determine the cause(s) of occasional bioaerosol peaks from open facilities; to improve exposure assessments through better modelling protocols; and to link enhanced exposure information to future health impact studies

A dominant allele of arabidopsis pectin-binding wall-associated kinase induces a stress response suppressed by MPK6 but not MPK3 mutations

The plant cell wall is composed of a matrix of cellulose fibers, flexible pectin polymers, and an array of assorted carbohydrates and proteins. The receptor-like Wall-Associated Kinases (WAKs) of Arabidopsis bind pectin in the wall, and are necessary both for cell expansion during development and for a response to pathogens and wounding. Mitogen Activated Protein Kinases (MPKs) form a major signaling link between cell surface receptors and both transcriptional and enzyme regulation in eukaryotes, and Arabidopsis MPK6 and MPK3 indeed have important roles in development and the response to stress and pathogens. A dominant allele of WAK2 requires kinase activity and activates a stress response that includes an increased ROS accumulation and the up-regulation of numerous genes involved in pathogen resistance, wounding, and cell wall biogenesis. This dominant allele requires a functional pectin binding and kinase domain, indicating that it is engaged in a WAK signaling pathway. A null mutant of the major plasma membrane ROS-producing enzyme complex, rbohd/f does not suppress the WAK2cTAP-induced phenotype. A mpk6, but not a mpk3, null allele is able to suppress the effects of this dominant WAK2 mutation, thus distinguishing MPK3 and MPK6, whose activity previously was thought to be redundant. Pectin activation of gene expression is abated in a wak2-null, but is tempered by the WAK-dominant allele that induces elevated basal stress-related transcript levels. The results suggest a mechanism in which changes to the cell wall can lead to a large change in cellular responses and help to explain how pathogens and wounding can have general effects on growth. The Author 2011. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS.2011 © The Author 2011. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS

Nutrient Acquisition, Rather Than Stress Response Over Diel Cycles, Drives Microbial Transcription in a Hyper-Arid Namib Desert Soil

Hot desert surface soils are characterized by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated by Actinobacteria. Metatranscriptomic analysis of samples taken at different times over 3 days indicated that functional diel variations were limited at the whole community level, and mostly affected the eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network

With a pinch of salt : metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities

DATA AVAILABILITY : Metagenomic data generated in this work can be accessed through the IMG/M database (https://img.jgi.doe.gov/) under GOLD Sequencing Project ID: Gp0293142 and IMG Genome IDs: 3300023218, 3300023197, 3300022725, 3300023214, 3300023202, 3300022723, 3300022777, 3300022719, 3300022719 and 3300022719. The unassembled reads from all datasets analyzed are available in the SRA database under BioProject PRJNA943124, accession numbers: SRR23862440, SRR23862446, SRR23862438, SRR23862439, SRR23862444, SRR23862445, SRR23862443, SRR23862437, SRR23862441, SRR23862442Salt pans or playas, which are saline-rich springs surrounded by halite evaporates in arid environments, have played an essential role in landscape erosion during the formation of the Namib Desert and are numerous in its central region. In this study, we used shotgun metagenomics to investigate the phylogenetic and functional capacities of the microbial communities from two salt pans (namely, Eisefeld and Hosabes) located in central Namib Desert, located in Southwest Africa. We studied the source and sink sediment mat communities of the saline streams, as well as those from two halites (crystallized structures on the stream margins). The microbial assemblages and potential functions were distinct in both niches. Independently from their localization (Eisfeld vs Hosabes and source vs sink), the sediment mat communities were dominated by members of the Alpha- and Gamma-proteobacteria classes, while halites were Archaea dominated and also contained high abundances of the extremely halophilic bacterium Salinibacter sp. (phylum Bacteroidota). Photoheterotrophy and chemoheterotrophy were the principal lifestyles in both niches, with halite communities having a reduced diversity of metabolic pathways. Intense microbial-virus interactions in both niches were implied by the widespread detection of CRISPR-Cas defense systems. We identified a putatively novel clade of type II CRISPR-Cas systems, as well as novel candidate viral lineages of the class Caudoviricetes and of Halobacteriales-infecting haloviruses. Putative gene transfer agent-like sequences within the Alphaproteobacteria were identified in the sediment mat communities. These horizontal gene transfer elements have the potential to drive genome plasticity and evolution of the Alphaproteobacteria in the Namib Desert salt pan microbiomes.The University of Pretoria and the National Research Foundation.http://aem.asm.org2024-05-16hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

‘Follow the Water’: Microbial Water Acquisition in Desert Soils

Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments

Monogenic conditions and central nervous system anomalies:A prospective study, systematic review and meta-analysis

Objectives: Determine the incremental diagnostic yield of prenatal exome sequencing (pES) over chromosome microarray (CMA) or G-banding karyotype in fetuses with central nervous system (CNS) abnormalities.Methods: Data were collected via electronic searches from January 2010 to April 2022 in MEDLINE, Cochrane, Web of Science and EMBASE. The NHS England prenatal exome cohort was also included. Incremental yield was calculated as a pooled value using a random-effects model. Results: Thirty studies were included (n = 1583 cases). The incremental yield with pES for any CNS anomaly was 32% [95%CI 27%–36%; I2 = 72%]. Subgroup analysis revealed apparent incremental yields in; (a) isolated CNS anomalies; 27% [95%CI 19%–34%; I2 = 74%]; (b) single CNS anomaly; 16% [95% CI 10%–23%; I2 = 41%]; (c) more than one CNS anomaly; 31% [95% Cl 21%–40%; I2 = 56%]; and (d) the anatomical subtype with the most optimal yield was Type 1 malformation of cortical development, related to abnormal cell proliferation or apoptosis, incorporating microcephalies, megalencephalies and dysplasia; 40% (22%–57%; I2 = 68%). The commonest syndromes in isolated cases were Lissencephaly 3 and X-linked hydrocephalus. Conclusions: Prenatal exome sequencing provides a high incremental diagnostic yield in fetuses with CNS abnormalities with optimal yields in cases with multiple CNS anomalies, particularly those affecting the midline, posterior fossa and cortex.</p

Human fetal dendritic cells promote prenatal T-cell immune suppression through arginase-2.

During gestation the developing human fetus is exposed to a diverse range of potentially immune-stimulatory molecules including semi-allogeneic antigens from maternal cells, substances from ingested amniotic fluid, food antigens, and microbes. Yet the capacity of the fetal immune system, including antigen-presenting cells, to detect and respond to such stimuli remains unclear. In particular, dendritic cells, which are crucial for effective immunity and tolerance, remain poorly characterized in the developing fetus. Here we show that subsets of antigen-presenting cells can be identified in fetal tissues and are related to adult populations of antigen-presenting cells. Similar to adult dendritic cells, fetal dendritic cells migrate to lymph nodes and respond to toll-like receptor ligation; however, they differ markedly in their response to allogeneic antigens, strongly promoting regulatory T-cell induction and inhibiting T-cell tumour-necrosis factor-α production through arginase-2 activity. Our results reveal a previously unappreciated role of dendritic cells within the developing fetus and indicate that they mediate homeostatic immune-suppressive responses during gestation