A multifaceted analysis of bacterial blotch diseases of mushrooms

Similar to most agro-ecological systems, cultivation of button mushrooms relies heavily on the dynamic interactions between the host, Agaricus bisporus, and soil microorganisms. Mushroom cropping systems are diverse ecosystems, inhabited by good (growth-promoters), bad (mushroom pathogens) and ugly (human pathogens) microorganisms together. In this research, we investigate bacterial pathogens of mushrooms, and their  interactions with the host and the soil microbiome, in order to better understand the key factors determining disease outbreaks in mushroom cultivation. To address these research questions, several genomic, microbial, physico-chemical and phytopathological experiments were performed, the results of which are described and discussed in seven chapters of this thesis. In Chapter 1, we introduce bacterial blotch a group of diseases that result in discoloration and disfiguration of mushroom caps of A. bisporus. Blotch not only reduces the total marketable crop due to compromised aesthetic value, it also lessens the overall yields due to pin death and lowers the shelf-life post-harvest, leading to severe economic losses globally. Despite being studied for over a century, the identity and taxonomy of blotch-causing organisms still remains unclear. Chapter 2 provides a detailed overview of genetic and regional diversity and the virulence of blotch causing organisms in Western Europe. It describes the molecular characterization of the phylogenetic and phenotypic diversity of bacteria colonizing the caps of diseased mushrooms, using prokaryotic genomics, with large implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management. Chapter 3 describes the development of multiplex TaqmanTM-qPCR assays for the detection of three blotch pathogens at low densities in environmental samples. It reports the diagnostic sensitivity and specificity, reproducibility and repeatability of the assays. Moreover, it includes successful validation and application of the assays for routine testing of samples associated with mushroom cropping systems, such as water, compost, peat source and casing soil. Chapter 4 investigates the infection dynamics and population dynamics of newly discovered brown blotch pathogen, P. salomonii, with that of ginger blotch pathogen, ‘P. gingeri’. It identifies the soil inoculum thresholds for both pathogens and elucidates the role of abiotic and biotic parameters such as casing soil composition and environmental humidity for their blotch outbreaks. It also studies the endemic and inoculated pathogen populations in various casing soils. Chapter 5 reports the development of soil suppressiveness to ginger blotch in consecutive mushroom cultivation cycles, despite increasing pathogen populations. It describes changes in the soil microbial community due to pathogen invasion, pathogen establishment and blotch suppression, and identifies specific bacterial and fungal genera that are associated with blotch suppression. It also reports on the transferability of blotch suppressiveness to conducive soils with aqueous soil extracts. Chapter 6 proposes three circular alternatives for replacement of peat in mushroom casing soils. It evaluates the agronomical performance, physico-chemical characteristics, and the soil microbiome of these peat-reduced growing media. It addresses trade-offs between productivity and disease pressure in these circular cropping systems, with regard to the diversity, composition and interactions within their microbiomes. It also comments on the accessibility and sustainability of these peat-alternatives. Chapter 7 discusses the main findings presented in this thesis, integrates these results with existing knowledge on bacterial blotch and elaborates on their advantages and limitations, with particular focus on blotch management. Finally, it places this research in context for localized and ecological management of soil-borne diseases in mushroom cropping systems, and the future research required to achieve sustainable and blotch-free mushroom cultivatio

Regulation of the antennal transcriptome of the dengue vector, Aedes aegypti, during the first gonotrophic cycle

BackgroundIn the light of dengue being the fastest growing transmissible disease, there is a dire need to identify the mechanisms regulating the behaviour of the main vector Aedes aegypti. Disease transmission requires the female mosquito to acquire the pathogen from a blood meal during one gonotrophic cycle, and to pass it on in the next, and the capacity of the vector to maintain the disease relies on a sustained mosquito population.ResultsUsing a comprehensive transcriptomic approach, we provide insight into the regulation of the odour-mediated host- and oviposition-seeking behaviours throughout the first gonotrophic cycle. We provide clear evidence that the age and state of the female affects antennal transcription differentially. Notably, the temporal- and state-dependent patterns of differential transcript abundance of chemosensory and neuromodulatory genes extends across families, and appears to be linked to concerted differential modulation by subsets of transcription factors.ConclusionsBy identifying these regulatory pathways, we provide a substrate for future studies targeting subsets of genes across disparate families involved in generating key vector behaviours, with the goal to develop novel vector control tools

Antennal transcriptome of Aedes aegypti during the first gonotrophic cycle

Using a comprehensive transcriptomic approach, we provide insight into the regulation of the odour-mediated host- and oviposition-seeking behaviours throughout the first gonotrophic cycle. We provide clear evidence that the age and state of the female affects antennal transcription differentially. Notably, the temporal- and state-dependent patterns of differential transcript abundance of chemosensory and neuromodulatory genes extends across families, and appears to be linked to concerted differential modulation by subsets of transcription factors

Antennal transcriptome of Aedes aegypti during the first gonotrophic cycle

Using a comprehensive transcriptomic approach, we provide insight into the regulation of the odour-mediated host- and oviposition-seeking behaviours throughout the first gonotrophic cycle. We provide clear evidence that the age and state of the female affects antennal transcription differentially. Notably, the temporal- and state-dependent patterns of differential transcript abundance of chemosensory and neuromodulatory genes extends across families, and appears to be linked to concerted differential modulation by subsets of transcription factors

Regulation of the antennal transcriptome of the dengue vector, Aedes aegypti, during the first gonotrophic cycle

Background In the light of dengue being the fastest growing transmissible disease, there is a dire need to identify the mechanisms regulating the behaviour of the main vector Aedes aegypti. Disease transmission requires the female mosquito to acquire the pathogen from a blood meal during one gonotrophic cycle, and to pass it on in the next, and the capacity of the vector to maintain the disease relies on a sustained mosquito population. Results Using a comprehensive transcriptomic approach, we provide insight into the regulation of the odour-mediated host- and oviposition-seeking behaviours throughout the first gonotrophic cycle. We provide clear evidence that the age and state of the female affects antennal transcription differentially. Notably, the temporal- and state-dependent patterns of differential transcript abundance of chemosensory and neuromodulatory genes extends across families, and appears to be linked to concerted differential modulation by subsets of transcription factors. Conclusions By identifying these regulatory pathways, we provide a substrate for future studies targeting subsets of genes across disparate families involved in generating key vector behaviours, with the goal to develop novel vector control tools

Blood meal induced regulation of the chemosensory gene repertoire in the southern house mosquito

Background: The southern house mosquito, Culex quinquefasciatus, is one of the most prevalent vectors of lymphatic filariasis and flavivirus-induced encephalitis. Its vectorial capacity is directly affected by its reproductive feeding behaviors, such as host seeking, blood feeding, resting, and egg laying. In mosquitoes, these gonotrophic behaviors are odor-mediated and regulated following blood feeding. Immediately after a blood meal, female mosquitoes show reduced olfactory responsiveness and flight activity, as they enter a resting state. Insights into antennal chemosensory gene regulation at this time period can provide a foundation to identify targets involved in the state switch between host seeking and resting. Results: This study used quantitative gene expression analyses to explore blood meal induced regulation of chemosensory gene families in the antennae of 6 days post-emergence C. quinquefasciatus females. Improved annotations for multiple chemosensory gene families, and a quantitative differential gene expression analysis between host seeking and 24 h post- blood fed females of the same age, allowed for the detection of transcripts that potentially play a role in the switch from host seeking to resting, in C. quinquefasciatus. The expression profiles of chemosensory genes varied significantly between the two treatments. Conclusions: Annotations for chemosensory gene repertoires in C. quinquefasciatus have been manually curated and corrected for 3' exon choice and transcript length, through sequence and transcriptome analyses. The gene expression analyses identified various molecular components of the peripheral olfactory system in C. quinquefasciatus, including odorant receptors, ionotropic receptors, odorant binding proteins and chemosensory proteins, that are regulated in response to blood feeding, and could be critical for the behavioral switch from host seeking to resting. Functional characterization of these proteins in the future can identify targets essential for the females' gonotrophic behaviors, and can be used to design novel vector control strategies.</p

Additional file 4: of Blood meal induced regulation of the chemosensory gene repertoire in the southern house mosquito

Lists the sequences, amplicon sizes, melting temperatures, GC % content and 3’ complementarity of the forward and reverse primer-pair for each of the reference genes and select ORs and IRs that were verified using qPCR analyses. (DOCX 29 kb

Additional file 5: of Blood meal induced regulation of the chemosensory gene repertoire in the southern house mosquito

Describes the sequencing depth and Pearson coefficients of the technical replicates from non-blood fed and blood fed libraries. (XLSX 10 kb

Circular alternatives to peat in growing media: A microbiome perspective

Peat use in horticulture is associated with a large ecological footprint. Peat is the predominant growing media in Europe. Modern cropping systems rely heavily on dynamic interactions of the crop with the microorganisms in the growing media and yet, in the search for sustainable peat-alternatives, the microbiome of the growing media has often been ignored. In mushroom cultivation, peat is a prime determinant of productivity, in the form of a casing soil which supplies beneficial microbes. In this study we describe the microbial composition, interactions, and activity of four circular substrates used to proportionally replace peat in mushroom growing media. We also evaluate various physico-chemical characteristics of the peat-alternatives. We characterize the impact of sanitary pre-treatments such as steaming and acidification on the microbiome as well as the agronomical performance of the peat-reduced growing media. We found that grass fibres from agricultural residue streams, peat-moss farmed in degraded peatlands, and spent casing soil recycled from previous cultivation cycles can be used to successfully replace peat in mushroom growing media. Peat moss and spent casing were expectedly similar to peat in physical, chemical, and microbiological properties. However, the grass fibres had unique characteristics, such as high organic matter content, low water holding capacity and a diverse and competitive microbiome. Pre-treatment of the substrates by acidification and steaming significantly affected the microbiome, and reduced the presence of pests, pathogens and competitive fungi in the peat-reduced media. Strong trade-offs existed between the productivity and disease pressure in the circular cropping system, which are also governed by the microbial composition of the growing media. Knowledge on the accessibility, sustainability, and economic viability of these peat-alternatives will further determine the transition away from peat use and towards sustainable growing media