Serratia
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335642 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR5039727_1.fastq.gz | Fastqsanger.gz | |||
| SRR5039727_2.fastq.gz | Fastqsanger.gz |
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Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
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Project description:Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. To understand the functional response of the fungal phytopathogen Rhizoctonia solani to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Transcriptome analysis revealed that approximately 10% of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had fold values exceeding 8x and for further analyses this cut-off value was used. Functional classification of DEGs revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. In conclusion, it was found out that most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.
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Project description:Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains however largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram towards division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during A. thaliana colonization compared to in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta. Using a multi-cell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.
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Project description:We bulit a pulmonary aspergillosis model in immunocompetent mice. Mice were inoculated intratracheally with 50 μL suspension of conidia , hyphal fragments or normal saline, respectively, after anesthesia. Lungs from were harvested and ground for RNA extraction 24 hours after fungal inoculation. The result of RNA-seq indicated both conidia and hyphae can activate a series of immunologically relevant pathways and these pathways were much more strongly activated by hyphae. Hyphae could promote Th2 cell differentiation and suppress Th1 cell differentiation. Both hyphae and conidia could activate Th17 cell differentiation.
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Project description:Laser Capture Microdissection (LCM) was used for expression analysis of three contrasted fungal tissues of uredinia corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to identify tissue-specific gene expression to gain insights into the genes specifically associated with the biotrophic phase and the sporulation phase of the rust fungus. We performed 9 hybridizations (NimbleGen) with samples derived from Laser Capture Microdissection (LCM) of three contrasted fungal tissues of uredinia, corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. Three replicates per tissue. All samples were labeled with Cy3.
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Project description:The fungal pathogen Aspergillus fumigatus is frequently cultured from the sputum of cystic fibrosis (CF) patients along with the bacterium, Pseudomonas aeruginosa. A. fumigatus secretes a range of secondary metabolites, and one of these, gliotoxin, has inhibitory effects on the host immune response. In this study, the effect of P. aeruginosa culture filtrate (CuF) on fungal growth and gliotoxin production was investigated. Exposure of A. fumigatus hyphae to P. aeruginosa cells induced increased production of gliotoxin and a decrease in fungal growth. In contrast exposure of A. fumigatus hyphae to P. aeruginosa CuF lead to increased growth and decreased gliotoxin production. Quantitative proteomic analysis was employed to characterize the proteomic response of A. fumigatus upon exposure to P. aeruginosa CuF. Changes in the profile of proteins involved with secondary metabolite biosynthesis (gliotoxin, fumagillin, pseurotin A), and changes to the abundance of proteins involved in oxidative stress (e.g. formate dehydrogenase) and detoxification (e.g. thioredoxin reductase) were observed, suggesting that the bacterial secretome has a profound effect on the fungal proteome. Alterations in the abundance of proteins involved in detoxification and oxidative stress, highlight the ability of A. fumigatus to differentially regulate protein synthesis in response to environmental stresses imposed by competitors such as P. aeruginosa. Such responses may ultimately have serious detrimental effects on the host.
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