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ABSTRACT: Canadian Bee Microbome Metagenomic Sequencing in Proximity to Highbush Blueberry

PROVIDER: PRJNA1124990 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29437400_1.fastq.gz	Fastqsanger.gz
	SRR29437400_2.fastq.gz	Fastqsanger.gz
	SRR29437401_1.fastq.gz	Fastqsanger.gz
	SRR29437401_2.fastq.gz	Fastqsanger.gz
	SRR29437402_1.fastq.gz	Fastqsanger.gz

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Project description:Honey bees (Apis mellifera) are essential pollinators in agricultural systems, particularly in fruit-producing agroecosystems such as highbush blueberry and cranberry. However, their health is increasingly compromised by multiple interacting stressors, including pesticide exposure, pathogen infections, and changing nutritional landscapes. To test the hypothesis that distinct agricultural ecosystems, with different combinations of agrochemical exposure, pathogen loads, and floral resources, elicit ecosystem specific, tissue level molecular responses in honey bees, we conducted an integrated multiomics analysis. We combined RNA sequencing, quantitative proteomics, and gut microbiome profiling across three key tissues: head, abdomen, and gut collected from bees in blueberry and cranberry agroecosystems over two field seasons. In parallel, we quantified pesticide residues and pathogen and parasite loads (e.g., Nosema spp., Varroa destructor, and several viruses). Notably, our weighted gene co-expression network analysis (WGCNA) revealed tissue specific coregulated protein modules with ecosystem associated patterns. Bees from blueberry agroecosystems exhibited elevated expression of modules in oxidative phosphorylation, and translation, while those from cranberry agroecosystems showed increased activity in immune pathways and endoplasmic reticulum associated protein processing, indicating potential as robust markers for ecosystem induced physiological adaptation. To further explore the molecular mechanisms underlying different ecosystems, we also conducted the integrative analysis of proteomics, transcriptomics and gut microbiome metagenomics. Gut microbiota composition also differed significantly, with key genera (e.g., Gilliamella, Snodgrassella, Bartonella) correlating with host metabolic and immune modules. These findings underscore the complex, environment-dependent impacts of agroecosystem conditions on bee health. Our study provides a systems level understanding of how combined pesticide, pathogen, and parasitic stressors, mediated by diet and microbiome, shape molecular phenotypes in honey bees, informing strategies for pollinator protection in managed landscapes.

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