Isolation and Characterization of Pesticidal Compounds from Green Microalgae: Integrating Metabolomics and Transcriptomics to Elucidate Biosynthetic Pathways Responsible for Bioactive Compound Production

Herbicide resistance is eroding the effectiveness of dominant chemistries, motivating the search for novel, sustainable modes of action. This dissertation investigates green microalgae as sources of pesticidal metabolites and establishes a discovery framework linking ecological triggers (nutrient limitation/aging) with multi-omics and bioassay-guided fractionation. A comparative screen of aged extracts from Chlamydomonas, Chlorella, and Chloroidium revealed consistent algicidal, herbicidal, and nematicidal activities, inhibition of Chlorella sorokiniana, suppression of Arabidopsis thaliana germination, activity against glyphosate-resistant Amaranthus palmeri, and lethality to Caenorhabditis elegans. Untargeted UHPLC–MS profiled ~45 chemical classes across active extracts, including fatty-acid amides, oxylipin-related species, coumarins, and alkaloid-like nodes. A stage-resolved dissection in Chlamydomonas reinhardtii (7, 14, 21, 30 days after inoculation, dai) showed that bioactivity emerges only at late stages (21–30 dai) under nutrient limitation. Transcriptomics indicated attenuation of photosynthesis and pigment biosynthesis alongside activation of stress-associated programs (oxylipin/jasmonate-like signaling, purine metabolism, ER-linked protein processing), while metabolomics revealed late enrichment of oxylipins, purines, and selected terpenoids. Preparative HPLC localized activity to a late-eluting fraction and a single active subfraction, compressing thousands of LC–MS features to a tractable candidate set. Together, the results show that microalgae can be steered into late-stage chemical states that yield agriculturally relevant activities, and that a stage-resolved, chemistry-first pipeline converts complex metabolomes into prioritized leads.