MICROBIAL LAB

Marine microorganisms are fundamental drivers of global biogeochemical cycles and form the base of marine food webs. However, their ecological roles remain incompletely understood because most marine microbes are difficult to cultivate and many genes detected in environmental sequencing datasets remain uncharacterized. This integrated research project builds upon the Taiwan Ocean Genes (TOG) database, a large-scale marine metagenomic resource established from systematic sampling of waters surrounding Taiwan. By integrating artificial intelligence (AI), multi-omics approaches, and molecular ecological analyses, this project aims to develop an advanced analytical framework to uncover microbial functional potential and translate genomic information into ecological mechanisms. The project consists of two complementary subprojects. Subproject 1 focuses on AI-driven genomic mining and methodological innovation to improve genome assembly, annotation, and functional prediction from large-scale marine metagenomic datasets. By developing deep-learning-based binning, gene annotation models, and predictive frameworks linking environmental factors with microbial functions, the study aims to enhance the discovery of novel genes, predict microbial cultivation conditions, identify emerging antimicrobial resistance genes, and resolve virus–host interactions in marine ecosystems. These efforts will transform the TOG database from a repository of sequence data into a knowledge-driven platform for marine microbial ecology and biotechnology. Subproject 2 investigates the ecological roles of mixotrophic plankton in marine ecosystems and their influence on biogeochemical cycles under changing environmental conditions. Through controlled laboratory experiments, transcriptomic analyses, and field observations across environmental gradients in the Northwest Pacific Ocean, the study will examine how mixotrophic strategies shift between phototrophy and phagotrophy in response to light, nutrient availability, and prey abundance. The project will further quantify the impacts of different nutritional strategies on carbon flow, microbial food-web dynamics, and elemental stoichiometry in marine ecosystems. By integrating AI-driven genomic exploration with ecological validation, this project will establish a comprehensive framework linking genes, microbial functions, ecological mechanisms, and biogeochemical impacts. The results will advance our understanding of marine microbial ecosystems in the Northwest Pacific and improve predictions of ecosystem responses to climate change, while also supporting marine biotechnology development and evidence-based ocean environmental management.