Aquatic phototrophs, with their metabolic diversity, bioproduct potential, and capacity to thrive on marginal land and water, offer a powerful complement to conventional agriculture and biomanufacturing. Unlike terrestrial crops, they require neither arable land nor freshwater, opening opportunities in food and feed production, biofuels, materials, wastewater treatment, and metal recovery. Yet, their adoption has lagged behind established platforms such as E. coli, S. cerevisiae, and model plants. Recent discoveries of new model species, together with advances in genetic engineering and synthetic biology, are now transforming these underutilized phototrophs into versatile biocatalysts and next-generation crops. Beyond their applied potential, aquatic phototrophs also provide exceptional model systems for exploring photosynthesis, organelle evolution, multicellularity, plant origins, and cellular stress responses.

The rationale for a dedicated collection on “From novel model phototrophs to cutting-edge genetic tools” arises from two converging drivers. First, while model organisms such as Synechocystis sp. PCC 6803, Synechococcus elongatus PCC 7942, and Chlamydomonas reinhardtii have laid the foundation, research is now expanding toward newly isolated, genetically tractable phototrophs, including marine microalgae, diatoms, extremophilic cyanobacteria, fast-growing green algae, macroalgae, and aquatic plants. These emerging systems promise new insights into biosynthetic pathways and stress tolerance, while diatoms and macroalgae, in particular, offer advantages in scalability, biomineralization, and structural robustness with strong industrial potential. Second, rapid advances in genetic and analytical technologies, from CRISPR and prime editing to chloroplast transformation, high-throughput pipelines, and multi-omics, are overcoming long-standing barriers to genome engineering. Demonstrations of homologous recombination in Nannochloropsis and Auxenochlorella exemplify this growing versatility. The integration of metabolic engineering, bioinformatics, and machine learning is further redefining synthetic biology, making phototroph manipulation more precise, scalable, and impactful.

We envision contributions spanning:

• Progress in genome engineering of both classical and emerging phototrophs, encompassing precise genetic modifications, synthetic pathways, and large-scale genome redesign

• Applications of systems biology frameworks and illustrative case studies that demonstrate successful bioproduction strategies in aquatic photosynthetic systems

• Exploration of diatoms and macroalgae as versatile model platforms, emphasizing their unique cell architectures, carbon-concentrating mechanisms, and potential for scalable biomanufacturing and biomaterial production

• Application of unconventional phototrophic systems in cross-disciplinary contexts, including materials science, bioenergy, and synthetic ecology

Collectively, these works will demonstrate how engineering aquatic phototrophs is moving beyond niche experimentation to become a central pillar of next-generation biomanufacturing and elucidation of basic science inquiries. We are interested in Original Research, Review, and Methods articles.

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Engineering Aquatic Phototrophs: From Novel Model Organisms to Cutting-Edge Genetic Tools