SAMMBA is a high-throughput pipeline for isolating and phenotyping macroalgal strains

Abstract Anthropogenic climate change is causing the decline of seaweed forests in many parts of the world. Despite successful preservation efforts, their immense biodiversity is still severely underrepresented in germplasm biobanks throughout the world. These culture libraries can preserve genetic diversity and provide inoculum for marine forest restoration and mariculture ventures, and potentially accelerate the selection and breeding of climate-resilient and high-yielding strains. However, the complex life cycles and body plans of seaweeds pose a huge challenge for the development of standardized phenotyping and isolating protocols for microscopic stages, especially with the efficiency necessary to deal with the current pace of global climatic changes. Here, we present SAMMBA (Seaweed Automatable Microplate Microscopy for Breeding Approaches), an end-to-end pipeline for the high-throughput isolation, phenotyping and storage of macroalgal cells in 384-well plates (384WP). By optimizing fluorescence microscopy imaging and analysis, along with a novel fragmentation method and dilution-to-extinction isolation, different unialgal seaweed tissues could be regrown after thousand-fold dilutions. In a single plate, we successfully isolated 68 singlet gametophyte fragments of Laminaria ochroleuca (39 males, 29 females; 17.7% efficiency) and 60 spores of Phyllariopsis purpurascens (31.25% efficiency). Furthermore, the taxonomic versatility of SAMMBA was demonstrated through the successful isolation of 60 unialgal cultures of red algae ( Halymenia sp., Hydrolithon sp., Erythrotrichia sp. ) and 10 strains of the green alga Ulva sp, without cross-contamination. The viability and unialgal nature of the isolated strains were verified by distributing a single L. ochroleuca strain across an entire 384-well plate and imaging each well over 30 days. We found that the average specific daily growth rates (daily SGR) per well were 0.130 ± 0.006 and 0.117 ± 0.01 day -1 for males and females, respectively, showing a significant difference between sexes (n = 768; p = 1.27e -53 ), while edge effects significantly reduced daily SGR in males but not in females. This approach dramatically increases experimental reproducibility and statistical power compared to conventional methods. Due to its modular design and cost-effectiveness, SAMMBA is readily adaptable to macroalgal repositories globally. It supports high-throughput, selective recovery of unialgal strains without reliance on robotic platforms, while remaining fully compatible with automation. This system significantly expands the experimental and operational capacity in macroalgal hatcheries, providing a scalable foundation for phenomics, domestication programs, and standardized, verifiable biobanking of unialgal strains. Ultimately, SAMMBA could provide critical support for breeding strategies required to ensure the resilience of marine forests and aquaculture in a rapidly changing ocean.