Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria

Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to the insufficient sampling across diverse inland waterbodies. In this study, we present 170 high-quality genomes of freshwater picocyanobacteria and 33 genomes of potential symbiotic partners from non-axenic cultures collected across Central Europe. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients, while providing detoxification of ROS. The global abundance patterns of picocyanobacterial genomes revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla.原绿球藻属（Prochlorococcus）、聚球藻属（Synechococcus）以及蓝杆藻属（Cyanobium）中的微微型光合蓝细菌（picocyanobacteria），是水生生态系统中分布最为广泛的光合生物。然而，由于对各类内陆水体采样不足，其淡水种群仍未得到充分探索。本研究从中欧各地采集的非无菌培养物中，获得了170株淡水微微型光合蓝细菌的高质量基因组，以及33株潜在共生伙伴的基因组。该共生互作的基因组基础体现为：异养共生伙伴可获取微微型光合蓝细菌衍生的营养物质，同时为宿主提供活性氧（Reactive Oxygen Species, ROS）的脱毒功能。对全球范围内微微型光合蓝细菌基因组的丰度分布模式分析显示，其存在具有重要生态意义的生态型，这类生态型与营养状态、温度及pH值这三类关键环境因子密切相关。微微型光合蓝细菌在（超）富营养化水体中的适应性，可归因于其集落生活方式与CRISPR-Cas系统（CRISPR-Cas）。该类微生物中占主导的CRISPR-Cas亚型为I-G型与I-E型，这类亚型似乎是通过从其他细菌门类获取的水平基因转移事件获得的。