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

Picocyanobacteria from the genera <i>Prochlorococcus</i>, <i>Synechococcus</i>, and <i>Cyanobium</i> 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.<br>

原绿球藻属（Prochlorococcus）、聚球藻属（Synechococcus）与蓝杆藻属（Cyanobium）所属的微微型蓝细菌（picocyanobacteria），是水生生态系统中分布最为广泛的光合生物。然而目前针对其淡水种群的相关研究仍有待深入，究其原因在于现有针对各类内陆水体的采样覆盖度不足。本研究报道了从中欧地区采集的混菌培养（non-axenic）物中获得的170个高质量淡水微微型蓝细菌基因组，以及33个潜在共生伙伴的基因组。这类共生互作的基因组基础为：异养生物可利用微微型蓝细菌产生的营养物质，同时为其提供活性氧（ROS）脱毒功能。全球范围内微微型蓝细菌基因组的丰度分布模式，揭示了具有重要生态学意义的生态型，这些生态型与营养状态、温度及pH等关键环境因子密切相关。微微型蓝细菌在（超）富营养化水体中的适应性，可归因于其群体生活方式与CRISPR-Cas系统。微微型蓝细菌中占主导的CRISPR-Cas亚型为I-G型与I-E型，这类亚型似乎通过水平基因转移从其他细菌门中获取而来。