Microorganisms play a central role in the structure and function of marine ecosystems. Its vast diversity makes the disentangling of the microbial taxonomic composition an essential task. Engaño Bay, a highly productive temperate region on the Patagonian Atlantic Coast, constitutes a remote uncharted area. Here, metabarcoding analyses revealed that the microbiome community (cells < 5 µm) of surface water is dominated by a few bacterial taxa along with diverse low frequency groups. A substantial number of sequences of photosynthetic picoeukaryotes (PPE) were also evidenced, yet no cyanobacterial sequences could be observed. Specific PCR-detection of cyanobacteria, monitoring of viruses specific for cyanobacteria and PPE, microbiological isolation, and molecular diet analyses confirmed these findings. Cyanobacteria were PCR detected in three out of thirteen samples, while virological monitoring indicated the presence of PPE viruses and the absence of cyanobacteria phages. Traditional culture methods allowed the isolation of Ostreococcus and Micromonas spp. from samples belonging to warm and cold seasons, respectively. Molecular diet analyses showed that PPE were grazed by nanoplankters and that grazing pressure on PPE was stronger than on bacteria. Phylogenetic characterization of viral sequences indicated the presence of Ostreococcus virus, four Micromonas virus lineages and a divergent clade of Phycodnavirus belonging to no known viral species, pointing out a complex scenario of its hosts. This work characterizes the marine microbiome from a temperate uncharted region at the Southern Hemisphere, demonstrating the prevalence of PPE as primary producers with a complex scenario which warrant further studies.

微生物在海洋生态系统的结构和功能中发挥着核心作用。其巨大的多样性使得解开微生物分类组成成为一项必不可少的任务。恩加诺湾是巴塔哥尼亚大西洋沿岸一个高产的温带地区，构成了一个偏远的未知区域。在这里，元条形码分析表明，地表水的微生物群落（细胞 < 5 µm）主要由一些细菌类群和不同的低频群组成。还证实了大量的光合微型核生物 ( PPE ) 序列，但没有观察到蓝藻序列。蓝藻特异性 PCR 检测，蓝藻和PPE特异性病毒监测、微生物分离和分子饮食分析证实了这些发现。在 13 个样本中的 3 个样本中检测到蓝藻，而病毒学监测表明存在PPE病毒并且不存在蓝藻噬菌体。传统的培养方法允许分离Ostreococcus和Micromonas spp。分别来自温暖和寒冷季节的样品。分子饮食分析表明，PPE被纳米浮游生物放牧，并且 PPE 上的放牧压力比细菌强。病毒序列的系统发育特征表明存在Ostreococcus 病毒，四种Micromonas 病毒谱系和不属于已知病毒物种的藻类病毒的不同进化枝，指出了其宿主的复杂情况。这项工作描述了南半球温带未知地区的海洋微生物组，证明了PPE作为初级生产者的普遍性，其复杂的情况值得进一步研究。